Keith R. Weninger

Works (76)

Updated: April 3rd, 2024 18:53

2023 journal article

A nanophotonic interferometer

NANOTECHNOLOGY, 34(18).

By: A. Ghaffari n, S. Kashani n, K. Do n, K. Weninger n  & R. Riehn n 

author keywords: zero mode waveguide; sub-wavelength aperture; interferometer
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: January 19, 2023

2023 journal article

Ex vivo analysis of ultraviolet radiation transmission through ocular media and retina in select species

Experimental Eye Research, 233, 109550.

By: N. Himebaugh n, J. Robertson n , K. Weninger n , B. Gilger n , B. Ekesten * & A. Oh n 

author keywords: Ultraviolet radiation; Ocular media; Canine; Feline; Human; Vision
TL;DR: The globes of cats and dogs allowed the most amount of UV radiation transmission, while those of pigs and humans allowed the least amount ofUV radiation transmission. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, Crossref
Added: June 25, 2023

2023 journal article

Frustration Between Preferred States of Complementary Trinucleotide Repeat DNA Hairpins Anticorrelates with Expansion Disease Propensity

JOURNAL OF MOLECULAR BIOLOGY, 435(10).

By: P. Xu n, J. Zhang  n, F. Pan n, C. Mahn n, C. Roland n, C. Sagui n, K. Weninger n 

author keywords: single molecule FRET; hairpin slippage; molecular dynamics; kinetics; trinucleotide interrupts; Huntington's disease
MeSH headings : Humans; DNA / genetics; DNA / chemistry; DNA, Complementary; Nucleic Acid Conformation; Trinucleotide Repeat Expansion / genetics; Trinucleotide Repeats; Neurodegenerative Diseases / genetics
TL;DR: Single molecule FRET experiments and molecular dynamics simulations are applied to determine conformational stabilities and slipping dynamics for CAG, CTG, GAC and GTC hairpins to determine Tetraloops and TTG interrupts near the loop in the CTG hairpin stabilize the hairpin against slipping. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: May 22, 2023

2023 review

Illuminating Intrinsically Disordered Proteins with Integrative Structural Biology

[Review of ]. BIOMOLECULES, 13(1).

By: R. Evans n, S. Ramisetty*, P. Kulkarni * & K. Weninger n 

author keywords: intrinsically disordered proteins; integrative structural biology; unfolded; unstructured; flexible; protein function
MeSH headings : Intrinsically Disordered Proteins / chemistry; Signal Transduction; Biology; Protein Conformation
TL;DR: Some of the recent applications of the integrative structural biology philosophy to study IDPs are reviewed. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: February 13, 2023

2022 article

A Nanophotonic Interferometer for small particle detection

INTERFEROMETRY XXI, Vol. 12223.

By: A. Ghaffari, K. Do n, S. Kashani n, K. Weninger n  & R. Riehn n 

author keywords: zero mode waveguide; sub-wavelength aperture; interferometer
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: November 7, 2022

2022 journal article

A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories

NATURE COMMUNICATIONS, 13(1).

By: M. Goetz, A. Barth *, S. Bohr *, R. Boerner, J. Chen *, T. Cordes *, D. Erie *, C. Gebhardt * ...

MeSH headings : Benchmarking; Fluorescence Resonance Energy Transfer / methods; Kinetics; Models, Theoretical
TL;DR: A blind benchmark study assessing eleven analysis tools used to infer kinetic rate constants from smFRET trajectories, testing on simulated and experimental data and identifying key targets for future developments to advance the understanding of biomolecular dynamics. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: October 3, 2022

2022 article

Non-ergodicity of a globular protein extending beyond its functional timescale

Li, J., Xie, J. F., Godec, A., Weninger, K. R., Liu, C., Smith, J. C., & Hong, L. (2022, August 4). CHEMICAL SCIENCE, Vol. 8.

By: J. Li *, J. Xie*, A. Godec *, K. Weninger n , C. Liu *, J. Smith *, L. Hong *

TL;DR: By performing single-molecule fluorescence resonance energy transfer experiments and molecular dynamics simulations of a multi-domain globular protein, cytoplasmic protein-tyrosine phosphatase (SHP2), it is demonstrated that the functional inter-domain motion is observationally non-ergodic over the time spans 10−12 to 10−7 s and 10−1 to 102 s. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 22, 2022

2021 journal article

Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25

CELL REPORTS PHYSICAL SCIENCE, 2(11).

By: N. Saikia *, I. Yanez-Orozco*, R. Qiu n, P. Hao n, S. Milikisiyants n, E. Ou n, G. Hamilton *, K. Weninger n  ...

TL;DR: An integrative method is reported to probe the structural dynamics of SNAP-25 by combining replica-exchange discrete molecular dynamics simulations and label-based experiments at ensemble and single-molecule levels and it is expected that this integrative approach may help further the understanding of IDPs. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: March 14, 2022

2021 review

Molecular conformations and dynamics of nucleotide repeats associated with neurodegenerative diseases: double helices and CAG hairpin loops

[Review of ]. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 19, 2819–2832.

By: F. Pan*, Y. Zhang *, P. Xu n, V. Man n, C. Roland n, K. Weninger n , C. Sagui n

author keywords: Trinucleotide hexanucleotide repeats; CAG; GAC; CTG; CUG; CCG; GGC; GGGGCC; GGCCCC; Hairpin loops; smFRET; Molecular dynamics
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 30, 2021

2021 journal article

Structure, dynamics, and regulation of TRF1-TIN2-mediated trans- and cis-interactions on telomeric DNA

JOURNAL OF BIOLOGICAL CHEMISTRY, 297(3).

By: H. Pan n, P. Kaur n, R. Barnes *, A. Detwiler *, S. Sanford*, M. Liu  n, P. Xu n, C. Mahn n ...

MeSH headings : Cell Adhesion Molecules / metabolism; Cell Adhesion Molecules / physiology; DNA / metabolism; DNA-Binding Proteins / metabolism; Humans; Microscopy, Atomic Force / methods; Models, Molecular; Multiprotein Complexes / metabolism; Protein Binding; Protein Isoforms / metabolism; Shelterin Complex / metabolism; Shelterin Complex / physiology; Telomere / metabolism; Telomere-Binding Proteins / metabolism; Telomere-Binding Proteins / physiology; Telomeric Repeat Binding Protein 1 / metabolism; Telomeric Repeat Binding Protein 1 / physiology; Telomeric Repeat Binding Protein 2 / metabolism; Telomeric Repeat Binding Protein 2 / physiology
TL;DR: Analysis of DNA molecular structures promoted by TRF1-TIN2 interaction supports a molecular model in which protein assemblies at telomeres are heterogeneous with distinct subcomplexes and full shelterin complexes playing distinct roles in telomere protection and elongation. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: October 26, 2021

2020 journal article

Dynamic human MutS alpha-MutL alpha complexes compact mismatched DNA

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 117(28), 16302–16312.

By: K. Bradford*, H. Wilkins*, P. Hao n, Z. Li*, B. Wang *, D. Burke*, D. Wu *, A. Smith* ...

author keywords: DNA repair; AFM; MutS; MutL; DREEM
MeSH headings : Adenosine Triphosphate / metabolism; DNA / chemistry; DNA / genetics; DNA / metabolism; DNA Mismatch Repair; DNA-Binding Proteins / chemistry; DNA-Binding Proteins / metabolism; Humans; Multiprotein Complexes / metabolism; MutL Proteins / chemistry; MutL Proteins / metabolism; MutS Homolog 2 Protein / chemistry; MutS Homolog 2 Protein / metabolism; Nucleic Acid Conformation; Nucleosomes / metabolism; Protein Folding; Protein Multimerization
TL;DR: Atomic force microscopy is utilized coupled with other methods to reveal time- and concentration-dependent stoichiometries and conformations of assembling human MutSα–MutLα–DNA complexes, and it is found that they assemble into multimeric complexes comprising three to eight proteins around a mismatch on DNA. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 17, 2020

2020 journal article

Dynamics of strand slippage in DNA hairpins formed by CAG repeats: roles of sequence parity and trinucleotide interrupts

Nucleic Acids Research, 1.

By: P. Xu n, F. Pan  n, C. Roland n, C. Sagui  n & K. Weninger n 

MeSH headings : Base Pairing; DNA / chemistry; Fluorescence Resonance Energy Transfer; Inverted Repeat Sequences; Kinetics; Molecular Dynamics Simulation; Nucleic Acid Conformation; Single Molecule Imaging; Thermodynamics; Trinucleotide Repeats
TL;DR: Reducing strand slipping in TR hairpins by sequence interruptions at the loop suggests disease-associated variations impact expansion mechanisms at the level of slipped hairpins. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: ORCID
Added: September 2, 2021

2020 journal article

How Membrane Geometry Regulates Protein Sorting Independently of Mean Curvature

ACS CENTRAL SCIENCE, 6(7), 1159–1168.

By: J. Larsen *, K. Rosholm *, C. Kennard *, S. Pedersen*, H. Munch*, V. Tkach*, J. Sakon n, T. Bjornholm* ...

TL;DR: The results reveal that distinct membrane geometries have specific physicochemical properties and thus establish a ubiquitous mechanistic foundation for unravelling the conserved correlations between biological function and membrane polymorphism. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 24, 2020

2020 journal article

Recurrent mismatch binding by MutS mobile clamps on DNA localizes repair complexes nearby

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 117(30), 17775–17784.

By: P. Hao n, S. LeBlanc n, B. Case*, T. Elston *, M. Hingorani *, D. Erie *, K. Weninger n 

author keywords: smFRET; MMR; mismatch repair; MutS
MeSH headings : Adenosine Triphosphatases / metabolism; Adenosine Triphosphate / metabolism; Base Pair Mismatch; DNA / chemistry; DNA / genetics; DNA / metabolism; DNA Mismatch Repair; Hydrolysis; Models, Molecular; Multiprotein Complexes / metabolism; MutL Proteins / chemistry; MutL Proteins / metabolism; MutS DNA Mismatch-Binding Protein / chemistry; MutS DNA Mismatch-Binding Protein / metabolism; Structure-Activity Relationship
TL;DR: It is revealed that after the initial mobile clamp formation event, MutS undergoes frequent cycles of mismatch rebinding and mobile clamp reformation without releasing DNA, and mechanisms that localize repair complexes to the vicinity of the mismatch are supported. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 17, 2020

2019 journal article

Investigating the Function of Mutl Conformational Changes in Mismatch Repair using smFRET

Biophysical Journal, 116(3), 49a–50a.

By: S. LeBlanc *, P. Hao n, M. Hinds*, A. Morgan*, K. Gbozah*, K. Weninger n , D. Erie *

Sources: Crossref, ORCID
Added: February 5, 2020

2019 review

Spontaneous Switching among Conformational Ensembles in Intrinsically Disordered Proteins

[Review of ]. BIOMOLECULES, 9(3).

By: U. Choi *, H. Sanabria *, T. Smirnova n , M. Bowen * & K. Weninger n 

author keywords: dynamic configuration; free energy landscape; intrinsically disordered protein; IDP
MeSH headings : Humans; Intrinsically Disordered Proteins / chemistry; Protein Conformation
TL;DR: A growing number of proteins that appear intrinsically disordered by biochemical and bioinformatic characterization but switch between restricted regions of conformational space are described. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: April 29, 2019

2019 journal article

Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level

Biomolecules, 9(2), 77.

By: X. Lin* , P. Kulkarni *, F. Bocci *, N. Schafer*, S. Roy *, M. Tsai *, Y. He *, Y. Chen * ...

author keywords: PAGE4; intrinsically disordered proteins; conformational plasticity; order-disorder transition; phosphorylation
MeSH headings : Antigens, Neoplasm / chemistry; Antigens, Neoplasm / metabolism; Humans; Intrinsically Disordered Proteins / chemistry; Intrinsically Disordered Proteins / metabolism; Molecular Dynamics Simulation; Protein Conformation
TL;DR: It is argued that, although the structural plasticity of an IDP is important in promoting promiscuous interactions, the modulation of the structural ordering is important for sculpting its interactions so as to rewire with agility biomolecular interaction networks with significant functional consequences. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, Crossref
Added: March 25, 2019

2019 journal article

TIN2 is an Architectural Protein Stabilizing TRF1 at Telomere

Biophysical Journal, 116(3), 211a–212a.

By: H. Pan  n, S. Dangi n, P. Kaur n, P. Hao n, K. Weninger n , R. Riehn n , P. Opresko *, H. Wang n 

Sources: Crossref, ORCID
Added: January 25, 2020

2019 journal article

Toward Single Molecule FRET Studies of DNA Mismatch Repair in Live Bacteria

Biophysical Journal, 116(3), 139a.

By: P. Xu n, A. Hensley n, E. Chan  n & K. Weninger n 

Sources: Crossref, ORCID
Added: February 5, 2020

2019 journal article

Untangling DNA Mismatch Repair Complexes with smFRET and Tethered Particle Motion Analysis

Biophysical Journal, 116(3), 77a.

By: P. Hao n, S. LeBlanc, D. Erie & K. Weninger n 

Sources: Crossref, ORCID
Added: February 5, 2020

2018 journal article

Coordinated protein and DNA conformational changes govern mismatch repair initiation by MutS

NUCLEIC ACIDS RESEARCH, 46(20), 10782–10795.

By: S. LeBlanc n, J. Gauer*, P. Hao n, B. Case*, M. Hingorani *, K. Weninger n , D. Erie *

MeSH headings : Base Pair Mismatch / genetics; Base Pairing / physiology; DNA / chemistry; DNA Mismatch Repair / genetics; Escherichia coli; Fluorescence Resonance Energy Transfer; Genomic Instability / genetics; Models, Molecular; MutS DNA Mismatch-Binding Protein / chemistry; MutS DNA Mismatch-Binding Protein / genetics; MutS DNA Mismatch-Binding Protein / metabolism; Mutant Proteins / chemistry; Mutant Proteins / metabolism; Nucleic Acid Conformation; Protein Binding / physiology; Protein Conformation; Protein Domains / genetics; Protein Isoforms / chemistry; Protein Isoforms / genetics; Protein Isoforms / metabolism
TL;DR: A unified model of coordinated MutS and DNA conformational changes wherein initiation of mismatch repair is governed by a balance of DNA bending/unbending energetics and MutS conformationalChanges coupled to its nucleotide binding properties is proposed. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: February 11, 2019

2018 journal article

Motor-like DNA motion due to an ATP-hydrolyzing protein under nanoconfinement

Scientific Reports, 8(1).

By: M. Roushan n, Z. Azad n, S. Movahed n, P. Ray n, G. Livshits n, S. Lim n , K. Weninger n , R. Riehn n 

MeSH headings : Adenosine Triphosphate / metabolism; DNA / metabolism; DNA Ligases / metabolism; DNA Ligases / physiology; DNA-Binding Proteins / genetics; Diffusion; Escherichia coli / genetics; Escherichia coli / metabolism; Escherichia coli Proteins / metabolism; Escherichia coli Proteins / physiology; Motion; MutS DNA Mismatch-Binding Protein / metabolism; MutS DNA Mismatch-Binding Protein / physiology; NAD / metabolism
TL;DR: It is reported that long double-stranded DNA confined to quasi-1D nanochannels undergoes superdiffusive motion under the action of the enzyme T4 DNA ligase in the presence of necessary co-factors. (via Semantic Scholar)
Sources: Crossref, ORCID, NC State University Libraries
Added: August 6, 2018

2018 journal article

PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer

Journal of Molecular Biology, 430(16), 2422–2438.

By: X. Lin* , S. Roy *, M. Jolly*, F. Bocci *, N. Schafer *, M. Tsai *, Y. Chen *, Y. He * ...

Contributors: X. Lin* , S. Roy *, M. Jolly*, F. Bocci *, N. Schafer *, M. Tsai *, Y. Chen *, Y. He * ...

author keywords: intrinsically disordered protein; PAGE4; AWSEM; order-disorder transition; non-genetic heterogeneity
MeSH headings : Antigens, Neoplasm / chemistry; Antigens, Neoplasm / metabolism; Fluorescence Resonance Energy Transfer; Humans; Male; Models, Molecular; Models, Theoretical; Molecular Dynamics Simulation; Phosphorylation; Prostatic Neoplasms / metabolism; Protein Conformation; Protein Serine-Threonine Kinases / metabolism; Protein-Tyrosine Kinases / metabolism; Receptors, Androgen / metabolism; Scattering, Small Angle; Signal Transduction; Single Molecule Imaging; Transcription Factor AP-1 / metabolism; X-Ray Diffraction
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Crossref, ORCID
Added: February 5, 2020

2018 review

Phenotypic Plasticity, Bet-Hedging, and Androgen Independence in Prostate Cancer: Role of Non-Genetic Heterogeneity

[Review of ]. FRONTIERS IN ONCOLOGY, 8.

By: M. Jolly *, P. Kulkarni *, K. Weninger n , J. Orban * & H. Levine *

author keywords: bet-hedging; stochasticity; androgen independence; non-genetic heterogeneity; phenotypic plasticity; intermittent androgen therapy
TL;DR: It is illustrated how phenotypic plasticity and consequent mutation-independent or non-genetic heterogeneity possibly driven by protein conformational dynamics can stochastically give rise to androgen independence in PCa, and it is suggested that dynamic phenotyping plasticity should be considered in devising therapeutic dosing strategies designed to treat and manage PCa. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2018 journal article

Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study

NATURE METHODS, 15(9), 669-+.

By: B. Hellenkamp *, S. Schmid *, O. Doroshenko*, O. Opanasyuk*, R. Kuehnemuth, S. Adariani *, B. Ambrose *, M. Aznauryan * ...

MeSH headings : Fluorescence Resonance Energy Transfer / methods; Laboratories / standards; Reproducibility of Results
TL;DR: A multi-laboratory study finds that single-molecule FRET is a reproducible and reliable approach for determining accurate distances in dye-labeled DNA duplexes. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: October 19, 2018

2018 review

Prostate-Associated Gene 4 (PAGE4): Leveraging the Conformational Dynamics of a Dancing Protein Cloud as a Therapeutic Target

[Review of ]. JOURNAL OF CLINICAL MEDICINE, 7(6).

By: R. Salgia*, M. Jolly *, T. Dorff *, C. Lau*, K. Weninger n , J. Orban *, P. Kulkarni *

author keywords: PAGE4; prostate cancer; symptomatic BPH; Cancer/Testis Antigen; ADT; IAD
TL;DR: This work discusses how PAGE4, a protein which appears to act both as an oncogenic factor as well as a metastasis suppressor, is a novel therapeutic target for PCa and suggests that inhibiting PAGE4 may be a viable strategy for low-risk PCa where it is highly upregulated. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2018 journal article

Publisher Correction: Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study

Nature Methods, 15(11), 984–984.

By: B. Hellenkamp *, S. Schmid *, O. Doroshenko*, O. Opanasyuk*, R. Kühnemuth*, S. Adariani *, B. Ambrose *, M. Aznauryan * ...

Sources: Crossref, ORCID
Added: February 5, 2020

2018 journal article

Single Molecule Experiments Reveal Molecular Level Details of MutS-MutL Interactions in DNA Mismatch Activated Sliding Clamp

Biophysical Journal, 114(3), 85a.

By: P. Hao n, S. LeBlanc *, D. Erie * & K. Weninger n 

UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Crossref, ORCID
Added: February 5, 2020

2018 journal article

Single Molecule FRET Observations of Folding for DNA Hairpins Containing Trinucleotide Repeats

Biophysical Journal, 114(3), 599a.

By: P. Xu n & K. Weninger n 

Sources: Crossref, ORCID
Added: February 5, 2020

2018 review

Single Molecule FRET: A Powerful Tool to Study Intrinsically Disordered Proteins

[Review of ]. BIOMOLECULES, 8(4).

By: S. LeBlanc n, P. Kulkarni * & K. Weninger n 

author keywords: single molecule biophysics; FRET; intrinsically disordered protein; IDP
MeSH headings : Fluorescence Resonance Energy Transfer; Intrinsically Disordered Proteins / chemistry; Intrinsically Disordered Proteins / metabolism; Phosphorylation; Single Molecule Imaging
TL;DR: The power of applyingsmFRET to IDPs is illustrated by discussing two cases in the literature of protein systems for which smFRET has successfully reported phosphorylation-induced modification (but not elimination) of the disordered properties that have been connected to impacts on the related biological function. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: January 14, 2019

2017 journal article

Dynamic Studies of MutS-MutL-DNA Complexes in Mismatch Repair

Biophysical Journal, 112(3), 516a–517a.

By: S. LeBlanc *, J. Gauer*, P. Hao n, T. Walser n, K. Weninger n  & D. Erie *

Sources: Crossref, ORCID
Added: February 5, 2020

2017 journal article

Mismatch Repair on the Go: Extending the Mechanical Model of DNA Mismatch Repair through Single Molecule Study

Biophysical Journal, 112(3), 514a–515a.

By: P. Hao n, R. Qiu*, D. Erie * & K. Weninger n 

Sources: Crossref, ORCID
Added: February 5, 2020

2017 journal article

Phosphorylation-induced conformational dynamics in an intrinsically disordered protein and potential role in phenotypic heterogeneity

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(13), E2644–E2653.

By: P. Kulkarni *, M. Jolly*, D. Jia *, S. Mooney*, A. Bhargava, L. Kagohara *, Y. Chen *, P. Hao n ...

author keywords: intrinsic disorder; androgen resistance; prostate cancer; PAGE-4; phenotypic heterogeneity
MeSH headings : Antigens, Neoplasm / chemistry; Antigens, Neoplasm / metabolism; Humans; Intrinsically Disordered Proteins / chemistry; Intrinsically Disordered Proteins / metabolism; Models, Molecular; Phenotype; Phosphorylation; Protein Conformation; Protein Serine-Threonine Kinases / genetics; Protein Serine-Threonine Kinases / metabolism; Protein Serine-Threonine Kinases / physiology; Protein-Tyrosine Kinases / genetics; Protein-Tyrosine Kinases / metabolism; Protein-Tyrosine Kinases / physiology; Proteome
TL;DR: Multiple biophysical approaches that report conformational preferences of the intrinsically disordered protein (IDP) Prostate-Associated Gene 4 with human cancer biology and nonlinear dynamics suggest that the phosphorylation-induced conformational dynamics of PAGE4 may play a role in modulating changes between PCa cell phenotypes. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2017 journal article

Single Molecule Fluorescence and Atomic Force Microscopy Studies of DNA Repair

Biophysical Journal, 112(3), 7a.

By: D. Erie *, K. Bradford*, H. Wilkins*, J. Bower *, Z. Wang *, J. Gauer*, M. Satusky *, R. Qiu n ...

TL;DR: How AFM, DREEM, and single-molecule fluorescence can be powerful tools to study the stoichiometries, conformations, and dynamic assembly of multi-component complexes is discussed. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: February 5, 2020

2016 review

Prostate-associated gene 4 (PAGE4), an intrinsically disordered cancer/testis antigen, is a novel therapeutic target for prostate cancer

[Review of ]. ASIAN JOURNAL OF ANDROLOGY, 18(5), 695–703.

By: P. Kulkarni *, A. Dunker *, K. Weninger*  & J. Orban  n

author keywords: prostate-associated Gene 4; cancer/testis antigen; intrinsically disordered protein; prostate cancer; c-Jun; AP-1; protein interaction networks; homeodomain-interacting protein 1
MeSH headings : Antigens, Neoplasm / metabolism; Antineoplastic Agents / therapeutic use; Humans; Intrinsically Disordered Proteins / metabolism; Male; Phosphorylation; Prostate / metabolism; Prostate / pathology; Prostatic Neoplasms / drug therapy; Prostatic Neoplasms / metabolism; Prostatic Neoplasms / pathology; Protein Conformation
TL;DR: The data suggest that PAGE4 may represent the first molecular link between stress and prostate cancer (PCa), and pharmacologically targeting PAGE 4 may be a novel opportunity for treating and managing patients with PCa, especially patients with low-risk disease. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

Single-molecule FRET to measure conformational dynamics of DNA mismatch repair proteins

Single-Molecule Enzymology: Fluorescence-Based and High-Throughput Methods, 581, 285–315.

By: J. Gauer, S. LeBlanc, P. Hao, R. Qiu, B. Case, M. Sakato, M. Hingorani, D. Erie, K. Weninger 

Source: NC State University Libraries
Added: August 6, 2018

2016 journal article

Venoms from Centruroides sp. Scorpions Cleave SNARE Proteins

Toxicon, 117, 109.

By: P. Fletcher*, M. Fletcher*, K. Weninger n  & B. Martin*

Sources: Crossref, ORCID
Added: February 5, 2020

2016 journal article

smFRET and DEER Distance Measurements as Applied to Disordered and Structured Proteins

Biophysical Journal, 110(3), 559a.

By: K. Weninger n , R. Qiu n, E. Ou n, S. Milikisiyants  n, H. Sanabria * & T. Smirnova n 

TL;DR: Single molecule (sm) FRET reports on conformation of individual protein molecules whereas DEER provides information on ensemble average while the distance ranges of these two methods overlaps, and direct comparison of FRET and DEER data is rarely found in the literature. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Crossref, ORCID
Added: February 5, 2020

2016 journal article

tN-Ras, Synaptotagmin1 C2Ab, Annexinb12 and Amphiphysin NBAR can Discriminate Spherical from Cylindrical Membrane Curvature

Biophysical Journal, 110(3), 357a.

By: A. Breuer *, J. Larsen *, K. Røskva Rosholm, S. Pedersenb*, H. Munch*, V. Tkach*, J. Sakon *, T. Bjørnholm* ...

TL;DR: The results reveal membrane curvature geometry as a novel regulator of protein recruitment during trafficking and sorting for a plethora of membrane-binding proteins, and thus suggest a novel functional role to the diversity of conserved organelle morphologies. (via Semantic Scholar)
UN Sustainable Development Goal Categories
10. Reduced Inequalities (OpenAlex)
Sources: Crossref, ORCID
Added: February 5, 2020

2016 journal article

“Metalloproteases in new world scorpion venoms cleave intracellular membrane fusion SNARE proteins VAMP2 and VAMP8”

“Metalloproteases in new world scorpion venoms cleave intracellular membrane fusion SNARE proteins VAMP2 and VAMP8.” Toxicon, 117, 104.

By: P. Fletcher*, M. Fletcher* & K. Weninger n 

Sources: Crossref, ORCID
Added: February 5, 2020

2015 journal article

MutL traps MutS at a DNA mismatch

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112(35), 10914–10919.

By: R. Qiu n, M. Sakato*, E. Sacho n, H. Wilkins*, X. Zhang*, P. Modrichd, M. Hingorani *, D. Erie *, K. Weninger n 

author keywords: DNA mismatch repair; MutS; MutL; FRET
MeSH headings : Bacterial Proteins / genetics; Base Pair Mismatch; Genes, Bacterial; Thermus / genetics
TL;DR: It is discovered that MutL fundamentally changes the properties of mismatch-bound MutS by preventing it from sliding away from the mismatch, which it normally does when isolated, and suggests a mechanism for localizing the activity of repair proteins near the mismatch. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2015 journal article

Phosphorylation-induced Conformational Ensemble Switching in an Intrinsically Disordered Cancer/Testis Antigen

JOURNAL OF BIOLOGICAL CHEMISTRY, 290(41), 25090–25102.

By: Y. He *, Y. Chen *, S. Mooney*, K. Rajagopalan *, A. Bhargava, E. Sacho n, keith, P. Bryan * ...

MeSH headings : Amino Acid Sequence; Antigens, Neoplasm / chemistry; Antigens, Neoplasm / metabolism; Cell Line, Tumor; Humans; Male; Models, Molecular; Molecular Sequence Data; Phosphorylation; Prostatic Neoplasms / pathology; Protein Conformation
TL;DR: It is shown that the PAGE4 polypeptide chain has local and long-range conformational preferences that are perturbed by site-specific phosphorylation at Thr-51, which is critical for potentiating c-Jun transactivation, an important factor in controlling cell growth, apoptosis, and stress response. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2015 journal article

Toward Adding Complexity in Single Molecule FRET Studies of DNA Mismatch Repair

Biophysical Journal, 108(2), 69a–70a.

By: k. weninger n , P. Hao n, Y. Yang  n, E. Sacho  n & R. Qiu n

TL;DR: Recent progress developing single molecule FRET assays for more complex studies of DNA repair is presented, including work using unnatural amino acid engineering and other methods for site-specific labeling of yeast repair proteins, detailed analysis of kinetics to reveal nucleotide regulation of protein conformations, and steps toward studies in live cells. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: February 5, 2020

2014 journal article

Cancer/Testis Antigen PAGE4, a Regulator of c-Jun Transactivation, Is Phosphorylated by Homeodomain-Interacting Protein Kinase 1, a Component of the Stress-Response Pathway

BIOCHEMISTRY, 53(10), 1670–1679.

By: S. Mooney*, R. Qiu n, J. Kim*, E. Sacho n, K. Rajagopalan *, D. Johng, T. Shiraishi *, P. Kulkarni, K. Weninger n 

MeSH headings : Amino Acid Motifs; Antigens, Neoplasm / chemistry; Antigens, Neoplasm / genetics; Antigens, Neoplasm / metabolism; Cell Line, Tumor; Humans; Male; Phosphorylation; Prostatic Neoplasms / enzymology; Prostatic Neoplasms / genetics; Prostatic Neoplasms / metabolism; Prostatic Neoplasms / physiopathology; Protein Binding; Protein Serine-Threonine Kinases / genetics; Protein Serine-Threonine Kinases / metabolism; Proto-Oncogene Proteins c-jun / genetics; Proto-Oncogene Proteins c-jun / metabolism; Signal Transduction; Stress, Physiological; Testis / metabolism; Transcriptional Activation
TL;DR: The present results clearly implicate PAGE4 as a component of the stress-response pathway and uncover a novel link between components of this pathway and prostatic development and disease. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 journal article

Dynamics of MutS-Mismatched DNA Complexes Are Predictive of Their Repair Phenotypes

BIOCHEMISTRY, 53(12), 2043–2052.

By: V. DeRocco*, L. Sass, R. Qiu n, K. Weninger n  & D. Erie

MeSH headings : Bacterial Proteins / chemistry; Bacterial Proteins / genetics; DNA Repair / genetics; Fluorescence Resonance Energy Transfer; INDEL Mutation; MutS DNA Mismatch-Binding Protein / chemistry; MutS DNA Mismatch-Binding Protein / genetics; Phenotype; Predictive Value of Tests; Signal Transduction / genetics; Thermus / enzymology; Thermus / genetics
TL;DR: Comparison of MutS and MutS-E41A dynamics on GT and the T-bulge suggests that hydrogen bonding to MutS facilitates the changes in base–base hydrogen bonding that are required to achieve the U state, which has been implicated in repair signaling. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 journal article

Investigation of Calcein for Reporting Content Mixing During Viral Membrane Fusion Experiments

Biophysical Journal, 106(2), 707a.

By: L. Wessels* & K. Weninger n 

TL;DR: It is reported that osmotic balancing of the interior and exterior of the calcein-loaded vesicles is essential for these experiments to reproduce native virus fusion behaviors. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: September 8, 2020

2014 journal article

Single molecule studies of DNA mismatch repair

DNA REPAIR, 20, 71–81.

By: D. Erie * & K. Weninger n 

author keywords: Mismatch repair; One-dimensional diffusion; Single-molecule fluorescence; FRET; Atomic force microscopy; AFM; Single particle tracking; Protein-DNA interactions
MeSH headings : Amino Acid Sequence; Animals; DNA Mismatch Repair; DNA Repair Enzymes / chemistry; Fluorescence Resonance Energy Transfer / methods; Humans; Microscopy, Atomic Force / methods; Molecular Sequence Data; Optical Tweezers
TL;DR: Applications of single molecule methodology including electron microscope, atomic force microscopy, particle tracking, FRET, and optical trapping to studies of DNA mismatch repair are discussed. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 journal article

The Stress-response protein prostate-associated gene 4, interacts with c-Jun and potentiates its transactivation

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE, 1842(2), 154–163.

By: K. Rajagopalan *, R. Qiu n, S. Mooney*, S. Rao*, T. Shiraishi *, E. Sacho n, H. Huang*, E. Shapiro* ...

author keywords: PAGE4; Cancer/Testis Antigen; c-Jun; smFRET; Prostate cancer; Intrinsically disordered protein
MeSH headings : 3' Untranslated Regions / genetics; Antigens, Neoplasm / chemistry; Antigens, Neoplasm / genetics; Antigens, Neoplasm / metabolism; Cell Line, Tumor; Cyclin-Dependent Kinase Inhibitor p27 / genetics; Cyclin-Dependent Kinase Inhibitor p27 / metabolism; Fluorescence Resonance Energy Transfer; Gene Expression Regulation, Neoplastic; Humans; Immunohistochemistry; Male; MicroRNAs / genetics; MicroRNAs / metabolism; Mutation; Prostate / embryology; Prostate / growth & development; Prostate / metabolism; Prostatic Neoplasms / genetics; Prostatic Neoplasms / metabolism; Prostatic Neoplasms / pathology; Protein Binding; Protein Conformation; Proto-Oncogene Mas; Proto-Oncogene Proteins c-jun / genetics; Proto-Oncogene Proteins c-jun / metabolism; Reverse Transcriptase Polymerase Chain Reaction; Stress, Physiological; Transcriptional Activation
TL;DR: PAGE4 specifically interacts with c-Jun and that, conformational dynamics may account for its observed pleiotropic functions, the first report demonstrating crosstalk between a CTA and a proto-oncogene. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2013 journal article

Dynamics of DNA Mismatch Repair Initiation Complex Revealed by Single Molecule Fluorescence

Biophysical Journal, 104(2), 368a.

By: R. Qiu n & K. Weninger n 

TL;DR: Single molecule fluorescence resonance energy transfer (smFRET) is used to characterize conformational changes in this ternary complex through the process of mismatch recognition, MutS-MutL interaction and large MutS and MutL assembly formation on DNA and found that the sliding clamp formation of MutS is inhibited by MutL interaction. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: September 8, 2020

2012 journal article

Conformational Changes in MutS during Mismtach Repair Signaling Determined with Single Molecule FRET

Biophysical Journal, 102(3), 283a.

By: R. Qiu n & K. Weninger n 

TL;DR: It is found that DNA binding domains of MutS undergo large movements as it is converted to sliding clamp in a two step process, which results in a ring conformation that allows MutS to slide on DNA. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Crossref, ORCID
Added: September 8, 2020

2012 journal article

Cooperative All-Or-None Recruitment of Synaptotagmin C2AB on Single Vesicles Explains Why Ca2+ Regulates the Amplitude of SNARE Mediated Vesicle Fusion

Biophysical Journal, 102(3), 318a–319a.

By: D. Stamou *, S. Christensen *, N. Ehrlich *, V. Tkach*, J. Sakon  n, U. Choi  n, K. Weninger n 

TL;DR: It is demonstrated that this striking phenotype originates from the highly cooperative binding of syt to membranes that results to an all-or-none recruitment at the single vesicle level1-4 which is regulated by Ca2+. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Crossref, ORCID
Added: September 8, 2020

2012 journal article

Dynamics of DNA Mismatch Repair Revealed by Single Molecule FRET

Biophysical Journal, 102(3), 235a.

By: K. Weninger n 

TL;DR: This work uses smFRET to determine dynamic DNA bending by MutS, concomitant conformational changes within MutS itself, motion of MutS scanning along DNA, ATP binding states that commit MutS:mismatch DNA complexes to convert to sliding states used in signaling, and the modulation of these MutS behaviors by interactions with MutL. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: December 27, 2020

2012 journal article

Large conformational changes in MutS during DNA scanning, mismatch recognition and repair signalling

EMBO JOURNAL, 31(11), 2528–2540.

By: R. Qiu n, V. DeRocco*, C. Harris*, A. Sharma*, M. Hingorani *, D. Erie *, K. Weninger n 

author keywords: DNA mismatch repair; MMR; MutS; protein conformational change; sliding clamp
MeSH headings : Adenosine Diphosphate / chemistry; Adenosine Triphosphate / chemistry; DNA Mismatch Repair / genetics; DNA Mismatch Repair / physiology; Fluorescence Resonance Energy Transfer; MutS DNA Mismatch-Binding Protein / chemistry; MutS DNA Mismatch-Binding Protein / genetics; MutS DNA Mismatch-Binding Protein / metabolism; Protein Conformation
TL;DR: It is found that the DNA‐binding domains of MutS dynamically interconvert among multiple conformations when the protein is free and while it scans homoduplex DNA. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2012 chapter

Macromolecular Models by Single Molecule FRET

In NATO Science for Peace and Security Series B: Physics and Biophysics (pp. 1–19).

By: A. Brunger*, P. Strop *, M. Vrljic*, M. Bowen *, S. Chu * & K. Weninger n 

TL;DR: Recent applications of single molecule FRET are discussed to obtain a model of the synaptotagmin-1:SNARE complex and to study the conformation of PSD-95. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: September 8, 2020

2012 journal article

Opacity and Transport Measurements Reveal That Dilute Plasma Models of Sonoluminescence Are Not Valid

PHYSICAL REVIEW LETTERS, 108(10).

By: S. Khalid, B. Kappus*, K. Weninger n  & S. Putterman *

TL;DR: It is suggested that the effects of strong Coulomb interactions are an essential component of a first principles theory of sonoluminescence and can be 1000 times more opaque than what follows from the Saha equation of statistical mechanics in the ideal plasma limit. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2012 journal article

Single Molecule FRET Studies of the DNA Mismatch Repair Protein MutSα using Specific Labeling with Unnatural Amino Acids

Biophysical Journal, 102(3), 282a.

By: E. Sacho  n & K. Weninger n 

TL;DR: This work seeks to understand the mechanism behind the initiation step of mismatch repair in eukaryotes: binding of MutSα (Msh2 - Msh6) to mismatched DNA, and reports progress using unnatural amino acid labeling approaches. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Crossref, ORCID
Added: September 8, 2020

2011 journal article

Beyond the Random Coil: Stochastic Conformational Switching in Intrinsically Disordered Proteins

STRUCTURE, 19(4), 566–576.

By: U. Choi n, J. McCann *, K. Weninger n  & M. Bowen *

TL;DR: Surprisingly, two proteins, neuroligin and the NMDAR-2B glutamate receptor, were observed to stochastically switch among distinct conformational states despite the fact that they appeared intrinsically disordered by other measures. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2011 article

Complexin arrests a neighbor

Weninger, K. R. (2011, August). NATURE STRUCTURAL & MOLECULAR BIOLOGY, Vol. 18, pp. 861–863.

By: K. Weninger n 

MeSH headings : Adaptor Proteins, Signal Transducing / physiology; Adaptor Proteins, Vesicular Transport / chemistry; Animals; Humans; Nerve Tissue Proteins / chemistry; SNARE Proteins / chemistry; Synaptotagmins / physiology; Vesicle-Associated Membrane Protein 2 / chemistry
TL;DR: A series of studies address the problem of complexin's contradictory double life by revealing a switchable complexin conformation in which fusion arrest occurs when complexin clamps neighboring SNAREs. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2011 journal article

Single Molecule FRET Study of Nucleotide Binding Effects on Muts Proteins

Biophysical Journal, 100(3), 223a.

By: R. Qiu & K. Weninger* 

TL;DR: Possible roles for ATP cycling that could regulate the function of MutS in DNA MMR are suggested and MutS-DNA conformations resulting from specific nucleotide bound states to be characterized are suggested. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Crossref, ORCID
Added: September 8, 2020

2011 journal article

Three-dimensional molecular modeling with single molecule FRET

JOURNAL OF STRUCTURAL BIOLOGY, 173(3), 497–505.

By: A. Brunger *, P. Strop *, M. Vrljic*, S. Chu * & K. Weninger n 

author keywords: Single molecule fluorescence; FRET; Molecular dynamics; Protein-protein interactions
MeSH headings : Computer Simulation; Fluorescence Resonance Energy Transfer / methods; Fluorescent Dyes / chemistry; Image Processing, Computer-Assisted; Macromolecular Substances / chemistry; Models, Molecular; Molecular Conformation
TL;DR: The experimental and computational methods used for three-dimensional modeling based on single molecule fluorescence resonance transfer are reviewed, and recent progress in pushing the limits of this approach to macromolecular complexes is described. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2010 journal article

Detecting the conformation of individual proteins in live cells

NATURE METHODS, 7(3), 203–U56.

By: J. Sakon n & K. Weninger n 

MeSH headings : Cells, Cultured; Fluorescence Resonance Energy Transfer; Humans; Membrane Fusion; Protein Conformation; Protein Folding; SNARE Proteins / chemistry; Synaptosomal-Associated Protein 25
TL;DR: Single-molecule fluorescence resonance energy transfer with single-particle tracking in live cells to detect the in vivo conformation of individual proteins shows the potential of this method to reveal dynamic interactions within cells. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2010 journal article

Four-color single-molecule fluorescence with noncovalent dye labeling to monitor dynamic multimolecular complexes

BIOTECHNIQUES, 49(5), 807-+.

By: V. DeRocco*, T. Anderson n, J. Piehler *, D. Erie * & K. Weninger n 

author keywords: FRET; MutS; Msh2; Msh6; DNA mismatch repair; SNARE proteins; Munc-18
MeSH headings : Coloring Agents; DNA / chemistry; DNA Mismatch Repair; Energy Transfer; Fluorescence Resonance Energy Transfer / methods; Histidine; Macromolecular Substances / chemistry; MutS DNA Mismatch-Binding Protein / analysis; MutS DNA Mismatch-Binding Protein / chemistry; MutS DNA Mismatch-Binding Protein / pharmacology; Nitrilotriacetic Acid; Nucleic Acid Conformation / drug effects; Protein Conformation / drug effects; SNARE Proteins / chemistry; Tromethamine
TL;DR: These methods are combined to colocalize the mismatch repair protein MutSα on DNA while monitoring MutS α-induced DNA bending using Förster resonance energy transfer (FRET) and to monitor assembly of membrane-tethered SNARE protein complexes. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2010 journal article

Optimizing Methods to Recover Absolute FRET Efficiency from Immobilized Single Molecules

BIOPHYSICAL JOURNAL, 99(3), 961–970.

By: J. McCann *, U. Choi n, L. Zheng*, K. Weninger n  & M. Bowen *

MeSH headings : Animals; Base Sequence; DNA / chemistry; DNA / genetics; Disks Large Homolog 4 Protein; Fluorescence Resonance Energy Transfer / methods; Immobilized Proteins / chemistry; Intracellular Signaling Peptides and Proteins / chemistry; Membrane Proteins / chemistry; Molecular Sequence Data; Mutant Proteins / chemistry; Photobleaching; Rats; Reference Standards
TL;DR: This is the first systematic study of methods to recover the true FRET efficiency using DNA rulers with known fluorophore separations and per-molecule gamma-normalization was the most effective depending on how it was applied. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2010 journal article

Recovering Absolute Fret Efficiency from Single Molecules: Comparing Methods of Gamma Correction

Biophysical Journal, 98(3), 186a–187a.

By: J. McCann *, U. Choi *, L. Zheng*, K. Weninger n  & M. Bowen *

TL;DR: It was found that gamma correction based on single molecule photobleaching was the most effective particularly when gamma was determined for each sample or even each molecule. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Crossref, ORCID
Added: September 8, 2020

2010 journal article

Single-Molecule FRET TACKLE Reveals Highly Dynamic Mismatched DNA-MutS Complexes

BIOCHEMISTRY, 49(14), 3174–3190.

By: L. Sass, C. Lanyi, K. Weninger n  & D. Erie

MeSH headings : Base Pair Mismatch; DNA / chemistry; Fluorescence Resonance Energy Transfer; Kinetics; MutS DNA Mismatch-Binding Protein / chemistry; Nucleic Acid Conformation; Protein Binding; Protein Conformation
TL;DR: The results suggest that the dynamics of the MutS-mismatch complex could govern the efficiency of repair of different DNA mismatches, and this FRET TACKLE method will enable the analysis of the complex dynamics of other biological systems. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2010 journal article

Single-molecule FRET-derived model of the synaptotagmin 1-SNARE fusion complex

NATURE STRUCTURAL & MOLECULAR BIOLOGY, 17(3), 318–U84.

By: U. Choi n, P. Strop *, M. Vrljic*, S. Chu *, A. Brunger * & K. Weninger n 

MeSH headings : Animals; Calcium / metabolism; Chromatography, Affinity; Chromatography, Gel; Chromatography, Ion Exchange; Fluorescence Resonance Energy Transfer; Protein Binding; Rats; Recombinant Fusion Proteins / chemistry; Recombinant Fusion Proteins / genetics; Recombinant Fusion Proteins / metabolism; SNARE Proteins / chemistry; SNARE Proteins / genetics; SNARE Proteins / metabolism; Synaptotagmin I / chemistry; Synaptotagmin I / genetics; Synaptotagmin I / metabolism
TL;DR: An experimentally determined model of the elusive Syt1–SNARE complex is obtained using a multibody docking approach with 34 FRET-derived distances as restraints, suggesting a common mechanism by which the interaction between synaptotagmins and SNAREs aids in Ca2+-triggered fusion. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2010 journal article

Vesicle-associated Membrane Protein (VAMP) Cleavage by a New Metalloprotease from the Brazilian Scorpion Tityus serrulatus

JOURNAL OF BIOLOGICAL CHEMISTRY, 285(10), 7405–7416.

By: P. Fletcher*, M. Fletcher*, K. Weninger n , T. Anderson n & B. Martin*

MeSH headings : Amino Acid Sequence; Animals; Guinea Pigs; Immunohistochemistry; Metalloproteases / metabolism; Metalloproteases / ultrastructure; Models, Molecular; Molecular Sequence Data; Pancreas, Exocrine / anatomy & histology; Pancreas, Exocrine / metabolism; Protein Conformation; Protein Isoforms / metabolism; R-SNARE Proteins / metabolism; R-SNARE Proteins / ultrastructure; SNARE Proteins / metabolism; Scorpion Venoms / enzymology; Scorpions / enzymology; Secretory Vesicles / chemistry; Secretory Vesicles / ultrastructure
TL;DR: Evidence is presented that venom from the Brazilian scorpion Tityus serrulatus and a purified fraction selectively cleave essential SNARE proteins within exocrine pancreatic tissue and the unique cleavages of VAMP2 and VAMP8 may be linked to pancreatitis that develops following scorpion envenomation. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2009 journal article

Fluorescence quenching effects of nanocrystalline diamond surfaces

DIAMOND AND RELATED MATERIALS, 18(1), 82–87.

By: J. Sakon, G. Ribeill, J. Garguilo*, J. Perkins, K. Weninger*  & R. Nemanich*

author keywords: Nanocrystalline; Diamond film; Biocompatibility; Optical properties
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2009 article

How Do Adhesion Proteins Stick?

Weninger, K. (2009, August 12). STRUCTURE, Vol. 17, pp. 1035–1036.

By: K. Weninger n 

MeSH headings : Binding Sites / genetics; Cadherins / chemistry; Cadherins / genetics; Cadherins / metabolism; Calcium / chemistry; Calcium / pharmacology; Cell Line; Fluorescence Resonance Energy Transfer; Humans; Microscopy, Atomic Force; Mutation; Protein Binding; Protein Conformation / drug effects; Protein Multimerization; Protein Structure, Tertiary; Transfection; Tryptophan / chemistry; Tryptophan / genetics; Tryptophan / metabolism
TL;DR: Combining single molecule fluorescence and force analyses allowed Sivasankar et al. to provide strong evidence for an induced fit pathway to dimerization. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2009 journal article

Photoinactivation of Sindbis Virus Infectivity Without Inhibition of Membrane Fusion

PHOTOCHEMISTRY AND PHOTOBIOLOGY, 85(3), 801–806.

By: W. Thongthai n & K. Weninger n 

MeSH headings : Animals; Cells, Cultured; Cricetinae; Electrophoresis, Polyacrylamide Gel; Liposomes; Membrane Fusion; Sindbis Virus / pathogenicity; Sindbis Virus / radiation effects; Virulence / radiation effects
TL;DR: It is shown that photobleaching of Sindbis virus labeled with the membrane localized dye, R18 (octadecyl rhodamine B) causes a dramatic loss of infectivity without observable changes in low‐pH triggered membrane fusion to liposomes, and electrophoretic gel analysis suggests no cross‐linking of viral fusion proteins following photobreaching of dye‐labeled Sindbis. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2009 review

Physical Aspects of Viral Membrane Fusion

[Review of ]. THESCIENTIFICWORLDJOURNAL, 9, 764–780.

By: L. Wessels n & K. Weninger n 

author keywords: viral membrane fusion; class I, II, and III fusion proteins; hemagluttin (HA); E1; gp64
MeSH headings : Membrane Fusion; Protein Conformation; Viral Proteins / chemistry; Virus Physiological Phenomena
TL;DR: This work focuses on the key dynamical aspects of fusion protein structure, along with some of the experimental and computational techniques presently being used to investigate viral-mediated membrane fusion. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2009 article

Single-Molecule Studies of the Neuronal SNARE Fusion Machinery

ANNUAL REVIEW OF BIOCHEMISTRY, Vol. 78, pp. 903–928.

By: A. Brunger *, K. Weninger n , M. Bowen * & S. Chu

author keywords: FRET; membrane fusion; neurotransmission; synaptic vesicle
MeSH headings : Animals; Fluorescence; Humans; Microscopy, Atomic Force; Neurons / chemistry; Neurons / metabolism; SNARE Proteins / chemistry; SNARE Proteins / metabolism; Spectrum Analysis / methods; Synaptotagmins / chemistry
TL;DR: Applications of single-molecule approaches to observe reconstituted SNAREs, their complexes, associated proteins, and their effect on biological membranes are discussed. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2008 journal article

Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1 : 1 syntaxin/SNAP-25 complex

STRUCTURE, 16(2), 308–320.

By: K. Weninger n , M. Bowen *, U. Choi n, S. Chu * & A. Brunger *

MeSH headings : Fluorescence Resonance Energy Transfer; Lipid Bilayers / metabolism; Protein Structure, Tertiary; Qa-SNARE Proteins / chemistry; Qa-SNARE Proteins / metabolism; R-SNARE Proteins / metabolism; SNARE Proteins / metabolism; Synaptosomal-Associated Protein 25 / chemistry; Synaptosomal-Associated Protein 25 / metabolism
TL;DR: The structure of the 1:1 syntaxin/SNAP-25 binary complex is variable, with states changing on the second timescale, and one state corresponds to a parallel three-helix bundle, whereas other states show one of the SNAP-25 SNARE domains dissociated. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2007 journal article

Infection of cells by Sindbis virus at low temperature

Virology, 362(2), 461–467.

By: G. Wang n, R. Hernandez n, keith & D. Brown n

MeSH headings : Animals; Cell Fusion; Cell Line; Cricetinae; Endocytosis; Microscopy, Immunoelectron; Neutral Red / metabolism; Sindbis Virus / physiology; Temperature; Time Factors; Viral Plaque Assay; Virus Internalization
TL;DR: The ability of Sind Bis virus to infect Baby Hamster Kidney cells at temperatures which block endocytosis is examined and it is found that under these conditions Sindbis virus infects cells in a temperature- and time-dependent fashion. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: NC State University Libraries, ORCID
Added: August 6, 2018

2007 journal article

Kinetics of complexin binding to the SNARE complex: Correcting single molecule FRET measurements for hidden events

BIOPHYSICAL JOURNAL, 93(6), 2178–2187.

By: Y. Li *, G. Augustine* & K. Weninger n 

MeSH headings : Animals; Binding Sites; Biophysical Phenomena; Biophysics; Fluorescence Resonance Energy Transfer; In Vitro Techniques; Kinetics; Ligands; Liposomes; Microscopy, Fluorescence; Models, Molecular; Multiprotein Complexes; Nerve Tissue Proteins / chemistry; Nerve Tissue Proteins / genetics; Nerve Tissue Proteins / metabolism; Protein Binding; Rats; Recombinant Fusion Proteins / chemistry; Recombinant Fusion Proteins / genetics; Recombinant Fusion Proteins / metabolism; SNARE Proteins / chemistry; SNARE Proteins / metabolism
TL;DR: These rate constants provide a quantitative framework for modeling of the cascade of reactions underlying exocytosis of SNARE complexes and establish a general approach for improving single-molecule measurements of intermolecular binding kinetics. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2007 journal article

Rapid membrane fusion of individual virus particles with supported lipid bilayers

BIOPHYSICAL JOURNAL, 93(2), 526–538.

By: L. Wessels n, M. Elting n , D. Scimeca n & K. Weninger n 

Contributors: L. Wessels n, M. Elting n , D. Scimeca n & K. Weninger n 

MeSH headings : Animals; Biophysical Phenomena; Biophysics; Chick Embryo; Cricetinae; Fluorescent Dyes; Hydrogen-Ion Concentration; In Vitro Techniques; Influenza A Virus, H3N2 Subtype / physiology; Lipid Bilayers / chemistry; Membrane Fusion / physiology; Models, Biological; Rhodamines; Sindbis Virus / physiology; Virion / physiology
TL;DR: A fluorescence assay using single particle tracking is introduced to observe lipid mixing between individual virus particles (influenza or Sindbis) and supported lipid bilayers to highlight the complex interaction between lipids, virus proteins, and buffer conditions in membrane fusion. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

Funding History

Funding history based on the linked ORCID record. Updated: February 16th, 2021 12:30

grant July 25, 2019 - May 31, 2023
Molecular mechanisms of DNA mismatch repair initiation
National Institute of General Medical Sciences
grant September 15, 2017 - August 31, 2021
Fast single-molecule refractive index binding sensor
National Institute of General Medical Sciences
grant July 1, 2016 - April 30, 2021
Trinucleotide Repeats: Atypical Structures, Diseases, and Evolution
National Institute of General Medical Sciences
grant June 1, 2014 - May 31, 2019
Quantitative analysis of transient DNA repair processes in vivo
National Institute of General Medical Sciences
grant May 1, 2006 - August 31, 2009
Detecting Individual Protein Conformation in Live Cells
National Institute of General Medical Sciences

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