Celeste Sagui

Works (68)

Updated: November 15th, 2024 05:01

2024 review

Structural and Dynamical Properties of Nucleic Acid Hairpins Implicated in Trinucleotide Repeat Expansion Diseases

[Review of ]. BIOMOLECULES, 14(10).

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

author keywords: trinucleotide repeats; expansion diseases; hairpin structure; single-molecule FRET; smFRET; molecular dynamics simulations; CAG and GAC; CTG and GTC
Sources: Web Of Science, NC State University Libraries
Added: November 12, 2024

2023 article

Conformationally Restricted Glycopeptide Backbone Inhibits Gas-Phase H/D Scrambling between Glycan and Peptide Moieties

Code, C., Qiu, D., Solov'yov, I. A., Lee, J.-G., Shin, H.-C., Roland, C., … Jorgensen, T. J. D. (2023, October 26). JOURNAL OF THE AMERICAN CHEMICAL SOCIETY.

By: C. Code *, D. Qiu*, I. Solov'yov *, J. Lee*, H. Shin *, C. Roland n, C. Sagui n, D. Houde *, K. Rand *, T. Jorgensen *

TL;DR: The results show that complete scrambling precedes the glycosidic bond cleavage in normal glycopeptides derived from a glycoprotein; i.e., all labile hydrogens have undergone positional randomization prior to loss of the glycan. (via Semantic Scholar)
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Source: Web Of Science
Added: November 20, 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)
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Sources: Web Of Science, NC State University Libraries
Added: May 22, 2023

2023 journal article

Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal

ELIFE, 12.

By: T. Kandola*, S. Venkatesan *, J. Zhang n, B. Lerbakken*, A. Von Schulze *, J. Blanck*, J. Wu*, J. Unruh * ...

author keywords: amyloid; phase separation; Huntington's disease; polyglutamine; aging; S. cerevisiae
TL;DR: By uncovering the physical nature of the rate-limiting event for polyQ aggregation in cells, the findings elucidate the molecular etiology of polyQ diseases and show that self-poisoning can be exploited to block amyloid formation. (via Semantic Scholar)
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Source: Web Of Science
Added: February 19, 2024

2023 article

Structure and Dynamics of DNA and RNA Double Helices Formed by d(CTG), d(GTC), r(CUG), and r(GUC) Trinucleotide Repeats and Associated DNA-RNA Hybrids

Fakharzadeh, A., Qu, J., Pan, F., Sagui, C., & Roland, C. (2023, September 8). JOURNAL OF PHYSICAL CHEMISTRY B.

By: A. Fakharzadeh n, J. Qu n, F. Pan*, C. Sagui n & C. Roland n

TL;DR: Molecular dynamics simulations of homoduplexes associated with myotonic dystrophy type 1 found that the U·U and T·T mismatches are dynamic, favoring anti-anti conformations inside the helical core, followed by anti-syn and syn-syn conformations. (via Semantic Scholar)
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Source: Web Of Science
Added: October 10, 2023

2023 journal article

Unpolarized laser method for infrared spectrum calculation of amide I C=O bonds in proteins using molecular dynamics simulation

COMPUTERS IN BIOLOGY AND MEDICINE, 159.

By: V. Man *, X. He *, P. Nguyen *, C. Sagui n, C. Roland n, X. Xie *, J. Wang *

author keywords: IR spectra; Amide I; Radiation absorption; External electric field; MD simulation
MeSH headings : Molecular Dynamics Simulation; Amides / chemistry; Spectrophotometry, Infrared / methods; Proteins / chemistry; Peptides / chemistry; Hydrogen Bonding
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Source: Web Of Science
Added: May 30, 2023

2022 article

Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats

Fakharzadeh, A., Zhang, J., Roland, C., & Sagui, C. (2022, May 10). NUCLEIC ACIDS RESEARCH.

By: A. Fakharzadeh n, J. Zhang n, C. Roland n & C. Sagui n

MeSH headings : Base Pairing; DNA / chemistry; DNA / genetics; DNA, Z-Form; Guanine / chemistry; Nucleic Acid Conformation; Trinucleotide Repeats / genetics
TL;DR: Characterization of the stability and structural features (especially overall left-handedness, higher-temperature and steered MD simulations) identified two novel Z-DNA helices: the most stable one displays alternately extruded Gs, and is followed by a helix with symmetrically extruded ZZ junctions. (via Semantic Scholar)
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Added: May 23, 2022

2022 journal article

RNA as a Major-Groove Ligand: RNA-RNA and RNA-DNA Triplexes Formed by GAA and UUC or TTC Sequences

ACS OMEGA, 7(43), 38728–38743.

By: J. Zhang n, A. Fakharzadeh n, C. Roland n & C. Sagui n

TL;DR: An in silico investigation of all possible triplexes that form by attaching a third RNA strand to an RNA:RNA or DNA:DNA duplex, complementing previous DNA-based triplex studies and allowing for the emergence of a complete picture of the stability and structural characteristics of triPlexes based on the GAA and TTC/UUC sequences. (via Semantic Scholar)
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Added: November 21, 2022

2021 journal article

Construction of DNA/RNA Triplex Helices Based on GAA/TTC Trinucleotide Repeats

BIO-PROTOCOL, 11(18).

By: J. Zhang n, A. Fakharzadeh n, F. Pan *, C. Roland n & C. Sagui n

author keywords: DNA/RNA; Triplex helices; Molecular dynamics; Trinucleotide repeats
TL;DR: This protocol illustrates how to build up more generalized DNA triplexes and DNA/RNA mixed hybrids formed from GAA/TTC trinucleotide repeats, which underlie Friedreich's ataxia. (via Semantic Scholar)
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Source: Web Of Science
Added: October 26, 2021

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
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Sources: Web Of Science, NC State University Libraries
Added: August 30, 2021

2021 journal article

The F19W mutation reduces the binding affinity of the transmembrane A beta(11-40) trimer to the membrane bilayer

RSC ADVANCES, 11(5), 2664–2676.

By: T. Tran *, F. Pan*, L. Tran *, C. Roland n & C. Sagui n

TL;DR: Experiments show that F19 mutations influence the aggregation rate, but maintain the fibril structures in the 3Aβ11–40 trimer immersed in DPPC lipid bilayers submerged in aqueous solution, suggesting the impact of mutations can be assessed, at least partially, by evaluating the interaction of the mutated peptides with the lipid membranes. (via Semantic Scholar)
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Source: Web Of Science
Added: February 15, 2021

2020 journal article

Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich's ataxia: DNA triplexes and RNA/DNA hybrids

NUCLEIC ACIDS RESEARCH, 48(17), 9899–9917.

By: J. Zhang n, A. Fakharzadeh n, F. Pan n, C. Roland n & C. Sagui n

MeSH headings : DNA / chemistry; Friedreich Ataxia / genetics; Humans; Nucleic Acid Heteroduplexes / chemistry; R-Loop Structures; Trinucleotide Repeats
TL;DR: A systematic in silico characterization of the possible DNA triplexes that could be assembled with GAA and TTC strands contributes to a systematic structural basis for the emerging field of quantitative R-loop biology. (via Semantic Scholar)
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Added: January 4, 2021

2018 journal article

Structure and Dynamics of DNA and RNA Double Helices Obtained from the CCG and GGC Trinucleotide Repeats

JOURNAL OF PHYSICAL CHEMISTRY B, 122(16), 4491–4512.

By: F. Pan n, V. Man  n, C. Roland n & C. Sagui n

MeSH headings : DNA / chemistry; Molecular Dynamics Simulation; Nucleic Acid Conformation; RNA / chemistry; Trinucleotide Repeats
TL;DR: Molecular dynamics simulations of (GCC) n and (GGC) n homoduplexes are performed in order to characterize their conformations, stability, and dynamics, and a novel technique based on fast melting by means of an infrared laser pulse is used to classify the relative stability of the different DNA-CCG and -GGC homodups. (via Semantic Scholar)
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Added: August 6, 2018

2017 journal article

E-motif formed by extrahelical cytosine bases in DNA homoduplexes of trinucleotide and hexanucleotide repeats

NUCLEIC ACIDS RESEARCH, 46(2), 942–955.

By: F. Pan  n, Y. Zhang n, V. Man  n, C. Roland n & C. Sagui n

MeSH headings : Base Pairing; Base Sequence; Cytosine / chemistry; DNA / chemistry; DNA / genetics; Guanine / chemistry; Hydrogen Bonding; Microsatellite Repeats / genetics; Molecular Dynamics Simulation; Nucleic Acid Conformation; Nucleotide Motifs; Trinucleotide Repeats / genetics
TL;DR: Detailed molecular dynamics simulations of C-rich TR and HR DNA homoduplexes are performed in order to characterize the conformations, stability and dynamics of formation of the e-motif, where the mismatched cytosines symmetrically flip out in the minor groove, pointing their base moieties towards the 5′-direction in each strand. (via Semantic Scholar)
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Added: August 6, 2018

2017 journal article

Structural and Dynamical Characterization of DNA and RNA Quadruplexes Obtained from the GGGGCC and GGGCCT Hexanucleotide Repeats Associated with C9FTD/ALS and SCA36 Diseases

ACS CHEMICAL NEUROSCIENCE, 9(5), 1104–1117.

By: Y. Zhang n, C. Roland n & C. Sagui n

author keywords: Quadruplex; hexanucleotide repeats; DNA; RNA; G-quartets
MeSH headings : Amyotrophic Lateral Sclerosis / genetics; C9orf72 Protein / genetics; Circular Dichroism / methods; DNA / genetics; DNA Repeat Expansion / genetics; G-Quadruplexes / radiation effects; Humans; Models, Molecular; Nerve Tissue Proteins / genetics; Nuclear Proteins; Nucleic Acid Conformation / drug effects; RNA / genetics
TL;DR: A (GGGGCC) hexanucleotide repeat (HR) expansion in the C9ORF72 gene has been considered the major cause behind both frontotemporal dementia and amyotrophic lateral sclerosis, while a (GGGCCT) is associated with spinocerebellar ataxia 36. (via Semantic Scholar)
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Added: August 6, 2018

2017 journal article

Structure and Dynamics of DNA and RNA Double Helices of CAG and GAC Trinucleotide Repeats

BIOPHYSICAL JOURNAL, 113(1), 19–36.

By: F. Pan n, V. Man n, C. Roland n & C. Sagui n

MeSH headings : Cations / chemistry; DNA / chemistry; Hydrogen-Ion Concentration; Molecular Dynamics Simulation; Nucleic Acid Conformation; Principal Component Analysis; RNA / chemistry; Sodium / chemistry; Trinucleotide Repeats
TL;DR: Free energy and molecular dynamics studies are carried out to determine the preferred conformations of the A-A noncanonical pairs in (CAG)n and (GAC)n trinucleotide repeats and the consequent changes in the overall structure of the RNA and DNA duplexes, finding that the global free energy minimum corresponds to A- A pairs stacked inside the core of the helix with anti-anti conformations in RNA and (high-anti)-( high-anti) (via Semantic Scholar)
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Added: August 6, 2018

2016 journal article

Amyloid Properties of Asparagine and Glutamine in Prion-like Proteins

ACS Chemical Neuroscience, 7(5), 576–587.

By: Y. Zhang  n, V. Man  n, C. Roland n & C. Sagui n

author keywords: Prion; amyloid; protein aggregation; intrinsically disordered proteins; polyglutamine disease
MeSH headings : Amyloidogenic Proteins / chemistry; Amyloidogenic Proteins / metabolism; Asparagine / chemistry; Asparagine / metabolism; GPI-Linked Proteins / chemistry; GPI-Linked Proteins / metabolism; Glutamine / chemistry; Glutamine / metabolism; Molecular Dynamics Simulation; Prion Proteins / chemistry; Prion Proteins / metabolism; Prions / chemistry; Prions / metabolism
TL;DR: A comprehensive theoretical study of N/Q-rich peptides, including sequences found in the yeast Sup35 PrD, in parallel and antiparallel β-sheet aggregates, and probe via fully atomistic molecular dynamics simulations all their possible steric-zipper interfaces in order to determine their protofibril structure and their relative stability. (via Semantic Scholar)
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Sources: Web Of Science, Crossref
Added: August 6, 2018

2016 journal article

Comparative melting and healing of B-DNA and Z-DNA by an infrared laser pulse

JOURNAL OF CHEMICAL PHYSICS, 144(14).

By: V. Man n, F. Pan n, C. Sagui n & C. Roland n

MeSH headings : DNA, B-Form / chemistry; DNA, Z-Form / chemistry; Lasers; Molecular Dynamics Simulation; Thermodynamics
TL;DR: It is proposed that fast melting by an infrared laser pulse could be used as a technique for a fast comparison of relative stabilities of same-sequence oligonucleotides with different secondary structures with full atomistic detail of the structures and solvent. (via Semantic Scholar)
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Added: August 6, 2018

2016 journal article

Contrasting Roles of Asparagine and Glutamine in the Aggregation of Prion-Like Proteins

Biophysical Journal, 110(3), 214a–215a.

By: Y. Zhang  n, V. Hoang Man  n, C. Roland n & C. Sagui n

TL;DR: A variety of N/Q-rich peptides are considered, including sequences found in the yeast Sup35 PrD, in parallel and antiparallel β-sheet aggregates, and all their possible steric-zipper interfaces are probed to determine their relative stability. (via Semantic Scholar)
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Added: February 24, 2020

2016 journal article

Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses

PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18(17), 11951–11958.

By: V. Man n, N. Van-Oanh *, P. Derreumaux *, M. Li *, C. Roland n, C. Sagui n, P. Nguyen *

MeSH headings : Biocompatible Materials / chemistry; Humans; Infrared Rays; Lasers; Molecular Dynamics Simulation; Poliomyelitis / virology; Poliovirus / chemistry; Poliovirus / radiation effects; Virion / chemistry; Virion / radiation effects
TL;DR: All-atom nonequilibrium molecular dynamics simulation, inspired by the recently developed mid-infrared free-electron laser pulse technology, is carried out to dissociate viruses, showing a proof of concept which may open a new, efficient way to cleave or to recycle virus-based materials. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2016 journal article

Stability and Ion Distributions Around Left- and Right-Handed DNA and RNA Duplexes: A Comparative Study

Biophysical Journal, 110(3), 407a.

By: F. Pan  n, V. Man  n, C. Roland n & C. Sagui n

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Added: February 24, 2020

2016 journal article

Structural Determinants of Polyqlutamine Protofibrils and Crystallites

Biophysical Journal, 110(3), 215a.

By: V. Man  n, C. Roland n & C. Sagui n

TL;DR: This work uses fully atomistic molecular dynamics simulations to probe the structural stability and conformational dynamics of both previously proposed and new polyglutamine aggregate models, and tests the relative stability of parallel and antiparallel β sheets. (via Semantic Scholar)
Source: Crossref
Added: February 24, 2020

2016 journal article

Structure and Dynamics of DNA and RNA Double Helices Obtained from the GGGGCC and CCCCGG Hexanucleotide Repeats That Are the Hallmark of C9FTD/ALS Diseases

ACS CHEMICAL NEUROSCIENCE, 8(3), 578–591.

By: Y. Zhang n, C. Roland n & C. Sagui n

author keywords: Nucleotide repeat disorder; hexanucleotide repeat; C-C and G-G mismatches; C9FTD; ALS; e-motif
MeSH headings : Amyotrophic Lateral Sclerosis / genetics; Base Pair Mismatch; C9orf72 Protein; Chromosomes, Human, Pair 9 / genetics; DNA / chemistry; DNA Repeat Expansion; Frontotemporal Dementia / genetics; Humans; Models, Molecular; Nucleic Acid Conformation; Principal Component Analysis; Proteins / genetics; RNA / chemistry; Repetitive Sequences, Nucleic Acid / genetics
TL;DR: Molecular dynamics simulations are performed to characterize the conformation and dynamics of the 12 duplexes that result from the three different reading frames in sense and antisense HRs for both DNA and RNA, showing atypical structures relevant for a molecular level understanding of these diseases. (via Semantic Scholar)
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Added: August 6, 2018

2015 article

Calculating transition and reaction rates with nonequilibrium work measurements

XXVI IUPAP CONFERENCE ON COMPUTATIONAL PHYSICS (CCP2014), Vol. 640.

By: M. Moradi *, C. Sagui n & C. Roland n

Source: Web Of Science
Added: August 6, 2018

2015 journal article

Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study

JOURNAL OF CHEMICAL PHYSICS, 143(15).

By: M. Viet  n, P. Derreumaux *, M. Li *, C. Roland n, C. Sagui n & P. Nguyen *

MeSH headings : Amyloid / chemistry; Amyloid / radiation effects; Infrared Rays; Lasers; Molecular Dynamics Simulation; Time Factors
TL;DR: A theoretical framework for this type of experiment based on laser-induced nonequilibrium all-atom molecular dynamics simulations is presented and it is shown that the fibril is destroyed due to the strong resonance between its amide I vibrational modes and the laser field. (via Semantic Scholar)
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Added: August 6, 2018

2015 journal article

Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study

PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17(41), 27275–27280.

By: M. Viet  n, P. Truong*, P. Derreumaux *, M. Li *, C. Roland n, C. Sagui n, P. Nguyen *

MeSH headings : Dipeptides; Freezing; Infrared Rays; Lasers; Molecular Dynamics Simulation; Nanotechnology; Nanotubes / chemistry; Peptides / chemistry; Phenylalanine / analogs & derivatives; Phenylalanine / chemistry; Time Factors
TL;DR: A theoretical framework, inspired by the recent developed mid-infrared free-electron laser pulse technology, to dissociate peptide nanotubes and shows a proof of concept and should provide a motivation for future experimental developments to open a new and efficient way to cleave or to recycle bio-inspired materials. (via Semantic Scholar)
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Added: August 6, 2018

2015 journal article

Structural Determinants of Polyglutamine Protofibrils and Crystallites

ACS CHEMICAL NEUROSCIENCE, 6(4), 632–645.

By: V. Man n, C. Roland n & C. Sagui n

author keywords: Aggregation; amyloid fibrils; parallel sheets; antiparallel sheets; polyglutamine diseases; steric zippers
MeSH headings : Amyloid / chemistry; Amyloid / genetics; Hydrogen Bonding; Models, Chemical; Molecular Dynamics Simulation; Peptides / chemistry; Protein Conformation; Protein Stability; Time Factors
TL;DR: This work uses fully atomistic molecular dynamics simulations to probe the structural stability and conformational dynamics of both previously proposed and new polyglutamine aggregate models, and explains and reconcile previously reported experimental and model discrepancies about polyglUTamine aggregate structures. (via Semantic Scholar)
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Added: August 6, 2018

2015 article

The Adaptively Biased Molecular Dynamics method revisited: New capabilities and an application

XXVI IUPAP CONFERENCE ON COMPUTATIONAL PHYSICS (CCP2014), Vol. 640.

By: M. Moradi *, V. Babin n, C. Roland n & C. Sagui n

TL;DR: The workings of the ABMD method are reviewed with an emphasis on recent software additions, along with a short summary of a selected ABMD application based on the B-to-Z DNA transition. (via Semantic Scholar)
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Added: August 6, 2018

2014 journal article

Correction to Classical Electrostatics for Biomolecular Simulations

Chemical Reviews, 114(9), 5116–5116.

By: G. Cisneros, M. Karttunen, P. Ren & C. Sagui*

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Added: February 24, 2020

2014 journal article

Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities

The Journal of Chemical Physics, 140(3), 034114.

By: M. Moradi  n, C. Sagui n & C. Roland n

MeSH headings : Cluster Analysis; Computer Simulation; Dimerization; Models, Chemical; Probability; Proline / chemistry; Thermodynamics
TL;DR: An extension of Crook's transient fluctuation theorem is derived, which relates the relative transition rates of driven systems in the forward and reverse directions, and allows for the calculation of these relative rates using work measurements. (via Semantic Scholar)
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Added: February 24, 2020

2014 article

Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities (vol 140, 034114, 2014)

Moradi, M., Sagui, C., & Roland, C. (2014, February 14). JOURNAL OF CHEMICAL PHYSICS, Vol. 140.

By: M. Moradi n, C. Sagui n & C. Roland n

Source: Web Of Science
Added: August 6, 2018

2014 journal article

Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates

The Journal of Chemical Physics, 140(3), 034115.

By: M. Moradi  n, C. Sagui n & C. Roland n

MeSH headings : Computer Simulation; Dipeptides / chemistry; Models, Chemical; Molecular Dynamics Simulation; Probability; Thermodynamics
TL;DR: The formalism is based on combining Transition Path Theory with the results ofNonequilibrium work relations, and shows that the equilibrium and nonequilibrium transition rates are in fact related, which allows for the calculation of relative equilibrium reaction rates with driven nonequ equilibrium simulations such as Steered Molecular Dynamics. (via Semantic Scholar)
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Added: February 24, 2020

2014 article

Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates (vol 140, 034115, 2014)

Moradi, M., Sagui, C., & Roland, C. (2014, February 14). JOURNAL OF CHEMICAL PHYSICS, Vol. 140.

By: M. Moradi n, C. Sagui n & C. Roland n

Source: Web Of Science
Added: August 6, 2018

2014 journal article

Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study

NUCLEIC ACIDS RESEARCH, 42(22), 13981–13996.

By: F. Pan  n, C. Roland n & C. Sagui n

MeSH headings : Cations / chemistry; Cations, Divalent / chemistry; Cations, Monovalent / chemistry; Chlorides / chemistry; DNA, A-Form / chemistry; DNA, B-Form / chemistry; DNA, Z-Form / chemistry; Magnesium / chemistry; Molecular Dynamics Simulation; Osmolar Concentration; Potassium / chemistry; RNA, Double-Stranded / chemistry; Sodium / chemistry
TL;DR: The results quantitatively describe the characteristics of the ionic distributions for different structures at varying ionic strengths, tracing these differences to nucleic acid structure and ion type. (via Semantic Scholar)
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Added: August 6, 2018

2014 journal article

Secondary structure assignment for conformationally irregular peptides: Comparison between DSSP, STRIDE and KAKSI

JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 55, 72–84.

By: Y. Zhang n & C. Sagui n

author keywords: Residual transient secondary structure; Intrinsically disordered proteins; gp41; Asparagine
MeSH headings : Amino Acid Sequence; Amino Acids / chemistry; Computer Simulation; Hydrogen Bonding; Peptides / chemistry; Protein Structure, Secondary; Software
TL;DR: Molecular Dynamics simulations of (relatively) disordered peptides, specifically gp41659-671 (ELLELDKWASLWN), the homopeptide polyasparagine (N18), and polyAsparagine dimers, are carried out and the resulting conformations with DSSP and STRIDE, based on hydrogen-bond patterns (and dihedral angles for STRIDE), and KAKSI, basedon α-Carbon distances are analyzed. (via Semantic Scholar)
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Added: August 6, 2018

2013 journal article

Binding Polymorphism in the DNA Bound State of the Pdx1 Homeodomain

PLOS COMPUTATIONAL BIOLOGY, 9(8).

By: V. Babin n, D. Wang n, R. Rose  n & C. Sagui n

TL;DR: Both the crystal and aqueous simulations support the existence of different stable binding conformers identified in the original crystallographic data with different degrees of specificity and propose that protein-protein and protein-DNA interactions favor a subset of the possible conformations. (via Semantic Scholar)
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Added: August 6, 2018

2013 review

Classical Electrostatics for Biomolecular Simulations

[Review of ]. CHEMICAL REVIEWS, 114(1), 779–814.

By: G. Cisneros *, M. Karttunen *, P. Ren * & C. Sagui n

MeSH headings : Molecular Dynamics Simulation; Monte Carlo Method; Proteins / chemistry; Proteins / metabolism; Quantum Theory; Static Electricity
TL;DR: The QCTFF embraces multipolar electrostatics as a way to overcome the inherent limitations of point charge Electrostatics, and captures polarisation effects (beyond dipole moments) through a machine learning method called kriging. (via Semantic Scholar)
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Added: August 6, 2018

2013 journal article

The gp41(659-671) HIV-1 Antibody Epitope: A Structurally Challenging Small Peptide

JOURNAL OF PHYSICAL CHEMISTRY B, 118(1), 69–80.

By: Y. Zhang  n & C. Sagui n

MeSH headings : Epitopes / chemistry; Epitopes / immunology; HIV Antibodies / immunology; HIV Antigens / chemistry; HIV Antigens / immunology; HIV Envelope Protein gp41 / chemistry; HIV Envelope Protein gp41 / immunology; HIV-1 / chemistry; HIV-1 / immunology; Molecular Dynamics Simulation; Peptide Fragments / chemistry; Peptide Fragments / immunology; Protein Conformation
TL;DR: Detailed molecular dynamics simulations of the tridecapeptide corresponding to residues 659-671 of the envelope glycoprotein gp41 of HIV-1, which spans the 2F5 monoclonal antibody epitope ELDKWA, report on the conformational ensembles of the peptide in solution both without applied restraints and under successive tensile restraints. (via Semantic Scholar)
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Added: August 6, 2018

2012 journal article

Reaction path ensemble of the B-Z-DNA transition: a comprehensive atomistic study

NUCLEIC ACIDS RESEARCH, 41(1), 33–43.

By: M. Moradi  n, V. Babin n, C. Roland n & C. Sagui n

MeSH headings : Base Pairing; DNA, B-Form / chemistry; DNA, Z-Form / chemistry; Models, Molecular; Molecular Dynamics Simulation
TL;DR: It is found that the B–Z-DNA transition—in absence of other molecular partners—can encompass more than one mechanism of comparable free energy, and is therefore better described in terms of a reaction path ensemble. (via Semantic Scholar)
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Added: August 6, 2018

2011 journal article

A Statistical Analysis of the PPII Propensity of Amino Acid Guests in Proline-Rich Peptides

Biophysical Journal, 100(4), 1083–1093.

By: M. Moradi  n, V. Babin n, C. Sagui n & C. Roland n

MeSH headings : Models, Statistical; Odds Ratio; Peptides / chemistry; Proline / chemistry; Protein Structure, Secondary
TL;DR: A comprehensive analysis of the conformational equilibria of the proline-based host oligopeptides with single guests with state-of-the-art force fields finds no evidence for an intrinsic PPII propensity in any of the guest amino acids other than proline. (via Semantic Scholar)
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Sources: Web Of Science, Crossref
Added: August 6, 2018

2011 journal article

Calculating relative transition rates with driven nonequilibrium simulations

CHEMICAL PHYSICS LETTERS, 518, 109–113.

By: M. Moradi n, C. Sagui n & C. Roland n

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Source: Web Of Science
Added: August 6, 2018

2011 journal article

PPII Propensity of Multiple-Guest Amino Acids in a Proline-Rich Environment

The Journal of Physical Chemistry B, 115(26), 8645–8656.

By: M. Moradi  n, V. Babin n, C. Sagui n & C. Roland n

MeSH headings : Amino Acid Sequence; Amino Acids / chemistry; Molecular Structure; Peptides / chemistry; Peptides / genetics; Protein Conformation
TL;DR: This work has used classical molecular dynamics simulations combined with replica-exchange methods to carry out a comprehensive analysis of the conformational equilibria of proline-based host oligopeptides with multiple guest amino acids including alanine, glutamine, valine, and asparagine and found that the more guests added to the system, the larger the increase in the trans content of the prolyl bonds, which results in an effective increase in. (via Semantic Scholar)
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Sources: Crossref, Web Of Science
Added: August 6, 2018

2010 journal article

A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers

JOURNAL OF CHEMICAL PHYSICS, 133(12).

By: M. Moradi n, V. Babin n, C. Roland n & C. Sagui n

MeSH headings : Molecular Dynamics Simulation; Peptides / chemistry; Phase Transition; Protein Conformation; Thermodynamics
TL;DR: This work characterized the conformations and the free energy landscapes of Ace-(Pro)(n)-Nme, n=2,3, ... ,9, and 13 peptides both in vacuo and in an implicit solvent environment and quantitatively investigate transition pathways and mechanisms for the PPII to PPI transitions. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2010 journal article

Conformational free energies of methyl-alpha-L-iduronic and methyl-beta-D-glucuronic acids in water

JOURNAL OF CHEMICAL PHYSICS, 132(10).

By: V. Babin n & C. Sagui n

author keywords: free energy; molecular dynamics method; organic compounds; simulation
MeSH headings : Algorithms; Carbohydrate Sequence; Computer Simulation; Glucuronic Acid / chemistry; Iduronic Acid / chemistry; Molecular Conformation; Molecular Sequence Data; Thermodynamics; Water / chemistry
TL;DR: A simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent is presented and applied to the study of the puckering landscapes of the methyl glycosides of alpha-L-iduronic acid and its C5 epimer beta-D-glucuronic Acid in water. (via Semantic Scholar)
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7. Affordable and Clean Energy (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2010 journal article

Dimerization free energy of vancomycin-group antibiotics and the cooperative effect: A density functional approach

International Journal of Quantum Chemistry, 110(15), 2894–2902.

By: J. Lee n, C. Sagui n & C. Roland n

author keywords: vancomycin; chloro-eremomycin; cooperative effect; ab initio QM; divide- and conquer; free energy
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Sources: Crossref, NC State University Libraries
Added: August 6, 2018

2010 journal article

Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation

International Journal of Quantum Chemistry, 110(15), 2865–2879.

By: M. Moradi n, J. Lee n, V. Babin n, C. Roland n & C. Sagui n

author keywords: polyproline; free energy; PPII
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7. Affordable and Clean Energy (OpenAlex)
Sources: Crossref, NC State University Libraries
Added: August 6, 2018

2010 journal article

The α-sheet: A missing-in-action secondary structure?

Proteins: Structure, Function, and Bioinformatics, 79(3), 937–946.

By: V. Babin n, C. Roland n & C. Sagui n

author keywords: protein structure; molecular mechanics; amyloid; polyglutamine; protein aggregation
MeSH headings : Molecular Dynamics Simulation; Peptides / chemistry; Protein Structure, Secondary
TL;DR: Molecular dynamics simulations support the existence of the α‐sheet as a stable, metastable, or long‐lived secondary structure in polyglutamine and, to a lesser extent, in polyasparagine aggregates. (via Semantic Scholar)
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Added: August 6, 2018

2009 article

Adaptively Biased Molecular Dynamics: An Umbrella Sampling Method With a Time-Dependent Potential

Babin, V., Karpusenka, V., Moradi, M., Roland, C., & Sagui, C. (2009, December). INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Vol. 109, pp. 3666–3678.

By: V. Babin n, V. Karpusenka n, M. Moradi n, C. Roland n & C. Sagui n

author keywords: free energy; nonequilibrium; simulation
TL;DR: The workings of the ABMD method are illustrated with a number of examples, including sugar puckering, and free energy landscapes for polymethionine and polyproline peptides, and for a short -turn peptide. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2009 journal article

Conformations and free energy landscapes of polyproline peptides

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106(49), 20746–20751.

By: M. Moradi n, V. Babin n, C. Roland n, T. Darden & C. Sagui n

author keywords: cis-trans isomerization; left-handed helix; molecular dynamics; PPI; PPII
MeSH headings : Peptides / chemistry; Protein Conformation; Thermodynamics
TL;DR: Results show the existence of several metastable isomers and therefore provide a complementary view to experimental conclusions based on photo-induced electron transfer experiments with regard to the exist of stable heterogeneous subpopulations in PPII polyproline. (via Semantic Scholar)
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7. Affordable and Clean Energy (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2008 journal article

Adaptively biased molecular dynamics for free energy calculations

Journal of Chemical Physics, 128(13).

By: V. Babin n, C. Roland n & C. Sagui n

TL;DR: The workings of the ABMD method are illustrated via a study of the folding of the Ace-GGPGGG-Nme peptide in a gaseous and solvated environment. (via Semantic Scholar)
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7. Affordable and Clean Energy (OpenAlex)
Source: NC State University Libraries
Added: August 6, 2018

2008 journal article

Amino acid adsorption on the Si(100) surface: The case of glycine

JOURNAL OF PHYSICAL CHEMISTRY C, 112(7), 2640–2648.

By: X. Luo n, G. Qian n, C. Sagui n & C. Roland n

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7. Affordable and Clean Energy (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2008 article

Electrostatics in biomolecular simulations: Where are we now and where are we heading?

COMPUTATIONAL MODELING OF MEMBRANE BILAYERS, Vol. 60, pp. 49–89.

By: M. Karttunen *, J. Rottler *, I. Vattulainen * & C. Sagui n

TL;DR: Current methods and developments in the treatment of electrostatic interactions in biomolecular and soft matter simulations, and also newer real-space methods such as multigrid methods, and local algorithms for Coulomb's law are discussed. (via Semantic Scholar)
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16. Peace, Justice and Strong Institutions (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2007 journal article

Theoretical investigation of the interaction of glycine with diamond C(100) and C(111) (2x1) surfaces

JOURNAL OF PHYSICAL CHEMISTRY C, 111(34), 12760–12767.

By: K. Odbadrakh n, X. Luo  n, J. Lee n, C. Sagui n & C. Roland n

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Source: Web Of Science
Added: August 6, 2018

2006 journal article

Deprotonation of solvated formic acid: Car-Parrinello and metadynamics simulations

JOURNAL OF PHYSICAL CHEMISTRY B, 110(5), 2325–2331.

By: J. Lee n, E. Asciutto n, V. Babin n, C. Sagui n, T. Darden n & C. Roland n

MeSH headings : Computational Biology; Computer Simulation; Formates / chemistry; Hydrogen / chemistry; Models, Molecular; Oxygen / chemistry; Protons; Solvents / chemistry; Thermodynamics; Time Factors
TL;DR: The microscopics of deprotonation and reprotonation of formic acid reveal the key role played by nearby water molecules in catalyzing the reactions, and reveal barriers similar to that obtained with the constrained free-energy calculation. (via Semantic Scholar)
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Added: August 6, 2018

2006 journal article

Molecular dynamics simulations of DNA with polarizable force fields: Convergence of an ideal B-DNA structure to the crystallographic structure

JOURNAL OF PHYSICAL CHEMISTRY B, 110(23), 11571–11581.

By: V. Babin n, J. Baucom n, T. Darden n & C. Sagui n

MeSH headings : Base Sequence; Crystallography; DNA / chemistry; Nucleic Acid Conformation
TL;DR: This is the first example of multiple nanosecond molecular dynamics trajectory that shows an ideal B-DNA model converging to an experimental structure, with a significant decay of RMSD. (via Semantic Scholar)
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Added: August 6, 2018

2006 journal article

Molecular dynamics simulations of polarizable DNA in crystal environment

International Journal of Quantum Chemistry, 106(15), 3260–3269.

By: V. Babin n, J. Baucom n, T. Darden* & C. Sagui n

author keywords: DNA; electrostatics; polarizable; crystal
TL;DR: By imposing the experimental unit cell environment, an initial configuration with ideal B-DNA duplexes in the unit cell acquires sequence-dependent features that very closely resemble the crystallographic ones. (via Semantic Scholar)
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Sources: Crossref, Web Of Science
Added: August 6, 2018

2006 journal article

The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections

JOURNAL OF CHEMICAL PHYSICS, 125(20).

By: V. Babin n, C. Roland n, T. Darden* & C. Sagui n

MeSH headings : Algorithms; Computer Simulation; Energy Transfer; Kinetics; Models, Chemical; Models, Molecular; Peptides / chemistry; Protein Conformation
TL;DR: It is shown that the accuracy of the free energy landscape calculated with the metadynamics method may be considerably improved when combined with umbrella sampling techniques, and is to be distributed in the next scheduled release of the code. (via Semantic Scholar)
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7. Affordable and Clean Energy (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2005 journal article

Exploring intramolecular reactions in complex systems with metadynamics: The case of the malonate anions

JOURNAL OF PHYSICAL CHEMISTRY A, 109(34), 7682–7687.

By: E. Asciutto n & C. Sagui n

TL;DR: For both malonates, new isomers (keto and enol structures) characterized by CO(2) rotations and intramolecular proton transfers characterize the keto-enol tautomerism that takes place both in the monoanion and dianion. (via Semantic Scholar)
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7. Affordable and Clean Energy (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2005 journal article

New and exotic self-organized patterns for modulated nanoscale systems

NANO LETTERS, 5(2), 389–395.

By: C. Sagui n, E. Asciutto n & C. Roland n

MeSH headings : Computer Simulation; Crystallization / methods; Models, Chemical; Models, Molecular; Molecular Conformation; Nanostructures / analysis; Nanostructures / chemistry; Nanostructures / ultrastructure; Nanotechnology / methods; Phase Transition
TL;DR: This work has generated a variety of new and exotic patterns, which represent either metastable or glassy states of modulated systems, as a compromise between the required equilibrium modulation period and the strain resulting from topologically constrained trajectories in phase space that effectively preclude the equilibrium configuration. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2005 journal article

Quantum simulations of the structure and binding of glycopeptide antibiotic aglycons to cell wall analogues

JOURNAL OF PHYSICAL CHEMISTRY B, 109(43), 20588–20596.

By: J. Lee n, C. Sagui n & C. Roland n

MeSH headings : Anti-Bacterial Agents / chemistry; Anti-Bacterial Agents / metabolism; Binding Sites; Cell Wall / metabolism; Computer Simulation; Dipeptides; Drug Resistance, Bacterial; Glycopeptides / chemistry; Glycopeptides / metabolism; Models, Molecular; Protein Conformation; Quantum Theory; Staphylococcus aureus / drug effects; Vancomycin / chemistry; Vancomycin / pharmacology
TL;DR: An extensive first principles investigation of the binding of vancomycin, avoparcin, teicoplanin, and ristocetin aglycons with dipetides with Dipetides, in liquid as well as gas phase finds the order of Gly and d-Ala binding is reversed in solution. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2005 journal article

Self-assembled patterns and strain-induced instabilities for modulated systems

PHYSICAL REVIEW E, 72(2).

By: E. Asciutto n, C. Roland n & C. Sagui n

TL;DR: The domains and instabilities that form in modulated systems are analyzed, and it is shown that a large variety of patterns--based on long-lived metastable or glassy states--may be formed as a compromise between the required equilibrium modulation period and the strain present in the system. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2004 journal article

Ab initio calculation of electrostatic multipoles with Wannier functions for large-scale biomolecular simulations

JOURNAL OF CHEMICAL PHYSICS, 120(9), 4530–4544.

By: C. Sagui n, P. Pomorski n, T. Darden* & C. Roland n

MeSH headings : Algorithms; Biopolymers / chemistry; Computer Simulation; Electrochemistry / methods; Models, Chemical; Models, Molecular; Static Electricity
TL;DR: Tests on isolated molecules and water dimers, show that the molecular electrostatic potentials generated by such a Wannier-function based approach are in excellent agreement with the density functional-based calculations. (via Semantic Scholar)
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Added: August 6, 2018

2004 journal article

First principles investigation of vancomycin and teicoplanin binding to bacterial cell wall termini

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 126(27), 8384–8385.

By: J. Lee n, C. Sagui n & C. Roland n

MeSH headings : Alanine / analogs & derivatives; Alanine / metabolism; Anti-Bacterial Agents / metabolism; Anti-Bacterial Agents / pharmacology; Bacteria / drug effects; Bacteria / metabolism; Cell Wall / drug effects; Cell Wall / metabolism; Dipeptides / metabolism; Kinetics; Lactates / metabolism; Teicoplanin / metabolism; Teicoplanin / pharmacology; Thermodynamics; Vancomycin / metabolism; Vancomycin / pharmacology
TL;DR: An extensive first principles investigation of the binding of vancomycin and teicoplanin with d-Ala-d-Lac (characteristic of VREs and non-VREs) was found to be stronger by about 3-5 kcal/mol and due primarily to the oxygen-oxygen lone-pair repulsion characteristic of the antibiotic/d-AlA-d.Lac complex. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2004 journal article

Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer in crystal environment: Comparison of atomic point-charge, extra-point, and polarizable force fields

JOURNAL OF CHEMICAL PHYSICS, 121(14), 6998–7008.

By: J. Baucom n, T. Transue*, M. Fuentes-Cabrera n, J. Krahn *, T. Darden* & C. Sagui n

MeSH headings : Computer Simulation; Crystallization; Nucleic Acid Conformation; Oligodeoxyribonucleotides / chemistry; Sequence Analysis, DNA; Thermodynamics
TL;DR: The polarizable force field provides the most accurate representation of the crystal structure and the sequence-dependent effects observed in the experiment, and points out the need of the inclusion of polarization for accurate descriptions of DNA. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2004 journal article

Surface solvation for an ion in a water cluster

JOURNAL OF CHEMICAL PHYSICS, 122(2).

By: D. Herce n, L. Perera *, T. Darden* & C. Sagui n

TL;DR: Molecular dynamics simulations are used to study the structural, dynamical, and thermodynamical properties of ions in water clusters to address controversial or unresolved issues, related to the underlying physical cause of surface solvation and the basic assumptions that go with it. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2003 journal article

Calculation of ionic charging free energies in simulation systems with atomic charges, dipoles, and quadrupoles

Journal of Chemical Physics, 119(15), 7621–7632.

By: H. Herce n, T. Darden* & C. Sagui n

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UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Source: NC State University Libraries
Added: August 6, 2018

2003 journal article

Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations

JOURNAL OF CHEMICAL PHYSICS, 120(1), 73–87.

By: C. Sagui n, L. Pedersen * & T. Darden*

MeSH headings : Algorithms; Computational Biology; Computer Simulation; Molecular Conformation; Static Electricity; Thermodynamics; Water / chemistry
TL;DR: An efficient formalism is presented for the treatment of higher order multipoles in Cartesian tensor formalism that provides a natural way to interface with continuous, Gaussian-based electrostatics in the future and considerably reduces the cost of the calculation with respect to the standard matrix implementation of multipole interactions. (via Semantic Scholar)
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Added: August 6, 2018

2001 journal article

Liquid-crystal phases of capped carbon nanotubes

PHYSICAL REVIEW B, 63(8).

By: A. Somoza *, C. Sagui n & C. Roland n

Source: Web Of Science
Added: August 6, 2018

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