Works (30)
Updated: August 20th, 2024 05:01
2024 journal article
Design of parallel β-sheet nanofibrils using Monte Carlo search, coarse-grained simulations, and experimental testing
PROTEIN SCIENCE, 33(8).
author keywords: amyloid beta-sheet fibrils; DMD/PRIME20 simulations; peptide assembly design; peptide self-assembly
open access via onlinelibrary.wiley.com (publisher PDF)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 14, 2024
2023 journal article
Design of 8-mer peptides that block <i>Clostridioides difficile</i> toxin A in intestinal cells
COMMUNICATIONS BIOLOGY, 6(1).
TL;DR:
An approach that combines a Pep tide B inding D esign (PepBD) algorithm, molecular-level simulations, a rapid screening assay, and surface plasmon resonance (SPR) measurements to develop peptide inhibitors that block Toxin A in colon epithelial cells is described.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
14. Life Below Water
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 27, 2023
2022 journal article
<p>De novo discovery of peptide-based affinity ligands for the fab fragment of human immunoglobulin G</p>
JOURNAL OF CHROMATOGRAPHY A, 1669.
author keywords: Affinity ligands; Ligand design; Biorecognition; Protein chromatography; Fragment antigen binding
MeSH headings : Humans; Immunoglobulin Fab Fragments / chemistry; Immunoglobulin G; Ligands; Peptides; Tissue Distribution
TL;DR:
An integrated computational and experimental scheme is described to de novo design 9-mer peptides that bind to Fab fragments that lay the groundwork for future development of these ligands towards biomanufacturing translation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: May 2, 2022
2022 journal article
Computational Design and Experimental Validation of ACE2-Derived Peptides as SARS-CoV-2 Receptor Binding Domain Inhibitors
JOURNAL OF PHYSICAL CHEMISTRY B, 126(41), 8129–8139.
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: November 7, 2022
2022 journal article
Sequence patterns and signatures: Computational and experimental discovery of amyloid-forming peptides
PNAS NEXUS, 1(5).
author keywords: peptide assembly design; discontinuous molecular dynamics; amyloid-forming peptides; fourier-transform infrared spectroscopy; transmission electron microscopy
TL;DR:
Experimental results from Fourier transform infrared spectroscopy, thioflavin T (ThT) fluorescence, circular dichroism (CD), and transmission electron microscopy, indicate that all the peptides predicted to assemble in silico assemble into antiparallel β-sheet nanofibers in a concentration-dependent manner.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: October 23, 2023
2021 journal article
De novo design of peptides that coassemble into beta sheet-based nanofibrils
SCIENCE ADVANCES, 7(36).
TL;DR:
Computational discoveries and experimental characterizations of coassembly peptides that form β sheet–based nanofibrils suggest that the polyene-like structure dominates in peptide-like structures while in the case of nanoporous materials, the polymethine-based structure is preferred.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: September 27, 2021
2021 journal article
Engineering β-Sheet Peptide Coassemblies for Biomaterial Applications
The Journal of Physical Chemistry B, 125(50), 13599–13609.
MeSH headings : Biocompatible Materials; Magnetic Resonance Spectroscopy; Nanostructures; Peptides; Protein Conformation, beta-Strand
TL;DR:
This perspective highlights recent advances and key challenges to understanding and controlling peptide coassembly and reveals that preconceived notions of structure and molecular organization are not always correct.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: January 3, 2022
2021 article
In Silico Identification and Experimental Validation of Peptide-Based Inhibitors Targeting Clostridium difficile Toxin A
Xiao, X., Sarma, S., Menegatti, S., Crook, N., Magness, S. T., & Hall, C. K. (2021, December 29). ACS CHEMICAL BIOLOGY, Vol. 17.
MeSH headings : Bacterial Toxins / antagonists & inhibitors; Bacterial Toxins / chemistry; Computer Simulation; Drug Design; Enterotoxins / antagonists & inhibitors; Enterotoxins / chemistry; Models, Molecular; Peptides / chemistry; Peptides / pharmacology; Protein Binding; Protein Conformation; Protein Domains; Reproducibility of Results
TL;DR:
This work used a computational strategy that integrates a peptide binding design algorithm and explicit-solvent atomistic molecular dynamics simulation to determine promising toxin A-targeting peptides that can recognize and bind to the catalytic site of the TcdA glucosyltransferase domain (GTD).
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: December 30, 2021
2020 journal article
Novel peptide ligands for antibody purification provide superior clearance of host cell protein impurities
JOURNAL OF CHROMATOGRAPHY A, 1625.
author keywords: Peptide affinity ligands; Protein A; mAb purification; Affinity chromatography; Peptide design
MeSH headings : Amino Acid Sequence; Animals; Antibodies, Monoclonal / isolation & purification; Antibodies, Monoclonal / metabolism; CHO Cells; Chromatography, Affinity / methods; Cricetinae; Cricetulus; Immunoglobulin G / isolation & purification; Immunoglobulin G / metabolism; Ligands; Peptides / chemical synthesis; Peptides / chemistry; Peptides / metabolism; Protein Binding; Staphylococcal Protein A / chemistry; Staphylococcal Protein A / metabolism
TL;DR:
WQRHGI-WorkBeads resin was finally characterized by purification of a monoclonal antibody from a Chinese Hamster Ovary cell culture harvest, affording a remarkable HCP LRV of 2.7, and consistent product yield and purity over 100 chromatographic cycles.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 10, 2020
2019 journal article
Computational Study of Thermosensitivity of Liposomes Modulated by Leucine Zipper-Structured Lipopeptides
ACTA PHYSICO-CHIMICA SINICA, 35(6), 598–606.
author keywords: Leucine zipper-structured lipopeptides; Thermosensitive liposomes; Cancer therapy; Drug carrier; Molecular dynamics simulation
TL;DR:
A series of computational techniques including quantum mechanics, implicit solvation replica exchange molecular dynamics simulations, dihedral principal component analysis (dPCA), and dictionary of protein secondary structure (DSSP) methods were applied in this work to examine the influence of the molecular structures on the phase transition behaviors of lipopeptides.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: April 20, 2020
2019 journal article
Computational study of transition states for reaction path of energetic material TKX-50
JOURNAL OF ENERGETIC MATERIALS, 37(2), 240–250.
author keywords: Energetic materials; TKX-50; density functional theory; transition states; equilibrium constants
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
11. Sustainable Cities and Communities
(Web of Science)
Source: Web Of Science
Added: May 6, 2019
2019 journal article
In Silico Discovery and Validation of Neuropeptide-Y-Binding Peptides for Sensors
The Journal of Physical Chemistry B, 124(1), 61–68.
MeSH headings : Algorithms; Amino Acid Sequence; Biomarkers / metabolism; Humans; Kinetics; Molecular Dynamics Simulation; Neuropeptide Y / analysis; Neuropeptide Y / chemistry; Neuropeptide Y / metabolism; Peptides / chemistry; Peptides / metabolism; Protein Binding; Protein Structure, Secondary
TL;DR:
This study discovers and compares 12-mer peptides that bind to neuropeptide Y (NPY), a stress and human health biomarker, using independent and complimentary experi-mental and computational approaches, suggesting its utility for discovering peptide binders to a variety of biomarker targets.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: February 3, 2020
2019 journal article
Insights into the solvation and dynamic behaviors of a lithium salt in organic- and ionic liquid-based electrolytes
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 21(35), 19216–19225.
TL;DR:
It was proved that the dissolution of LiTFSI in the IL solvents is an anion-driven process with higher conductivity than the [TFSI]-type IL electrolytes, especially [C4mim][BF4] with the highest conductivity among the IL-based electrolytes.
(via Semantic Scholar)
Source: Web Of Science
Added: October 7, 2019
2018 journal article
Advancing Peptide-Based Biorecognition Elements for Biosensors Using in-Silico Evolution
ACS SENSORS, 3(5), 1024–1031.
author keywords: troponin I; biorecognition elements; biosensor; phage displayed peptides; LSPR; computational modeling
MeSH headings : Amino Acid Sequence; Biomarkers / analysis; Biosensing Techniques / methods; Circular Dichroism; Computer Simulation; Dielectric Spectroscopy; Humans; Immunoassay; Limit of Detection; Microscopy, Electron, Scanning; Peptides / chemistry; Reproducibility of Results; Surface Plasmon Resonance; Troponin I / chemistry
TL;DR:
An in-silico approach to evolve higher sensitivity peptide-based BREs for the detection of cardiac event marker protein troponin I from a previously identified BRE as the parental affinity peptide is described.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2018 journal article
All-silica zeolites screening for capture of toxic gases from molecular simulation
CHINESE JOURNAL OF CHEMICAL ENGINEERING, 27(1), 174–181.
author keywords: All-silica zeolites; Toxic gases; Adsorption isotherm; GCMC simulation
Source: Web Of Science
Added: February 11, 2019
2018 article
Capture of pure toxic gases through porous materials from molecular simulations
MOLECULAR PHYSICS, Vol. 116, pp. 2095–2107.
author keywords: GCMC simulation; adsorption; MOFs; COFs; toxic gas
Source: Web Of Science
Added: August 6, 2018
2017 journal article
Extended Concerted Rotation Technique Enhances the Sampling Efficiency of the Computational Peptide-Design Algorithm
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 13(11), 5709–5720.
MeSH headings : Algorithms; Molecular Dynamics Simulation; Peptides / chemistry
TL;DR:
Three of the evolved peptides, viz.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2017 journal article
Potent aromatase inhibitors and molecular mechanism of inhibitory action
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 143, 426–437.
author keywords: Estrogen; Breast cancer; Aromatase inhibitors (AIs); Letrozole; Molecular mechanism of inhibitory action
MeSH headings : Antineoplastic Agents / chemical synthesis; Antineoplastic Agents / chemistry; Antineoplastic Agents / pharmacology; Aromatase / metabolism; Aromatase Inhibitors / chemical synthesis; Aromatase Inhibitors / chemistry; Aromatase Inhibitors / pharmacology; Cell Proliferation / drug effects; Dose-Response Relationship, Drug; Drug Screening Assays, Antitumor; Humans; MCF-7 Cells; Models, Molecular; Molecular Structure; Structure-Activity Relationship
TL;DR:
A combination of experimental and computational approaches facilitates us to understand the molecular mechanism of inhibitory action and discover more potent non-steroidal AIs against aromatase, thereby opening up a novel therapeutic strategy for hormone-dependent breast cancer.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2016 journal article
Adding energy minimization strategy to peptide-design algorithm enables better search for RNA-binding peptides: Redesigned N peptide binds boxB RNA
JOURNAL OF COMPUTATIONAL CHEMISTRY, 37(27), 2423–2435.
author keywords: peptide-design algorithm; N peptide-boxB RNA; RNA-binding peptide; RNA tethering; energy minimization strategy
MeSH headings : Algorithms; Molecular Dynamics Simulation; Peptide Library; Peptides / chemistry; RNA, Viral / chemistry; RNA-Binding Proteins / chemistry
TL;DR:
Simulation results demonstrated that the evolved peptides are better at binding to boxB RNA than the λ N peptide, and sequence searches using the old and new algorithm confirm that the new algorithm is more effective at finding good RNA‐binding peptides than the old algorithm.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2016 journal article
Computational insights into the destabilization of alpha-helical conformations formed by leucine zipper peptides in response to temperature
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18(36), 25465–25473.
TL;DR:
Analysis of conformation and energy of the folded peptides showed that the increase of temperature gives rise to a notable decrease in the number of intra-chain hydrogen bonds and a significant increase in the potentialenergy of the peptides, thereby reducing the folding stability of the two peptides.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2016 journal article
Introducing folding stability into the score function for computational design of RNA-binding peptides boosts the probability of success
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 84(5), 700–711.
author keywords: peptide design; search algorithm; atomistic molecular dynamics simulation; tRNA(UUU)(Lys3); binding affinity and specificity
MeSH headings : Algorithms; Computational Biology / methods; Drug Design; Humans; Molecular Dynamics Simulation; Peptides / chemistry; Peptides / metabolism; Protein Binding; Protein Folding; Protein Stability; RNA, Transfer, Lys / chemistry; RNA, Transfer, Lys / metabolism; RNA-Binding Proteins / chemistry; RNA-Binding Proteins / metabolism; Thermodynamics
TL;DR:
Simulation results demonstrated that setting an intermediate value of λ achieves a good balance between optimizing the peptide's binding ability and stabilizing its folded conformation during the sequence evolution process, and hence leads to optimal binding to the target ASLLys3.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2016 journal article
Probe the Binding Mode of Aristololactam-beta-D-glucoside to Phenylalanine Transfer RNA in Silico
CHEMISTRYSELECT, 1(17), 5430–5439.
author keywords: Aristololactam-beta-D-glucoside; Binding of drug molecule and RNA; Molecular docking and simulations; Molecular recognition mechanism; Phenylalanine transfer RNA
TL;DR:
An integrated computational strategy combining quantum mechanics calculation, molecular docking and atomistic molecular dynamics simulation was present in this work, and it was identified that the aristololactam of ADG provides binding specificity to the tRNAPhe, and the D-glucoce contributes to the affinity for binding with the tRNA.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2016 journal article
Simulation study of the ability of a computationally-designed peptide to recognize target tRNA(Lys3) and other decoy tRNAs
PROTEIN SCIENCE, 25(12), 2243–2255.
author keywords: binding uniqueness; target tRNA(Lys3) UUU; binding of RNA and peptide; molecular recognition mechanism
MeSH headings : Humans; Molecular Dynamics Simulation; Peptides / chemistry; RNA, Transfer, Lys / chemistry; Thermodynamics
TL;DR:
Results indicated that Pept10 recognizes and binds to the target ASLLys3 through residues W3 and R7 which interact with the nucleotides mcm5s2U34, U35, and ms2t6A37 via the interchain VDW energy.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2015 journal article
Designing Peptide Sequences in Flexible Chain Conformations to Bind RNA: A Search Algorithm Combining Monte Carlo, Self-Consistent Mean Field and Concerted Rotation Techniques
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11(2), 740–752.
MeSH headings : Algorithms; Amino Acid Sequence; Anti-HIV Agents / chemical synthesis; Anti-HIV Agents / chemistry; Binding Sites; Humans; Molecular Dynamics Simulation; Monte Carlo Method; Peptides / chemical synthesis; Peptides / chemistry; Protein Conformation; RNA / chemistry; RNA, Transfer / chemistry; Rotation; Thermodynamics
TL;DR:
A search algorithm combining Monte Carlo, self-consistent mean field, and concerted rotation techniques was developed to discover peptide sequences that are reasonable HIV drug candidates due to their exceptional binding to human tRNAUUU(Lys3), the primer of HIV replication.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2015 journal article
Effect of curvature on properties of diblock copolymers confined between two coaxial cylinders: 1. Layer thickness of a curved monolayer
CHEMICAL PHYSICS LETTERS, 633, 58–64.
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
6. Clean Water and Sanitation
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2015 journal article
Effect of curvature on properties of diblock copolymers confined between two coaxial cylinders: 2. Domain adjustment in a curved bilayer
CHEMICAL PHYSICS LETTERS, 639, 326–334.
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
6. Clean Water and Sanitation
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2014 journal article
Amino Acid Signature Enables Proteins to Recognize Modified tRNA
Biochemistry, 53(7), 1125–1133.
MeSH headings : Algorithms; Amino Acid Sequence; Amino Acids / metabolism; Humans; Models, Molecular; Monte Carlo Method; RNA, Transfer, Lys / chemistry; RNA, Transfer, Lys / metabolism; Substrate Specificity; gag Gene Products, Human Immunodeficiency Virus / metabolism
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018
2014 journal article
Molecular recognition mechanism of peptide chain bound to the tRNA(Lys3) anticodon loop in silico
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33(1), 14–27.
author keywords: molecular recognition; binding free energy; atomistic molecular dynamics simulation; binding affinity and specificity; peptide and tRNA(Lys3)
MeSH headings : Algorithms; Amino Acid Sequence; Amino Acids / chemistry; Amino Acids / metabolism; Anticodon / chemistry; Anticodon / genetics; Anticodon / metabolism; Computer Simulation; Humans; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Peptides / chemistry; Peptides / metabolism; Phenylalanine / chemistry; Phenylalanine / metabolism; Protein Binding; Protein Folding; Protein Structure, Secondary; Protein Structure, Tertiary; RNA, Transfer, Lys / chemistry; RNA, Transfer, Lys / metabolism; Static Electricity; Thermodynamics
TL;DR:
The metastable folded peptide was found to bind to hASLLys3 much easier than the stable Folded peptide in the binding simulations, and an energetic analysis reveals that the VDW energy favors the binding, whereas the ELE + EGB energies disfavor the binding.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2014 journal article
Phase Separation Behavior of Mixed Lipid Systems at Neutral and Low pH: Coarse-Grained Simulations with DMD/LIME
LANGMUIR, 31(3), 1086–1094.
MeSH headings : Hydrogen-Ion Concentration; Kinetics; Lipid Bilayers / chemistry; Molecular Dynamics Simulation; Phosphatidylcholines / chemistry; Phosphoserine / chemistry; Temperature; Thermodynamics
TL;DR:
These are the first molecular-level simulations of the phase separation in mixed lipid bilayers induced by a change in pH, and consistent with experimental findings of Sofou and co-workers.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
6. Clean Water and Sanitation
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2013 journal article
The design of a peptide sequence to inhibit HIV replication: a search algorithm combining Monte Carlo and self-consistent mean field techniques
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32(10), 1523–1536.
author keywords: protein design; Monte Carlo technique; self-consistent mean field theory; search algorithm; binding affinity and specificity
MeSH headings : Algorithms; Amino Acid Sequence; Anticodon; Computational Biology / methods; Drug Design; HIV-1 / drug effects; Humans; Molecular Sequence Data; Monte Carlo Method; Peptides / pharmacology; Protein Structure, Secondary; Protein Structure, Tertiary; Thermodynamics; Virus Replication / drug effects; Water
TL;DR:
A search algorithm combining Monte Carlo (MC) and self-consistent mean field techniques to evolve a peptide sequence that has good binding capability to the anticodon stem and loop of human lysine tRNA species, tRNALys3, with the ultimate purpose of breaking the replication cycle of human immunodeficiency virus-1.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
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