Cargando…

Length Dependent Folding Kinetics of Alanine-Based Helical Peptides from Optimal Dimensionality Reduction

We present a computer simulation study of helix folding in alanine homopeptides (ALA)n of length n = 5, 8, 15, and 21 residues. Based on multi-microsecond molecular dynamics simulations at room temperature, we found helix populations and relaxation times increasing from about 6% and ~2 ns for ALA5 t...

Descripción completa

Detalles Bibliográficos
Autores principales:	Kuczera, Krzysztof, Szoszkiewicz, Robert, He, Jinyan, Jas, Gouri S.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	MDPI 2021
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8170890/ https://www.ncbi.nlm.nih.gov/pubmed/33923197 http://dx.doi.org/10.3390/life11050385

Ejemplares similares

Analytical Approaches for Deriving Friction Coefficients for Selected α-Helical Peptides Based Entirely on Molecular Dynamics Simulations
por: Wosztyl, Aleksandra, et al.
Publicado: (2022)

Dissecting Multiple Pathways in the Relaxation Dynamics of Helix <==> Coil Transitions with Optimum Dimensionality Reduction
por: Jas, Gouri S., et al.
Publicado: (2021)

To Fold or Not to Fold: Diastereomeric Optimization of an α-Helical Antimicrobial Peptide
por: Personne, Hippolyte, et al.
Publicado: (2023)

Thermodynamics of Deca-alanine Folding in Water
por: Hazel, Anthony, et al.
Publicado: (2014)

Slow Dissolution Kinetics of Model Peptide Fibrils
por: Koder Hamid, Mona, et al.
Publicado: (2020)

Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models
por: Hummer, Gerhard, et al.
Publicado: (2014)

Folding and Insertion of Transmembrane Helices at the ER
por: Whitley, Paul, et al.
Publicado: (2021)

Co‐translational folding of α‐helical proteins: structural studies of intermediate‐length variants of the λ repressor
por: Hanazono, Yuya, et al.
Publicado: (2018)

Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations
por: Zhou, Hongyi, et al.
Publicado: (2005)

Two Dimensional Oblique Molecular Packing within a Model Peptide Ribbon Aggregate
por: Kuczera, Stefan, et al.
Publicado: (2020)

Energetics and structure of alanine-rich α-helices via adaptive steered molecular dynamics
por: Zhuang, Yi, et al.
Publicado: (2021)

Autonomously folded α-helical lockers promote RNAi*
por: Guyader, Christian P. E., et al.
Publicado: (2016)

Transmembrane but not soluble helices fold inside the ribosome tunnel
por: Bañó-Polo, Manuel, et al.
Publicado: (2018)

Polyamines Mediate Folding of Primordial Hyperacidic Helical Proteins
por: Despotović, Dragana, et al.
Publicado: (2020)

Evolutionary Pareto-optimization of stably folding peptides
por: Gronwald, Wolfram, et al.
Publicado: (2008)

Molecular basis for the folding of β-helical autotransporter passenger domains
por: Yuan, Xiaojun, et al.
Publicado: (2018)

Probing Protein Folding with Sequence-Reversed α-Helical Bundles
por: Kefala, Aikaterini, et al.
Publicado: (2021)

Methods to study folding of alpha-helical membrane proteins in lipids
por: Harris, Nicola J., et al.
Publicado: (2022)

Kinetics and Optimization of the Photocatalytic Reduction of Nitrobenzene
por: Patzsch, Julia, et al.
Publicado: (2019)

A minimal length rigid helical peptide motif allows rational design of modular surfactants
por: Mondal, Sudipta, et al.
Publicado: (2017)

Role of Helicity on the Anticancer Mechanism of Action of Cationic-Helical Peptides
por: Huang, Yi-Bing, et al.
Publicado: (2012)

Role of helicity of α-helical antimicrobial peptides to improve specificity
por: Huang, Yibing, et al.
Publicado: (2014)

Similar Structures to the E-to-H Helix Unit in the Globin-Like Fold are Found in Other Helical Folds
por: Matsuoka, Masanari, et al.
Publicado: (2014)

Folding kinetics of an entangled protein
por: Salicari, Leonardo, et al.
Publicado: (2023)

Dimerization Drives Proper Folding of Human Alanine:Glyoxylate Aminotransferase But Is Dispensable for Peroxisomal Targeting
por: Dindo, Mirco, et al.
Publicado: (2021)

Crystalline structures of polymeric hydrocarbon with 3,4-fold helical chains
por: Lian, Chao-Sheng, et al.
Publicado: (2015)

Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water
por: Duan, Lili, et al.
Publicado: (2019)

Dependence of α-helical and β-sheet amino acid propensities on the overall protein fold type
por: Fujiwara, Kazuo, et al.
Publicado: (2012)

KineticDB: a database of protein folding kinetics
por: Bogatyreva, Natalya S., et al.
Publicado: (2009)

Hydrophobicity and Helicity Regulate the Antifungal Activity of 14-Helical β-Peptides
por: Lee, Myung-Ryul, et al.
Publicado: (2014)

Polymorphic self-assembly of helical tubules is kinetically controlled
por: Fang, Huang, et al.
Publicado: (2022)

Kinetics and Thermodynamics of Membrane Protein Folding
por: Roman, Ernesto A., et al.
Publicado: (2014)

Simulation of Folding Kinetics for Aligned RNAs
por: Huang, Jiabin, et al.
Publicado: (2021)

Combination of Markov State Models and Kinetic Networks for the Analysis of Molecular Dynamics Simulations of Peptide Folding
por: Radford, Isolde H., et al.
Publicado: (2011)

α-Synuclein occurs physiologically as a helically folded tetramer that resists aggregation
por: Bartels, Tim, et al.
Publicado: (2011)

Exposing the distinctive modular behavior of β-strands and α-helices in folded proteins
por: Wang, Huabing, et al.
Publicado: (2020)

TmAlphaFold database: membrane localization and evaluation of AlphaFold2 predicted alpha-helical transmembrane protein structures
por: Dobson, Laszlo, et al.
Publicado: (2022)

Order through Disorder: Hyper-Mobile C-Terminal Residues Stabilize the Folded State of a Helical Peptide. A Molecular Dynamics Study
por: Patapati, Kalliopi K., et al.
Publicado: (2010)

Alanine Scanning Studies of the Antimicrobial Peptide Aurein 1.2
por: Migoń, Dorian, et al.
Publicado: (2018)

Force-Dependent Folding Kinetics of Single Molecules with Multiple Intermediates and Pathways
por: Rico-Pasto, Marc, et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_icgrken7u1ocongfi44rvq8n3a