Molecular dynamics of folding of secondary structures in Go-type models of proteins

We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic amino acid–amino acid potential is Lennard–Jones for the native contacts and a soft repulsion for the non-native contacts. The interactions are chosen to make the target secondary structure be the native state of the system. We provide a thorough equilibrium and kinetic characterization of the sequences through the molecular dynamics simulations with the Langevin noise. Models with the steric constraints are found to be better folders and to be more stable, especially in the case of the β structures. Phononic spectra for vibrations around the native states have low frequency gaps that correlate with the thermodynamic stability. Folding of the secondary structures proceeds through a well-defined sequence of events. For instance, α helices fold from the ends first. The closer to the native state, the faster establishment of the contacts. Increas...

• Publication year

  1999

• Venue

  Journal of Chemical Physics

• Publication date

  1999-11-30

• Fields of study

  Biology, Physics, Chemistry

• Identifiers
  DOI 10.1063/1.481261arXiv cond-mat/9911488
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides

  1999cited by this paper
• Folding in two-dimensional off-lattice models of proteins

  1999cited by this paper
• DELINEATION OF THE NATIVE BASIN IN CONTINUUM MODELS OF PROTEINS

  1999cited by this paper
• Interpreting the folding kinetics of helical proteins

  1999cited by this paper
• Energy landscapes, supergraphs, and "folding funnels" in spin systems.

  1999cited by this paper
• Scaling of Folding Properties in Simple Models of Proteins

  1999cited by this paper
• Energy Landscape of a Model Protein

  1999cited by this paper
• Brownian dynamics simulations of protein folding

  1998cited by this paper
• Formation and stability of β-hairpin structures in polypeptides

  1998cited by this paper
• Master Equation Approach to Protein Folding and Kinetic Traps

  1998cited by this paper
• Protein Structures and Optimal Folding from a Geometrical Variational Principle

  1998cited by this paper
• FOLDING, DESIGN, AND DETERMINATION OF INTERACTION POTENTIALS USING OFF-LATTICE DYNAMICS OF MODEL HETEROPOLYMERS

  1998cited by this paper
• Discrete molecular dynamics studies of the folding of a protein-like model.

  1998cited by this paper
• Identifying the protein folding nucleus using molecular dynamics.

  1998cited by this paper
• Protein folding in the landscape perspective: Chevron plots and non‐arrhenius kinetics

  1998cited by this paper
• Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution.

  1998cited by this paper
• Cell dynamics of folding in two-dimensional model proteins.

  1997cited by this paper
• The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics

  1997cited by this paper
• Viscosity Dependence of the Folding Rates of Proteins

  1997cited by this paper
• STABILITY THRESHOLD AS A SELECTION PRINCIPLE FOR PROTEIN DESIGN

  1997cited by this paper
• Folding dynamics and mechanism of β-hairpin formation

  1997cited by this paper
• Chain Length Scaling of Protein Folding Time.

  1996cited by this paper
• Emergence of Preferred Structures in a Simple Model of Protein Folding

  1996cited by this paper
• Criterion that determines the foldability of proteins.

  1996cited by this paper
• Identification of amino acid sequences with good folding properties in an off-lattice model

  1996cited by this paper
• First-Order Disorder-to-Order Transition in an Isolated Homopolymer Model.

  1996cited by this paper
• Local interactions and protein folding: A three-dimensional off-lattice approach

  1996cited by this paper
• Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties.

  1996cited by this paper
• Local interactions dominate folding in a simple protein model.

  1996cited by this paper
• Symmetry and the energy landscapes of biomolecules.

  1996cited by this paper
• From Minimal Models to Real Proteins: Time Scales for Protein Folding Kinetics

  1995cited by this paper
• Principles of protein folding — A perspective from simple exact models

  1995cited by this paper
• A reduced model of short range interactions in polypeptide chains

  1995cited by this paper
• First-principles calculation of the folding free energy of a three-helix bundle protein.

  1995cited by this paper
• Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2.

  1994cited by this paper
• How does a protein fold?

  1994cited by this paper
• Transition states and folding dynamics of proteins and heteropolymers

  1994cited by this paper
• Folding kinetics of proteinlike heteropolymers

  1994cited by this paper
• Kinetics and thermodynamics of folding in model proteins.

  1993cited by this paper
• Random self-interacting chains: A mechanism for protein folding

  1991cited by this paper
• Numerical Recipes: FORTRAN

  1990cited by this paper
• Computer simulation of liquids

  1989cited by this paper
• Molecular Dynamics Simulations of Proteins

  1987cited by this paper
• Molecular dynamics simulation for polymers in the presence of a heat bath.

  1986cited by this paper
• Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation

  1985cited by this paper
• Biopolymers

  1984cited by this paper
• Noninteracting local‐structure model of folding and unfolding transition in globular proteins. I. Formulation

  1981cited by this paper
• Macromolecules.

  1976cited by this paper
• Quantum theory of the solid state

  1974cited by this paper

• Coarse‐Grained DNA Models: Bridging Scales Through Extended Dynamics

  2025cites this paper
• Solvation enhances folding cooperativity and the topology dependence of folding rates in a lattice protein model.

  2025cites this paper
• Contact-based molecular dynamics of structured and disordered proteins in a coarse-grained model: Fixed contacts, switchable contacts and those described by pseudo-improper-dihedral angles

  2023cites this paper
• Hydrophobic and electrostatic interactions modulate protein escape at the ribosomal exit tunnel.

  2021cites this paper
• Nascent Folding of Proteins Across the Three Domains of Life

  2021cites this paper
• Extraction of kinetics from equilibrium distributions of states using the Metropolis Monte Carlo method.

  2021cites this paper
• Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry

  2021cites this paper
• Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

  2021cites this paper
• Protein mechanics probed using simple molecular models.

  2020cites this paper
• First-passage times in protein folding: exploring the native-like states vs. overcoming the free energy barrier.

  2020cites this paper
• Coarse-grained implicit solvent lipid force field with a compatible resolution to the Cα protein representation

  2020cites this paper
• Protein escape at the ribosomal exit tunnel: Effect of the tunnel shape.

  2020cites this paper
• Transient knots in intrinsically disordered proteins and neurodegeneration.

  2020cites this paper
• Pseudo-Improper-Dihedral Model for Intrinsically Disordered Proteins

  2020cites this paper
• Protein escape at an atomistic model of the ribosomal exit tunnel

  2020cites this paper
• Go-Kit: A Tool To Enable Energy Landscape Exploration of Proteins

  2019cites this paper
• Size Effect in Grand-canonical Monte-Carlo Simulation of Solutions of Electrolyte

  2019cites this paper
• Alternation of phases of regular and irregular dynamics in protein folding.

  2019cites this paper
• How the dyes affect folding of small proteins in single-molecule FRET experiments: A simulation study.

  2019cites this paper
• Computational methods in the study of self-entangled proteins: a critical appraisal

  2019cites this paper
• Protein Folding Dynamics in the Space of Experimentally Measured Variables: Turbulence Phenomena

  2018cites this paper
• Mechanostability of Virus Capsids and Their Proteins in Structure-Based Coarse-Grained Models

  2018cites this paper
• Protein Folding Dynamics in the Space of Experimentally Measured Variables: Turbulence Phenomena

  2018cites this paper
• Disordered peptide chains in an α-C-based coarse-grained model.

  2018cites this paper
• Modeling Nucleic Acids at the Residue–Level Resolution

  2018cites this paper
• Modeling of Multicolor Single-Molecule Förster Resonance Energy-Transfer Experiments on Protein Folding.

  2018cites this paper
• Protein escape at the ribosomal exit tunnel: Effects of native interactions, tunnel length, and macromolecular crowding.

  2018cites this paper
• Frequency-control of protein translocation across an oscillating nanopore.

  2017cites this paper
• Folding and escape of nascent proteins at ribosomal exit tunnel.

  2016cites this paper
• Unfolding knots by proteasome-like systems: simulations of the behaviour of folded and neurotoxic proteins.

  2016cites this paper
• Understanding biopharmaceutical aggregation using minimalist models based on square-well potential

  2016cites this paper
• Polarizable coarse‐grained models for molecular dynamics simulation of liquid cyclohexane

  2015cites this paper
• Knotted proteins: A tangled tale of Structural Biology

  2015cites this paper
• Modeling Nucleic Acids at the Residue-Level Resolution

  2014cites this paper
• Citrate synthase proteins in extremophilic organisms: studies within a structure-based model.

  2014cites this paper
• Mechanostability of Virus Capsids and Their Proteins in Structure-Based Models

  2014cites this paper
• DNA Duplex Formation with a Coarse-Grained Model

  2014cites this paper
• Recent successes in coarse‐grained modeling of DNA

  2013cites this paper
• Protein folding: complex potential for the driving force in a two-dimensional space of collective variables.

  2013cites this paper
• Interplay between native topology and non-native interactions in the folding of tethered proteins

  2013cites this paper
• Multiple molecule effects on the cooperativity of protein folding transitions in simulations.

  2012cites this paper
• 1.21 Computation of Structure, Dynamics, and Thermodynamics of Proteins

  2012cites this paper
• Développement d’une méthode de simulation multi-échelle pour l’étude des grandes transformations dans les protéines

  2012cites this paper
• Structure-Based Models of Biomolecules: Stretching of Proteins, Dynamics of Knots, Hydrodynamic Effects, and Indentation of Virus Capsids

  2011cites this paper
• Mechanical stability of multidomain proteins and novel mechanical clamps

  2011cites this paper
• A coarse-grain three-site-per-nucleotide model for DNA with explicit ions.

  2011cites this paper
• Coarse-Grained Models of Proteins: Theory and Applications

  2011cites this paper
• Universal distribution of protein evolution rates as a consequence of protein folding physics

  2010cites this paper
• BSDB: the biomolecule stretching database

  2010cites this paper
• Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome

  2010cites this paper
• Hexameric helicase deconstructed: interplay of conformational changes and substrate coupling.

  2010cites this paper
• Protein simulations combining an all-atom force field with a Go term

  2009cites this paper
• Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways

  2009cites this paper
• Molecular simulations of peptides: a useful tool for the development of new drugs and for the study of molecular recognition.

  2009cites this paper
• A mesoscale model of DNA and its renaturation.

  2009cites this paper
• Protein Mechanics at the Single-Molecule Level

  2009cites this paper
• Thermal and mechanical multistate folding of ribonuclease H.

  2009cites this paper
• REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform

  2009cites this paper
• Peptide Microarrays

  2009cites this paper
• Peptide Microarrays: Methods and Protocols

  2009cites this paper
• An entropic perspective of protein stability on surfaces.

  2008cites this paper
• Topologically Based Multipolar Reconstruction of Electrostatic Interactions in Multiscale Simulations of Proteins.

  2008cites this paper
• Hydrodynamic interactions in protein folding.

  2008cites this paper
• Selection of optimal variants of Gō-like models of proteins through studies of stretching.

  2008cites this paper
• Effects of confinement and crowding on folding of model proteins

  2008cites this paper
• A coarse grain model for DNA.

  2007cites this paper
• Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes.

  2007cites this paper
• Mechanical stretching of proteins—a theoretical survey of the Protein Data Bank

  2007cites this paper
• Protein-folding dynamics: overview of molecular simulation techniques.

  2007cites this paper
• Proteins in a shear flow.

  2007cites this paper
• Relationships between unfolded configurations of proteins and dynamics of folding to the native state

  2006cites this paper
• Confinement effects on the thermodynamics of protein folding: Monte Carlo simulations.

  2006cites this paper
• Evaluation of free energy landscapes from manipulation experiments

  2006cites this paper
• Folding with downhill behavior and low cooperativity of proteins

  2006cites this paper
• Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment.

  2006cites this paper
• Protein folding in a force clamp.

  2006cites this paper
• Dependence of folding dynamics and structural stability on the location of a hydrophobic pair in β‐hairpins

  2006cites this paper
• Structure and stability of a model three‐helix‐bundle protein on tailored surfaces

  2005influential citation
• Mechanical unfolding of ubiquitin molecules.

  2005cites this paper
• Permeation of particle through a four-helix-bundle model channel.

  2005cites this paper
• Folding behavior of chaperonin‐mediated substrate protein

  2005cites this paper
• Protein Folding in Nano-Sized Cylinders

  2005cites this paper
• Minimal model for the secondary structures and conformational conversions in proteins

  2005cites this paper
• Folding Behaviour for Proteins BBL and E3BD with Gō-like Models

  2005cites this paper
• Mechanical properties of the domains of titin in a Go-like model.

  2004cites this paper
• Stretching of homopolymers and contact order.

  2004cites this paper
• THE "FOLDING" BEHAVIORS OF HOMOPOLYMERS WITH ONE END FIXED

  2004cites this paper
• Folding Dynamics of Proteins from Denatured to Native State: Principal Component Analysis

  2004cites this paper
• Study of the Villin headpiece folding dynamics by combining coarse‐grained Monte Carlo evolution and all‐atom molecular dynamics

  2004cites this paper
• Chirality and protein folding

  2004cites this paper
• Correction to the article “Study of the Villin Headpiece folding dynamics by combining coarse‐grained Monte Carlo evolution and all‐atom molecular dynamics”

  2004cites this paper
• Mechanical stretching of proteins: calmodulin and titin

  2004cites this paper
• Simulated dynamics and biological macromolecules

  2003cites this paper
• Self-consistent Knowledge-Based Approach to Protein Design

  2003cites this paper
• Stretching of proteins in the entropic limit.

  2003cites this paper
• Thermal effects in stretching of Go‐like models of titin and secondary structures

  2003cites this paper
• Folding of proteins in Go models with angular interactions

  2003cites this paper
• Simulated dynamics and biological macromolecules

  2003cites this paper
• Folding pathways of prion and doppel.

  2002cites this paper
• Elastic properties of proteins: insight on the folding process and evolutionary selection of native structures.

  2002cites this paper