Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins

No abstract is available for this paper.

• Publication year

  2010

• Venue

  Proceedings of the National Academy of Sciences of the United States of America

• Publication date

  2010-01-29

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1073/pnas.0911844107PMID 20133730PMCID PMC2840274
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Confinement effects on the kinetics and thermodynamics of protein dimerization

  2009cited by this paper
• Native topology of the designed protein Top7 is not conducive to cooperative folding.

  2009influential reference
• Desolvation barrier effects are a likely contributor to the remarkable diversity in the folding rates of small proteins.

  2009cited by this paper
• Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions.

  2008cited by this paper
• Origins of barriers and barrierless folding in BBL

  2008cited by this paper
• Probing invisible, low-populated States of protein molecules by relaxation dispersion NMR spectroscopy: an application to protein folding.

  2008cited by this paper
• Simulation of Top7-CFr: A transient helix extension guides folding

  2008cited by this paper
• Probing possible downhill folding: native contact topology likely places a significant constraint on the folding cooperativity of proteins with approximately 40 residues.

  2008cited by this paper
• Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding

  2008influential reference
• Intermediates: ubiquitous species on folding energy landscapes?

  2007cited by this paper
• Hydrophobic association of α-helices, steric dewetting, and enthalpic barriers to protein folding

  2007cited by this paper
• Mechanical control of the directional stepping dynamics of the kinesin motor

  2007cited by this paper
• The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection.

  2007influential reference
• Hydrophobic association of alpha-helices, steric dewetting, and enthalpic barriers to protein folding.

  2007cited by this paper
• Polyelectrostatic interactions of disordered ligands suggest a physical basis for ultrasensitivity

  2007cited by this paper
• Folding with downhill behavior and low cooperativity of proteins

  2006cited by this paper
• Water mediation in protein folding and molecular recognition.

  2006cited by this paper
• Criteria for downhill protein folding: Calorimetry, chevron plot, kinetic relaxation, and single‐molecule radius of gyration in chain models with subdued degrees of cooperativity

  2006cited by this paper
• Small proteins fold through transition states with native-like topologies.

  2006cited by this paper
• Desolvation is a likely origin of robust enthalpic barriers to protein folding.

  2005cited by this paper
• Antagonism, non-native interactions and non-two-state folding in S6 revealed by double-mutant cycle analysis.

  2005cited by this paper
• Solvation and desolvation effects in protein folding: native flexibility, kinetic cooperativity and enthalpic barriers under isostability conditions

  2005cited by this paper
• A protein folding pathway with multiple folding intermediates at atomic resolution.

  2005cited by this paper
• Cooperativity principles in protein folding.

  2004cited by this paper
• Correspondence between anomalous m- and DeltaCp-values in protein folding.

  2004cited by this paper
• Sparsely populated folding intermediates of the Fyn SH3 domain: matching native-centric essential dynamics and experiment.

  2004cited by this paper
• Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection.

  2004influential reference
• Simulation, experiment, and evolution: understanding nucleation in protein S6 folding.

  2004cited by this paper
• Gatekeepers in the ribosomal protein s6: thermodynamics, kinetics, and folding pathways revealed by a minimalist protein model.

  2004cited by this paper
• Correspondence between anomalous m‐ and Δ Cp‐values in protein folding

  2004cited by this paper
• Faculty Opinions recommendation of Design of a novel globular protein fold with atomic-level accuracy.

  2003cited by this paper
• Temperature dependence of the distribution of the first passage time: results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G.

  2003cited by this paper
• Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

  2003cited by this paper
• Origins of chevron rollovers in non-two-state protein folding kinetics.

  2003cited by this paper
• Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: how adequate is native-centric topological modeling?

  2002cited by this paper
• Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse

  2002cited by this paper
• Experimental evaluation of topological parameters determining protein-folding rates

  2002cited by this paper
• On hydrophobicity correlations in protein chains.

  2000cited by this paper
• Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins.

  2000cited by this paper
• Speeding protein folding beyond the Gō model: How a little frustration sometimes helps

  2000cited by this paper
• Protein misfolding, evolution and disease.

  1999cited by this paper
• Protein folding in the landscape perspective: Chevron plots and non‐arrhenius kinetics

  1998cited by this paper
• The changing nature of the protein folding transition state: implications for the shape of the free-energy profile for folding.

  1998cited by this paper
• Contact order, transition state placement and the refolding rates of single domain proteins.

  1998cited by this paper
• Emergence of Preferred Structures in a Simple Model of Protein Folding

  1996cited by this paper
• Comparing folding codes for proteins and polymers

  1996cited by this paper
• Kinetics of Folding of Proteins and RNA

  1996cited by this paper
• Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding

  1995cited by this paper
• Impact of local and non-local interactions on thermodynamics and kinetics of protein folding.

  1995cited by this paper
• Funnels, pathways, and the energy landscape of protein folding: A synthesis

  1994cited by this paper
• Crystal structure of the ribosomal protein S6 from Thermus thermophilus.

  1994cited by this paper
• Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition.

  1991cited by this paper
• Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation

  1985cited by this paper

• On the role of native contact cooperativity in protein folding

  2024cites this paper
• Probing the Energy Landscape of Spectrin R15 and R16 and the Effects of Non-native Interactions.

  2023cites this paper
• Exploring the Folding Mechanism of Dimeric Superoxide Dismutase.

  2023cites this paper
• Reframing prosegment‐dependent folding and limits on natural protein folding landscapes from an evolutionary perspective

  2023cites this paper
• Effects of sequence-dependent non-native interactions in equilibrium and kinetic folding properties of knotted proteins

  2023cites this paper
• Effects of Surface Tethering on the Thermodynamics and Kinetics of Frustrated Protein Folding.

  2022cites this paper
• Coordinate-Dependent Drift-Diffusion Reveals the Kinetic Intermediate Traps of Top7-Based Proteins.

  2022cites this paper
• Biotinylation Eliminates the Intermediate State of Top7 Designed with an HIV-1 Epitope.

  2022cites this paper
• A Method for Assessing the Robustness of Protein Structures by Randomizing Packing Interactions

  2022cites this paper
• The folding and misfolding mechanisms of multidomain proteins

  2022cites this paper
• A hierarchy of coupling free energies underlie the thermodynamic and functional architecture of protein structures

  2021cites this paper
• Fuzziness and Frustration in the Energy Landscape of Protein Folding, Function, and Assembly

  2021cites this paper
• Single molecule force spectroscopy reveals the context dependent folding pathway of the C-terminal fragment of Top7

  2020cites this paper
• The Molecular Mechanism of Domain Swapping of the C-Terminal Domain of the SARS-Coronavirus Main Protease

  2020cites this paper
• The influence of intrinsic folding mechanism of an unfolded protein on the coupled folding‐binding process during target recognition

  2019cites this paper
• Stability and Strain in Hisactophilin and Mechanism of the Myristoyl Switch

  2019cites this paper
• Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias

  2018cites this paper
• Disordered linkers in multidomain allosteric proteins: Entropic effect to favor the open state or enhanced local concentration to favor the closed state?

  2018cites this paper
• Effects of Non-native Interactions on Frustrated Proteins Folding under Confinement.

  2018cites this paper
• Nonnative Energetic Frustrations in Protein Folding at Residual Level: A Simulation Study of Homologous Immunoglobulin-like β-Sandwich Proteins

  2018cites this paper
• The folding pathways and thermodynamics of semiflexible polymers.

  2018cites this paper
• Assessing AMBER force fields for protein folding in an implicit solvent.

  2018cites this paper
• Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields

  2018cites this paper
• The role of solvent quality and chain stiffness on the end-to-end contact kinetics of semiflexible polymers.

  2018cites this paper
• Energy Landscape of the Designed Protein Top7.

  2018cites this paper
• Non-Native Cooperative Interactions Modulate Protein Folding Rates.

  2018cites this paper
• The Sensitivity of Computational Protein Folding to Contact Map Perturbations: The Case of Ubiquitin Folding and Function.

  2018cites this paper
• 1 Modeling of disordered protein structures using 2 Monte Carlo simulations and knowledge-based 3 statistical force fields 4

  2018cites this paper
• Non-native Interactions Explain the Folding Rate Differences in α-Spectrin Domains and the Origin of Internal Friction Effects

  2017cites this paper
• Molecular recognition and packing frustration in a helical protein

  2017cites this paper
• The low populated folding intermediate of a mutant of the Fyn SH3 domain identified by a simple model.

  2017cites this paper
• Energetic frustrations in protein folding at residue resolution: a simulation study of homologous immunoglobulin-like \b{eta}-sandwich proteins

  2017cites this paper
• A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding.

  2017cites this paper
• The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations

  2016cites this paper
• Using natural sequences and modularity to design common and novel protein topologies.

  2016cites this paper
• Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches

  2016cites this paper
• As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy

  2016cites this paper
• Dimensions, energetics, and denaturant effects of the protein unstructured state

  2016cites this paper
• Influences of heterogeneous native contact energy and many-body interactions on the prediction of protein folding mechanisms.

  2016cites this paper
• Quantifying Nonnative Interactions in the Protein-Folding Free-Energy Landscape.

  2016cites this paper
• Interplay between binding affinity and kinetics in protein–protein interactions

  2016cites this paper
• Coarse-Grained Protein Models and Their Applications.

  2016cites this paper
• Constructing sequence‐dependent protein models using coevolutionary information

  2016cites this paper
• Computational Design of Protein Structure and Prediction of Ligand Binding

  2016cites this paper
• Native Contact Density and Nonnative Hydrophobic Effects in the Folding of Bacterial Immunity Proteins

  2015cites this paper
• Theoretical perspectives on nonnative interactions and intrinsic disorder in protein folding and binding.

  2015influential citation
• Einzelmolekülexperimente zum Einfluss von Knoten und makromolekularem Crowding auf die Faltung von Proteinen

  2015cites this paper
• Domains of Pyrococcus furiosusl-asparaginase fold sequentially and assemble through strong intersubunit associative forces

  2015cites this paper
• Energetic Frustrations in Protein Folding at Residue Resolution: A Homologous Simulation Study of Im9 Proteins

  2014cites this paper
• Correction: Energetic Frustrations in Protein Folding at Residue Resolution: A Homologous Simulation Study of Im9 Proteins

  2014cites this paper
• CHARMM-GUI PACE CG Builder for Solution, Micelle, and Bilayer Coarse-Grained Simulations

  2014cites this paper
• A hybrid MD-kMC algorithm for folding proteins in explicit solvent.

  2014cites this paper
• biophysicsof protein evolution and evolutionary protein

  2014cites this paper
• Effects of desolvation barriers and sidechains on local-nonlocal coupling and chevron behaviors in coarse-grained models of protein folding.

  2014cites this paper
• Site-specific thermodynamic stability and unfolding of a de novo designed protein structural motif mapped by 13C isotopically edited IR spectroscopy.

  2014cites this paper
• Designing cooperativity into the designed protein Top7

  2014cites this paper
• How the folding rates of two‐ and multistate proteins depend on the amino acid properties

  2014cites this paper
• Multi-scale simulations of intrinsically disordered proteins and development of enhanced sampling techniques

  2014cites this paper
• Biophysics of protein evolution and evolutionary protein biophysics

  2014cites this paper
• Modeling Non‐Native Interactions in Designed Proteins

  2014cites this paper
• Spatial ranges of driving forces are a key determinant of protein folding cooperativity and rate diversity.

  2013cites this paper
• How well does a funneled energy landscape capture the folding mechanism of spectrin domains?

  2013cites this paper
• Perspective: Coarse-grained models for biomolecular systems.

  2013cites this paper
• Atomistic description of the folding of a dimeric protein.

  2013cites this paper
• Folding and association of a homotetrameric protein complex in an all-atom Go model.

  2013cites this paper
• Slow and bimolecular folding of a de novo designed monomeric protein DS119.

  2013cites this paper
• Funneling and frustration in the energy landscapes of some designed and simplified proteins.

  2013cites this paper
• Activity and steady‐state kinetics of one‐dimensional kinetic Ising model

  2013cites this paper
• Learning To Fold Proteins Using Energy Landscape Theory.

  2013cites this paper
• Frustration in biomolecules

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

  2013cites this paper
• Coarse‐grained models of protein folding as detailed tools to connect with experiments

  2013cites this paper
• Protein structural dynamics and thermodynamics from advanced simulation techniques

  2013cites this paper
• Analyzing the effect of homogeneous frustration in protein folding

  2013cites this paper
• Polycation-π Interactions Are a Driving Force for Molecular Recognition by an Intrinsically Disordered Oncoprotein Family

  2013cites this paper
• Quantitative analysis of the effects of photoswitchable distance constraints on the structure of a globular protein.

  2012cites this paper
• Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot

  2012cites this paper
• Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2 ouf-knot

  2012cites this paper
• Hydrogen bond models for the simulation of protein folding and aggregation

  2012cites this paper
• Synergistic folding of two intrinsically disordered proteins: searching for conformational selection.

  2012cites this paper
• Kinetic consequences of native state optimization of surface‐exposed electrostatic interactions in the Fyn SH3 domain

  2012cites this paper
• Electrostatically accelerated coupled binding and folding of intrinsically disordered proteins.

  2012cites this paper
• De novo prediction of protein folding pathways and structure using the principle of sequential stabilization

  2012cites this paper
• Kinetic studies of the folding of heterodimeric monellin: evidence for switching between alternative parallel pathways.

  2012cites this paper
• Nonnative interactions regulate folding and switching of myristoylated protein

  2012cites this paper
• Transition paths, diffusive processes, and preequilibria of protein folding

  2012cites this paper
• The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function.

  2012cites this paper
• Denaturant-dependent folding of GFP

  2012cites this paper
• Determining the native and nonnative effects of myristoylation on the folding and switching of hisactophilin

  2012cites this paper
• Collapse kinetics and chevron plots from simulations of denaturant-dependent folding of globular proteins

  2011cites this paper
• Comparison of chemical and thermal protein denaturation by combination of computational and experimental approaches. II.

  2011cites this paper
• Taming the complexity of protein folding.

  2011cites this paper
• Folding dynamics of Trp-cage in the presence of chemical interference and macromolecular crowding. I.

  2011cites this paper
• The folding of single domain proteins--have we reached a consensus?

  2011cites this paper
• Cooperativity, local-nonlocal coupling, and nonnative interactions: principles of protein folding from coarse-grained models.

  2011cites this paper
• Effectiveness of Φ-value analysis in the binding process of Arc repressor dimer.

  2011cites this paper
• Hydrophobic interactions in the formation of secondary structures in small peptides.

  2011cites this paper
• Nonnative Interactions in Coupled Folding and Binding Processes of Intrinsically Disordered Proteins

  2010influential citation
• Smoothing molecular interactions: The “kinetic buffer” effect of intrinsically disordered proteins

  2010cites this paper
• Non‐native interactions play an effective role in protein folding dynamics

  2010cites this paper