Reply to Comment on "Criterion that Determines the Foldability of Proteins"

Abstract

We point out that the correlation between folding times and $\sigma =(T_{\theta }-T_f)/T_{\theta }$ in protein-like heteropolymer models where $T_{\theta }$ and $T_f$ are the collapse and folding transition temperatures was already established in 1993 before the other presumed equivalent criterion (folding times correlating with $T_f$ alone) was suggested. We argue that the folding times for these models show no useful correlation with the energy gap even if restricted to the ensemble of compact structures as suggested by Karplus and Shakhnovich (cond-mat/9606037).

6 pages, Latex, 2 Postscript figures. Plots explicitly showing the lack of correlation between folding time and energy gap are added

Cited by in corpus (44)

• The double-funnel energy landscape of the 38-atom Lennard-Jones cluster
• Positive and negative design in stability and thermal adaptation of natural proteins
• Protein design: A perspective from simple tractable models
• Molecular dynamics of folding of secondary structures in Go-type models of proteins
• The effect of chain stiffness on the phase behaviour of isolated homopolymers
• Sequencing of folding events in Go-like proteins
• Multi-Self-Overlap Ensemble for protein folding: ground state search and thermodynamics
• Linking Rates of Folding in Lattice Models of Proteins with Underlying Thermodynamic Characteristics
• Folding and Aggregation of Designed Proteins
• Characteristic Temperatures of Folding of a Small Peptide
• Folding and Misfolding of Designed Heteropolymer Chains with Mutations
• Protein folding using contact maps
• Energy landscapes, supergraphs, and "folding funnels" in spin systems
• Unified perspective on proteins: A physics approach
• Optimal enumeration of state space of finitely buffered stochastic molecular networks and exact computation of steady state landscape probability
• The Scaling Behaviour of Stochastic Minimization Algorithms in a Perfect Funnel Landscape
• Modeling study on the validity of a possibly simplified representation of proteins
• Stability of Designed Proteins Against Mutations
• Statistical Geometry of Packing Defects of Lattice Chain Polymer from Enumeration and Sequential Monte Carlo Method
• Stability Threshold as a Selection Principle for Protein Design
• Folding in two-dimenensional off-lattice models of proteins
• Folding of the Protein Domain hbSBD
• Steric constraints in model proteins
• Protein folding dynamics via quantification of kinematic energy landscape
• Statistical Mechanics of Membrane Protein Conformation: A Homopolymer Model
• Criteria for folding in structure-based models of proteins
• Exactness of the Annealed and the Replica Symmetric Approximations for Random Heteropolymers
• Designability of lattice model heteropolymers
• Thermodynamically Important Contacts in Folding of Model Proteins
• Delineation of the Native Basin in Continuum Models of Proteins
• The Origin of the Designability of Protein Structures
• Design Equation: A Novel Approach to Heteropolymer Design
• Design of amino acid sequences to fold into C_alpha-model proteins
• A coarse-grained, ``realistic'' model for Protein Folding
• What thermodynamic features characterize good and bad folders? Results from a simplified off-lattice protein model
• Spin analogs of proteins: scaling of "folding" properties
• Note on irreducible approach to reducible second-class constraints
• Folding lattice proteins confined on minimal grids using a quantum-inspired encoding
• Glass Transition Temperature and Fractal Dimension of Protein Free Energy Landscapes
• Protein Folding Kinetics: Time Scales, Pathways, and Energy Landscapes in Terms of Sequence Dependent Properties
• Factors that Affect the Folding Ability of Proteins
• Cooperativity in Protein Folding: From Lattice Models with Side Chains to Real Proteins
• Structural Susceptibilities in Toy Models of Proteins
• Selecting fast folding proteins by their rate of convergence