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Protein folding is a complex process by which polypeptides form their functional 3D structures, involving various theories and approaches. Quantum folding theory explores how photon interactions influence folding rates, while statistical physics views it as a stochastic process shaped by energy landscapes. Rapid, single-exponential kinetics observed in protein folding are attributed to smooth energy landscapes, and methodologies like discrete path sampling help understand folding pathways, particularly in complex structures like knotted proteins.
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arxiv.org
Protein Photo-folding and Quantum Folding Theory

The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from the quantum folding theory by use of standard field-theoretical method. All these protein photo-folding processes are compared with common protein folding…

arxiv.org
Cooperativity and the origins of rapid, single-exponential kinetics in protein folding

The folding of naturally occurring, single domain proteins is usually well-described as a simple, single exponential process lacking significant trapped states. Here we further explore the hypothesis that the smooth energy landscape this implies, and the rapid kinetics it engenders, arises due to th…

q-bio.BM
arxiv.org
Introduction to Protein Folding

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which…

q-bio.BM
arxiv.org
Protein Folding: A Perspective From Statistical Physics

In this paper, we introduce an approach to the protein folding problem from the point of view of statistical physics. Protein folding is a stochastic process by which a polypeptide folds into its characteristic and functional 3D structure from random coil. The process involves an intricate interplay…

cond-mat.stat-mech cond-mat.soft physics.bio-ph q-bio.BM
arxiv.org
The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein

The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling approach, and the resulting potential energy surface is visual…

q-bio.BM cond-mat.soft
arxiv.org
Thermodynamics of Protein Folding

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which…

q-bio.BM
arxiv.org
Introducing Protein Folding Using Simple Models

We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use of lattice models to understand the selection of the limited …

cond-mat.soft q-bio
arxiv.org
The effects of non-native interactions on protein folding rates: Theory and simulation

Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free energy barrier. We present an analytic theory to account fo…

q-bio.BM
arxiv.org
Discrete molecular dynamics studies of the folding of a protein-like model

Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical properties of the proteins (lattice models), while others are …

cond-mat.stat-mech q-bio
arxiv.org
Remarks on homo- and hetero-polymeric aspects of protein folding

Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common approach to diversity is randomness, which is usually implemente…

cond-mat.soft cond-mat.dis-nn cond-mat.stat-mech q-bio.BM