Theory of protein folding: the energy landscape perspective

JN Onuchic, Z Luthey-Schulten… - Annual review of …, 1997 - annualreviews.org
▪ Abstract The energy landscape theory of protein folding is a statistical description of a
protein's potential surface. It assumes that folding occurs through organizing an ensemble of …

Principles of protein folding—a perspective from simple exact models

KA Dill, S Bromberg, K Yue, HS Chan… - Protein …, 1995 - Wiley Online Library
General principles of protein structure, stability, and folding kinetics have recently been
explored in computer simulations of simple exact lattice models. These models represent …

[HTML][HTML] Finding low-energy conformations of lattice protein models by quantum annealing

A Perdomo-Ortiz, N Dickson, M Drew-Brook, G Rose… - Scientific reports, 2012 - nature.com
Lattice protein folding models are a cornerstone of computational biophysics. Although
these models are a coarse grained representation, they provide useful insight into the …

Navigating the folding routes

PG Wolynes, JN Onuchic, D Thirumalai - Science, 1995 - science.org
A theory of helix formation in collapsed polymers relates the measured amount of helix in the
collapsed states to the conformational entropy associated with different chain topologies …

Molten globule and protein folding

OB Ptitsyn - Advances in protein chemistry, 1995 - Elsevier
Publisher Summary This chapter describes the present state of the studies of the molten
globule state and its role in protein folding and physiological processes. Recent data on the …

[HTML][HTML] A theoretical method to compute sequence dependent configurational properties in charged polymers and proteins

L Sawle, K Ghosh - The Journal of chemical physics, 2015 - pubs.aip.org
A general formalism to compute configurational properties of proteins and other
heteropolymers with an arbitrary sequence of charges and non-uniform excluded volume …

Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes

S Paul, SK Bag, S Das, ET Harvill, C Dutta - Genome biology, 2008 - Springer
Background Halophilic prokaryotes are adapted to thrive in extreme conditions of salinity.
Identification and analysis of distinct macromolecular characteristics of halophiles provide …

Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet

E Shakhnovich - Chemical reviews, 2006 - ACS Publications
As was noted in our recent review, 1 the protein folding field underwent a cyclic
development. Initially, protein folding was viewed as a strictly experimental field belonging to …

Rules of physical mathematics govern intrinsically disordered proteins

K Ghosh, J Huihui, M Phillips… - Annual Review of …, 2022 - annualreviews.org
In stark contrast to foldable proteins with a unique folded state, intrinsically disordered
proteins and regions (IDPs) persist in perpetually disordered ensembles. Yet an IDP …

Protein and DNA sequence determinants of thermophilic adaptation

KB Zeldovich, IN Berezovsky… - PLoS computational …, 2007 - journals.plos.org
There have been considerable attempts in the past to relate phenotypic trait—habitat
temperature of organisms—to their genotypes, most importantly compositions of their …