Fast-folding eriments and the topography of protein folding energy landscapes

PG Wolynes, Z Luthey-Schulten, JN Onuchic - Chemistry & biology, 1996 - cell.com
The rapid folding of certain proteins can be described theoretically using an energy
landscape in the shape of a folding funnel. New techniques have allowed the examination of …

Deconstructing the native state: energy landscapes, function, and dynamics of globular proteins

PI Zhuravlev, CK Materese… - The Journal of Physical …, 2009 - ACS Publications
Proteins are highly complex molecules with features exquisitely selected by nature to carry
out essential biological functions. Physical chemistry and polymer physics provide us with …

Energy landscapes and the collapse dynamics of homopolymers

HS Chan, KA Dill - The Journal of chemical physics, 1993 - pubs.aip.org
What is the shape of the conformational free energy landscape for the collapse of a single
homopolymer molecule? We model the dynamics of homopolymer collapse in a poor …

Watching solvent friction impede ultrafast barrier crossings: A direct test of Kramers theory

JM Anna, KJ Kubarych - The Journal of chemical physics, 2010 - pubs.aip.org
A systematic investigation of the solvent's dynamic influence on activated barrier crossings
on an electronic ground state is performed using ultrafast two-dimensional infrared chemical …

Ion condensation onto ribozyme is site specific and fold dependent

N Hori, NA Denesyuk, D Thirumalai - Biophysical Journal, 2019 - cell.com
The highly charged RNA molecules, with each phosphate carrying a single negative charge,
cannot fold into well-defined architectures with tertiary interactions in the absence of ions …

Physical basis of the disorder-order transition

A Soranno - Archives of biochemistry and biophysics, 2020 - Elsevier
Intrinsically disordered proteins do not adopt well-defined structures, yet they still play
functional roles in many different aspects of biology. Their lack of stable conformations …

Topography of the free-energy landscape probed via mechanical unfolding of proteins

S Kirmizialtin, L Huang, DE Makarov - The Journal of chemical physics, 2005 - pubs.aip.org
Single-molecule experiments in which proteins are unfolded by applying mechanical
stretching forces generally force unfolding to proceed along a reaction coordinate that is …

Theoretical and computational validation of the Kuhn barrier friction mechanism in unfolded proteins

SM Avdoshenko, A Das, R Satija, GA Papoian… - Scientific Reports, 2017 - nature.com
A long time ago, Kuhn predicted that long polymers should approach a limit where their
global motion is controlled by solvent friction alone, with ruggedness of their energy …

Protein aggregation in silico

T Cellmer, D Bratko, JM Prausnitz, HW Blanch - Trends in biotechnology, 2007 - cell.com
Protein aggregation is a challenge to the successful manufacture of protein therapeutics; it
can impose severe limitations on purification yields and compromise formulation stability …

Factors governing the foldability of proteins

DK Klimov, D Thirumalai - Proteins: Structure, Function, and …, 1996 - Wiley Online Library
We use a three‐dimensional lattice model of proteins to investigate systematically the global
properties of the polypeptide chains that determine the folding to the native conformation …