Fast-folding eriments and the topography of protein folding energy landscapes
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 …
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 …
out essential biological functions. Physical chemistry and polymer physics provide us with …
Energy landscapes and the collapse dynamics of homopolymers
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 …
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 …
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 …
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 …
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 …
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
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 …
global motion is controlled by solvent friction alone, with ruggedness of their energy …
Protein aggregation in silico
Protein aggregation is a challenge to the successful manufacture of protein therapeutics; it
can impose severe limitations on purification yields and compromise formulation stability …
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 …
properties of the polypeptide chains that determine the folding to the native conformation …