Theory of free energy and entropy in noncovalent binding

HX Zhou, MK Gilson - Chemical reviews, 2009 - ACS Publications
Noncovalent binding provides an invisible wiring diagram for biomolecular pathways and is
the essence of host-guest and supramolecular chemistry. Decades of theoretical and …

Protein binding specificity versus promiscuity

G Schreiber, AE Keating - Current opinion in structural biology, 2011 - Elsevier
Interactions between macromolecules in general, and between proteins in particular, are
essential for any life process. Examples include transfer of information, inhibition or …

[ΒΙΒΛΙΟ][B] Introduction to proteins: structure, function, and motion

A Kessel, N Ben-Tal - 2018 - taylorfrancis.com
Introduction to Proteins provides a comprehensive and state-of-the-art introduction to the
structure, function, and motion of proteins for students, faculty, and researchers at all levels …

Protein flexibility and conformational entropy in ligand design targeting the carbohydrate recognition domain of galectin-3

C Diehl, O Engstrom, T Delaine… - Journal of the …, 2010 - ACS Publications
Rational drug design is predicated on knowledge of the three-dimensional structure of the
protein− ligand complex and the thermodynamics of ligand binding. Despite the …

Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition

J Wereszczynski, JA McCammon - Quarterly reviews of biophysics, 2012 - cambridge.org
Molecular recognition plays a central role in biochemical processes. Although well studied,
understanding the mechanisms of recognition is inherently difficult due to the range of …

The binding mechanisms of intrinsically disordered proteins

J Dogan, S Gianni, P Jemth - Physical Chemistry Chemical Physics, 2014 - pubs.rsc.org
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins
are very common and instrumental for cellular signaling. Recently, a number of studies have …

Targeting disordered proteins with small molecules using entropy

GT Heller, P Sormanni, M Vendruscolo - Trends in biochemical sciences, 2015 - cell.com
The human proteome includes many disordered proteins. Although these proteins are
closely linked with a range of human diseases, no clinically approved drug targets them in …

Hot spots and transient pockets: predicting the determinants of small-molecule binding to a protein–protein interface

A Metz, C Pfleger, H Kopitz… - Journal of chemical …, 2012 - ACS Publications
Protein–protein interfaces are considered difficult targets for small-molecule protein–protein
interaction modulators (PPIMs). Here, we present for the first time a computational strategy …

Ancestral protein reconstruction yields insights into adaptive evolution of binding specificity in solute-binding proteins

BE Clifton, CJ Jackson - Cell chemical biology, 2016 - cell.com
The promiscuous functions of proteins are an important reservoir of functional novelty in
protein evolution, but the molecular basis for binding promiscuity remains elusive. We used …

Protein thermostability is owing to their preferences to non-polar smaller volume amino acids, variations in residual physico-chemical properties and more salt-bridges

AS Panja, B Bandopadhyay, S Maiti - PloS one, 2015 - journals.plos.org
Introduction Protein thermostability is an important field for its evolutionary perspective of
mesophilic versus thermophilic relationship and for its industrial/therapeutic applications …