Rigidity theory for biomolecules: concepts, software, and applications

SMA Hermans, C Pfleger, C Nutschel… - Wiley …, 2017 - Wiley Online Library
The mechanical heterogeneity of biomolecular structures is intimately linked to their diverse
biological functions. Applying rigidity theory to biomolecules identifies this heterogeneous …

Constraint Network Analysis (CNA): a Python software package for efficiently linking biomacromolecular structure, flexibility,(thermo-) stability, and function

C Pfleger, PC Rathi, DL Klein, S Radestock, H Gohlke - 2013 - ACS Publications
For deriving maximal advantage from information on biomacromolecular flexibility and
rigidity, results from rigidity analyses must be linked to biologically relevant characteristics of …

A critical evaluation of correlated mutation algorithms and coevolution within allosteric mechanisms

DR Livesay, KE Kreth, AA Fodor - Allostery: Methods and Protocols, 2012 - Springer
The notion of using the evolutionary history encoded within multiple sequence alignments to
predict allosteric mechanisms is appealing. In this approach, correlated mutations are …

Ensemble-and rigidity theory-based perturbation approach to analyze dynamic allostery

C Pfleger, A Minges, M Boehm… - Journal of Chemical …, 2017 - ACS Publications
Allostery describes the functional coupling between sites in biomolecules. Recently, the role
of changes in protein dynamics for allosteric communication has been highlighted. A …

Distinct allosteric pathways in imidazole glycerol phosphate synthase from yeast and bacteria

F Maschietto, A Gheeraert, A Piazzi, VS Batista… - Biophysical …, 2022 - cell.com
Understanding the relationship between protein structures and their function is still an open
question that becomes very challenging when allostery plays an important functional role …

Rigid residue scan simulations systematically reveal residue entropic roles in protein allostery

R Kalescky, H Zhou, J Liu, P Tao - PLoS computational biology, 2016 - journals.plos.org
Intra-protein information is transmitted over distances via allosteric processes. This
ubiquitous protein process allows for protein function changes due to ligand binding events …

Changes in lysozyme flexibility upon mutation are frequent, large and long-ranged

D Verma, DJ Jacobs, DR Livesay - PLoS computational biology, 2012 - journals.plos.org
We investigate changes in human c-type lysozyme flexibility upon mutation via a Distance
Constraint Model, which gives a statistical mechanical treatment of network rigidity …

Rigidity emerges during antibody evolution in three distinct antibody systems: evidence from QSFR analysis of Fab fragments

T Li, MB Tracka, S Uddin, J Casas-Finet… - PLoS computational …, 2015 - journals.plos.org
The effects of somatic mutations that transform polyspecific germline (GL) antibodies to
affinity mature (AM) antibodies with monospecificity are compared among three GL-AM Fab …

Redistribution of flexibility in stabilizing antibody fragment mutants follows Le Chatelier's principle

T Li, MB Tracka, S Uddin, J Casas-Finet, DJ Jacobs… - Biophysical …, 2014 - cell.com
Redistribution of Flexibility in Stabilizing Antibody Fragment Mutants Follows Le Chatelier's
Principle Page 1 are believed to be contributed by the rotational motion of the side methyl …

CheY's acetylation sites responsible for generating clockwise flagellar rotation in Escherichia coli

M Fraiberg, O Afanzar, CK Cassidy… - Molecular …, 2015 - Wiley Online Library
Stimulation of E scherichia coli with acetate elevates the acetylation level of the chemotaxis
response regulator CheY. This elevation, in an unknown mechanism, activates CheY to …