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 …
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
For deriving maximal advantage from information on biomacromolecular flexibility and
rigidity, results from rigidity analyses must be linked to biologically relevant characteristics of …
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
The notion of using the evolutionary history encoded within multiple sequence alignments to
predict allosteric mechanisms is appealing. In this approach, correlated mutations are …
predict allosteric mechanisms is appealing. In this approach, correlated mutations are …
Ensemble-and rigidity theory-based perturbation approach to analyze dynamic allostery
Allostery describes the functional coupling between sites in biomolecules. Recently, the role
of changes in protein dynamics for allosteric communication has been highlighted. A …
of changes in protein dynamics for allosteric communication has been highlighted. A …
Distinct allosteric pathways in imidazole glycerol phosphate synthase from yeast and bacteria
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 …
question that becomes very challenging when allostery plays an important functional role …
Rigid residue scan simulations systematically reveal residue entropic roles in protein allostery
Intra-protein information is transmitted over distances via allosteric processes. This
ubiquitous protein process allows for protein function changes due to ligand binding events …
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
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 …
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 …
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 …
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
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 …
response regulator CheY. This elevation, in an unknown mechanism, activates CheY to …