Linking protein structural and functional change to mutation using amino acid networks
C Sotomayor-Vivas, E Hernández-Lemus… - Plos one, 2022 - journals.plos.org
The function of a protein is strongly dependent on its structure. During evolution, proteins
acquire new functions through mutations in the amino-acid sequence. Given the advance in …
acquire new functions through mutations in the amino-acid sequence. Given the advance in …
Energy transport across interfaces in biomolecular systems
DM Leitner, HD Pandey, KM Reid - The Journal of Physical …, 2019 - ACS Publications
Energy transport during chemical reactions or following photoexcitation in systems of
biological molecules is mediated by numerous interfaces that separate chemical groups and …
biological molecules is mediated by numerous interfaces that separate chemical groups and …
A general mechanism for the propagation of mutational effects in proteins
Mutations in the hydrophobic interior of proteins are generally thought to weaken the
interactions only in their immediate neighborhood. This forms the basis of protein …
interactions only in their immediate neighborhood. This forms the basis of protein …
Exploring allosteric pathways of a v-type enzyme with dynamical perturbation networks
Elucidation of the allosteric pathways in proteins is a computational challenge that strongly
benefits from combination of atomistic molecular dynamics (MD) simulations and coarse …
benefits from combination of atomistic molecular dynamics (MD) simulations and coarse …
Connected Component Analysis of Dynamical Perturbation Contact Networks
A Gheeraert, C Lesieur, VS Batista… - The Journal of …, 2023 - ACS Publications
Describing protein dynamical networks through amino acid contacts is a powerful way to
analyze complex biomolecular systems. However, due to the size of the systems, identifying …
analyze complex biomolecular systems. However, due to the size of the systems, identifying …
Scaling of rates of vibrational energy transfer in proteins with equilibrium dynamics and entropy
Theoretical arguments and results of molecular dynamics (MD) simulations of myoglobin at
300 K are presented to relate rates of vibrational energy transfer across nonbonded contacts …
300 K are presented to relate rates of vibrational energy transfer across nonbonded contacts …
Mapping energy transport networks in proteins
DM Leitner, T Yamato - Rev. Comput. Chem, 2018 - books.google.com
The response to chemical reactions or impulsive excitations that occur within protein
molecules has fascinated chemists for decades. 1–3 In recent years, ultrafast X-ray studies …
molecules has fascinated chemists for decades. 1–3 In recent years, ultrafast X-ray studies …
Variation of energy transfer rates across protein–water contacts with equilibrium structural fluctuations of a homodimeric hemoglobin
Molecular dynamics simulations of the homodimeric hemoglobin from Scapharca
inaequivalvis (HbI) have been carried out to examine relations between rates of vibrational …
inaequivalvis (HbI) have been carried out to examine relations between rates of vibrational …
Dissecting mutational allosteric effects in alkaline phosphatases associated with different Hypophosphatasia phenotypes: An integrative computational investigation
F Xiao, Z Zhou, X Song, M Gan, J Long… - PLoS Computational …, 2022 - journals.plos.org
Hypophosphatasia (HPP) is a rare inherited disorder characterized by defective bone
mineralization and is highly variable in its clinical phenotype. The disease occurs due to …
mineralization and is highly variable in its clinical phenotype. The disease occurs due to …
Large-scale in silico mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness
Background How, and the extent to which, evolution acts on DNA and protein sequences to
ensure mutational robustness and evolvability is a long-standing open question in the field …
ensure mutational robustness and evolvability is a long-standing open question in the field …