Correlation of fitness landscapes from three orthologous TIM barrels originates from sequence and structure constraints

Autor: Yvonne H. Chan, Sergey V. Venev, Konstantin B. Zeldovich, C. Robert Matthews

Publikováno v: Nature Communications, Vol 8, Iss 1, Pp 1-12 (2017)

The TIM barrel fold is an evolutionarily conserved motif found in proteins with a variety of enzymatic functions. Here the authors explore the fitness landscape of the TIM barrel protein IGPS and uncover evolutionary constraints on both sequence and

Externí odkaz: https://doaj.org/article/384072a0261e4a018bae7414c6c3b0e8

The Adaptive Potential of the Middle Domain of Yeast Hsp90

Autor: Inês Fragata, Claudia Bank, Pamela A. Cote-Hammarlof, Konstantin B. Zeldovich, Julia M. Flynn, David Mavor, Daniel N. Bolon

Publikováno v: Molecular Biology and Evolution
bioRxiv
Cote-Hammarlof, Pamela A; Fragata, Inês; Flynn, Julia; Mavor, David; Zeldovich, Konstantin B; Bank, Claudia; Bolon, Daniel N A (2021). The Adaptive Potential of the Middle Domain of Yeast Hsp90. Molecular Biology and Evolution, 38(2), pp. 368-379. Oxford University Press 10.1093/molbev/msaa211
Repositório Científico de Acesso Aberto de Portugal
Repositório Científico de Acesso Aberto de Portugal (RCAAP)
instacron:RCAAP

The distribution of fitness effects (DFEs) of new mutations across different environments quantifies the potential for adaptation in a given environment and its cost in others. So far, results regarding the cost of adaptation across environments have

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::39761b9e0b94c90cd9be380f02d0aeeb
http://europepmc.org/articles/PMC7826181

Characterizing Protein-Ligand Binding Using Atomistic Simulation and Machine Learning: Application to Drug Resistance in HIV-1 Protease

Autor: Debra A. Ragland, Celia A. Schiffer, Troy W. Whitfield, Konstantin B. Zeldovich

Publikováno v: J Chem Theory Comput

Over the past several decades, atomistic simulations of biomolecules, whether carried out using molecular dynamics or Monte Carlo techniques, have provided detailed insights into their function. Comparing the results of such simulations for a few clo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::960083f0f9b0a027b506bf63bf7eadc8
https://pubmed.ncbi.nlm.nih.gov/31877249

Protein and DNA sequence determinants of thermophilic adaptation.

Autor: Konstantin B Zeldovich, Igor N Berezovsky, Eugene I Shakhnovich

Publikováno v: PLoS Computational Biology, Vol 3, Iss 1, p e5 (2007)

There have been considerable attempts in the past to relate phenotypic trait--habitat temperature of organisms--to their genotypes, most importantly compositions of their genomes and proteomes. However, despite accumulation of anecdotal evidence, an

Externí odkaz: https://doaj.org/article/5f0e1f8e960d4b079f416fcfd3453764

The Combined Effect of Oseltamivir and Favipiravir on Influenza A Virus Evolution

Autor: Claudia Bank, Nicholas Renzette, Sebastian Matuszewski, Robert W. Finberg, Timothy F. Kowalik, Daniel N. Bolon, Louise Ormond, Jennifer P. Wang, Jeffrey D. Jensen, Ping Liu, Konstantin B. Zeldovich

Publikováno v: Genome Biology and Evolution
Repositório Científico de Acesso Aberto de Portugal
Repositório Científico de Acesso Aberto de Portugal (RCAAP)
instacron:RCAAP

This deposit is composed by the main article plus the supplementary materials of the publication. Influenza virus inflicts a heavy death toll annually and resistance to existing antiviral drugs has generated interest in the development of agents with

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::196a7fe93d3022d2db66ed415f370fde
http://europepmc.org/articles/PMC5570085