83 citations · 219 across the 28 of their papers we have counts for
23 papers · 1 filter
Multi-scale sequence correlations increase proteome structural disorder and promiscuity
Ariel Afek, Eugene I. Shakhnovich, David B. Lukatsky
Numerous experiments demonstrate a high level of promiscuity and structural disorder in organismal proteomes. Here we ask the question what makes a protein promiscuous, i.e., prone…
Lethal Mutagenesis in Viruses and Bacteria
Peiqiu Chen, Eugene I. Shakhnovich
Here we study how mutations which change physical properties of cell proteins (stability) impact population survival and growth. In our model the genotype is presented as a set of…
Adaptation through stochastic switching into transient mutators in finite asexual populations
Muyoung Heo, Louis Kang, Eugene Shakhnovich
The importance of mutator clones in the adaptive evolution of asexual populations is not fully understood. Here we address this problem by using an ab initio microscopic model of l…
Emergence of mutationally robust proteins in a microscopic model of evolution
Konstantin B. Zeldovich, Eugene I. Shakhnovich
The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computation…
Identifying critical residues in protein folding: Insights from phi-value and Pfold analysis
P. F. N. Faisca, R. D. M. Travasso, R. C. Ball +1
We apply a simulational proxy of the phi-value analysis and perform extensive mutagenesis experiments to identify the nucleating residues in the folding reactions of two small latt…
Emergence of clonal selection and affinity maturation in an ab initio microscopic model of immunity
Muyoung Heo, Konstantin B. Zeldovich, Eugene I. Shakhnovich
Mechanisms of immunity, and of the host-pathogen interactions in general are among the most fundamental problems of medicine, ecology, and evolution studies. Here, we present a mic…