A5029418807- Heat shock proteins research
- Evolution and Genetic Dynamics
- Protein Structure and Dynamics
- HIV Research and Treatment
- RNA and protein synthesis mechanisms
- HIV/AIDS drug development and treatment
- Computational Drug Discovery Methods
- Influenza Virus Research Studies
- Ubiquitin and proteasome pathways
- Enzyme Structure and Function
- thermodynamics and calorimetric analyses
- Fungal and yeast genetics research
- SARS-CoV-2 and COVID-19 Research
- vaccines and immunoinformatics approaches
- CRISPR and Genetic Engineering
- Hepatitis C virus research
- Protein Degradation and Inhibitors
- Endoplasmic Reticulum Stress and Disease
- Genetics, Bioinformatics, and Biomedical Research
- Bacteriophages and microbial interactions
- Signaling Pathways in Disease
- ATP Synthase and ATPases Research
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- Complex Systems and Decision Making
University of Massachusetts Chan Medical School
2015-2024
Massachusetts Academy of Math and Science
2022
Ohio University
1994-2017
Cat Tien National Park
2010
Massachusetts Institute of Technology
2003-2007
Charoenkrung Pracharak Hospital
2007
Howard Hughes Medical Institute
2001-2005
RMIT University
2005
California Institute of Technology
2001-2003
Virginia Tech
1993
We report the development and initial experimental validation of a computational design procedure aimed at generating enzyme-like protein catalysts called “protozymes.” Our approach utilizes “compute build” strategy that is based on physical/chemical principles governing stability catalytic mechanism. By using catalytically inert 108-residue Escherichia coli thioredoxin as scaffold, histidine-mediated nucleophilic hydrolysis p -nitrophenyl acetate model reaction, ORBIT software to compute...
The genes of all organisms have been shaped by selective pressures. relationship between gene sequence and fitness has tremendous implications for understanding both evolutionary processes functional constraints on the encoded proteins. Here, we exploited deep sequencing technology to experimentally determine possible individual point mutants under controlled conditions a nine-amino acid region Hsp90. Over past five decades, limited glimpses into function sparked long debate regarding...
With the continual evolution of new strains severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that are more virulent, transmissible, and able to evade current vaccines, there is an urgent need for effective anti-viral drugs. The SARS-CoV-2 main protease (M
Abstract Coronaviruses can evolve and spread rapidly to cause severe disease morbidity mortality, as exemplified by SARS-CoV-2 variants of the COVID-19 pandemic. Although currently available vaccines remain mostly effective against variants, additional treatment strategies are needed. Inhibitors that target essential viral enzymes, such proteases polymerases, represent key classes antivirals. However, clinical use antiviral therapies inevitably leads emergence drug resistance. In this study...
The challenge of distinguishing genetic drift from selection remains a central focus population genetics. Time-sampled data may provide powerful tool for these processes, and we here propose approximate Bayesian, maximum likelihood, analytical methods the inference demography time course data. Utilizing novel statistical computational tools, evaluate whole-genome datasets an influenza A H1N1 strain in presence absence oseltamivir (an inhibitor neuraminidase) collected at thirteen points....
Abstract The role of adaptation in the evolutionary process has been contentious for decades. At heart century-old debate between neutralists and selectionists lies distribution fitness effects (DFE)—that is, selective effect all mutations. Attempts to describe DFE have varied, occupying theoreticians experimentalists alike. New high-throughput techniques stand make important contributions empirical efforts characterize DFE, but usefulness such approaches depends on availability robust...
Mutations are the source of evolutionary variation. The interactions multiple mutations can have important effects on fitness and trajectories. We recently described distribution all single for a nine-amino-acid region yeast Hsp90 (Hsp82) implicated in substrate binding. Here, we report discuss intragenic epistatic within this seven point mutant backgrounds neutral to slightly deleterious effect, resulting an analysis more than 1,000 double mutants. find negative epistasis between...
The role of adaptation in molecular evolution has been contentious for decades. Here, we shed light on the adaptive potential Saccharomyces cerevisiae by presenting systematic fitness measurements all possible point mutations a region Hsp90 under four environmental conditions. Under elevated salinity, observe numerous beneficial with growth advantages up to 7% relative wild type. All these were observed be associated high costs adaptation. We thus demonstrate that an essential protein can...
Significance When mutations within a protein change each other’s functional effects—a phenomenon called epistasis—the paths available to evolution at any moment in time depend on the specific set of changes that previously occurred protein. The extent which epistasis has shaped historical evolutionary trajectories is unknown. Using high-precision bulk fitness assay and ancestral reconstruction, we measured effects extant sequences all substitutions during billion-year trajectory an essential...
To probe the mechanism of Hsp90 chaperone that is required for maturation many signaling proteins in eukaryotes, we analyzed effects all individual amino acid changes ATPase domain on yeast growth rate. The sensitivity a position to mutation was strongly influenced by proximity phosphates ATP, indicating ATPase-driven conformational impose stringent physical constraints Hsp90. investigate how these may vary different clients, performed biochemical analyses panel mutants spanning full range...
Ubiquitin is essential for eukaryotic life and varies in only 3 amino acid positions between yeast humans. However, recent deep sequencing studies indicate that ubiquitin highly tolerant to single mutations. We hypothesized this tolerance would be reduced by chemically induced physiologic perturbations. To test hypothesis, a class of first year UCSF graduate students employed mutational scanning determine the fitness landscape all possible residue mutations presence five different small...
Gene-environment interactions have long been theorized to influence molecular evolution. However, the environmental dependence of most mutations remains unknown. Using deep mutational scanning, we engineered yeast with all 44,604 single codon changes encoding 14,160 amino acid variants in Hsp90 and quantified growth effects under standard conditions five stress conditions. To our knowledge, these are largest determined comprehensive fitness maps point mutants. The many differed between...
Drugs that target the main protease (Mpro) of SARS-CoV-2 are effective therapeutics have entered clinical use. Wide-scale use these drugs will apply selection pressure for evolution resistance mutations. To understand potential in Mpro, we performed comprehensive surveys amino acid changes can cause to nirmatrelvir (Pfizer), and ensitrelvir (Xocova) a yeast screen. We identified 142 mutations 177 ensitrelvir, many which not been previously reported. Ninety-nine caused apparent both...
Protein–protein interactions can be designed computationally by using positive strategies that maximize the stability of desired structure and/or negative seek to destabilize competing states. Here, we compare efficacy these methods in reengineering a protein homodimer into heterodimer. The stability-design (positive design only) was experimentally more stable than specificity-design heterodimer and design). By contrast, only assembled as homogenous solution, whereas formed mixture species....
Heat shock protein 90 (Hsp90) plays a central role in signal transduction and has emerged as promising target for anti-cancer therapeutics, but its molecular mechanism is poorly understood. At physiological concentration, Hsp90 predominantly forms dimers, the function of full-length monomers cells not clear. contains three domains: N-terminal middle domains contribute directly to ATP binding hydrolysis C domain mediates dimerization. To study monomers, we used single-chain strategy that...
In natural systems, selection acts on both protein sequence and expression level, but it is unclear how integrates over these two dimensions. We recently developed the EMPIRIC approach to systematically determine fitness effects of all possible point mutants for important regions essential genes in yeast. Here, we investigated mutations a putative substrate binding loop yeast Hsp90 (Hsp82) broad range strengths. Negative epistasis between reduced strength amino acid substitutions was common,...