D. Bolon

发表

Enzyme-like proteins by computational design

S. L. Mayo, D. Bolon, Daniel N. A. Bolon, 2001, Proceedings of the National Academy of Sciences of the United States of America.

Quantifying and understanding the fitness effects of protein mutations: Laboratory versus nature

Dan S. Tawfik, D. Bolon, J. Boucher, 2016, Protein science : a publication of the Protein Society.

Analyses of the effects of all ubiquitin point mutants on yeast growth rate.

Kelly M. Thayer, Benjamin P. Roscoe, D. Bolon, 2013, Journal of molecular biology.

Systematic exploration of ubiquitin sequence, E1 activation efficiency, and experimental fitness in yeast.

Benjamin P. Roscoe, D. Bolon, Daniel N. A. Bolon, 2014, Journal of molecular biology.

Systematic Mutant Analyses Elucidate General and Client-Specific Aspects of Hsp90 Function.

D. Bolon, J. Flynn, Parul Mishra, 2016, Cell reports.

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting

Kyle A. Barlow, Benjamin P. Roscoe, Benjamin A. Barad, 2015, bioRxiv.

Polar residues in the protein core of Escherichia coli thioredoxin are important for fold specificity.

S. L. Mayo, D. Bolon, 2001, Biochemistry.

SHIFTING FITNESS LANDSCAPES IN RESPONSE TO ALTERED ENVIRONMENTS

Claudia Bank, D. Bolon, J. Jensen, 2013, Evolution; international journal of organic evolution.

Molecular Basis for Differential Patterns of Drug Resistance in Influenza N1 and N2 Neuraminidase.

Kelly M. Thayer, C. Schiffer, D. Bolon, 2016, Journal of chemical theory and computation.

An experimental evaluation of drug-induced mutational meltdown as an antiviral treatment strategy

D. Bolon, J. Jensen, K. Zeldovich, 2016, bioRxiv.

Computational Enzyme Design

D. Bolon, Daniel N. A. Bolon, 2002 .

pM to µM - Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance.

Shuntai Zhou, C. Schiffer, D. Bolon, 2019, ACS chemical biology.

Picomolar to Micromolar: Elucidating the Role of Distal Mutations in HIV ‑ 1 Protease in Conferring Drug Resistance

D. Bolon, R. Swanstrom, E. Nalivaika, 2019 .

Designed Hsp90 heterodimers reveal an asymmetric ATPase-driven mechanism in vivo.

D. Bolon, Parul Mishra, Daniel N. A. Bolon, 2014, Molecular cell.

Chapter 8: Hsp90 and Client Protein Maturation

D. Bolon, Parul Mishra, Daniel N. A. Bolon, 2016 .

Post-translational modification and conformational state of Heat Shock Protein 90 differentially affect binding of chemically diverse small molecule inhibitors

D. Bolon, L. Neckers, Tony Taldone, 2013, Oncotarget.

Posttranslational modification and conformational state of heat shock protein 90 differentially affect binding of chemically diverse small molecule inhibitors.

D. Bolon, L. Neckers, Tony Taldone, 2013 .

A complete allosteric map of a GTPase switch in its native network

Christopher J. P. Mathy, D. Bolon, T. Kortemme, 2022, bioRxiv.

Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance

C. Schiffer, D. Bolon, J. Flynn, 2022, Nature Communications.

Molecular Basis for Di ff erential Patterns of Drug Resistance in In fl uenza N 1 and N 2 Neuraminidase

Kelly M. Thayer, D. Bolon, Ayşegül Özen, 2016 .

Sculpting the Proteome with AAA+ Proteases and Disassembly Machines

Greg L. Hersch, T. Baker, R. Sauer, 2004, Cell.

A Bayesian MCMC Approach to Assess the Complete Distribution of Fitness Effects of New Mutations: Uncovering the Potential for Adaptive Walks in Challenging Environments

A. Wong, D. Bolon, J. Jensen, 2014, Genetics.

A systematic survey of an intragenic epistatic landscape

Claudia Bank, D. Bolon, J. Jensen, 2014, bioRxiv.

Experimental illumination of a fitness landscape

D. Bolon, J. Jensen, Ryan T. Hietpas, 2011, Proceedings of the National Academy of Sciences.

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

D. Bolon, J. Jensen, K. Zeldovich, 2017, Genome biology and evolution.

Influenza Virus Drug Resistance: A Time-Sampled Population Genetics Perspective

Daniel R. Caffrey, C. Schiffer, D. Bolon, 2014, PLoS genetics.

Evolution of the Influenza A Virus Genome during Development of Oseltamivir Resistance In Vitro

Alyssa J. Porter, Daniel R. Caffrey, C. Schiffer, 2013, Journal of Virology.

The Adaptive Potential of the Middle Domain of Yeast Hsp90

D. Bolon, J. Flynn, K. Zeldovich, 2020, Molecular biology and evolution.

The adaptive potential of the M-domain of yeast Hsp90

D. Bolon, J. Flynn, K. Zeldovich, 2019, bioRxiv.

Comprehensive fitness maps of Hsp90 show widespread environmental dependence

D. Bolon, J. Flynn, David Mavor, 2020, eLife.

Investigating the influence of environment on the evolution of Hsp90 using comprehensive fitness maps

D. Bolon, J. Flynn, David Mavor, 2019, bioRxiv.

Latent Effects of Hsp90 Mutants Revealed at Reduced Expression Levels

Konstantin B. Zeldovich, D. Bolon, K. Zeldovich, 2013, PLoS genetics.

A Balance between Inhibitor Binding and Substrate Processing Confers Influenza Drug Resistance.

Claudia Bank, Daniel R. Caffrey, Celia A Schiffer, 2016, Journal of molecular biology.

CRISPR-Cas9–mediated saturated mutagenesis screen predicts clinical drug resistance with improved accuracy

Michael R. Green, C. Schiffer, D. Bolon, 2017, Proceedings of the National Academy of Sciences.

Systematic analyses of the resistance potential of drugs targeting SARS-CoV-2 main protease

C. Schiffer, D. Bolon, J. Flynn, 2023, bioRxiv.

Pervasive contingency and entrenchment in a billion years of Hsp90 evolution

D. Bolon, J. Flynn, Parul Mishra, 2017, Proceedings of the National Academy of Sciences.

Quantitative structural analysis of influenza virus by cryo-electron tomography and convolutional neural networks.

C. Schiffer, D. Bolon, R. Finberg, 2022, Structure.

Quantitative Structural Analysis of Influenza Virus by Cryo-electron Tomography and Convolutional Neural Networks

C. Schiffer, D. Bolon, R. Finberg, 2021, bioRxiv.

Saturation Mutagenesis of the HIV-1 Envelope CD4 Binding Loop Reveals Residues Controlling Distinct Trimer Conformations

D. Bolon, P. Clapham, Daniel N. A. Bolon, 2016, PLoS pathogens.

Evolutionary mechanisms studied through protein fitness landscapes.

D. Bolon, J. Flynn, Pamela A. Cote-Hammarlof, 2018, Current opinion in structural biology.

Viewing Protein Fitness Landscapes Through a Next-Gen Lens

Benjamin P. Roscoe, D. Bolon, J. Flynn, 2014, Genetics.

Synonymous Mutations at the Beginning of the Influenza A Virus Hemagglutinin Gene Impact Experimental Fitness.

Daniel R. Caffrey, C. Schiffer, D. Bolon, 2018, Journal of molecular biology.

Mutations in Influenza A Virus Neuraminidase and Hemagglutinin Confer Resistance against a Broadly Neutralizing Hemagglutinin Stem Antibody

C. Schiffer, D. Bolon, W. Marasco, 2018, Journal of Virology.

Solubility-Promoting Function of Hsp90 Contributes to Client Maturation and Robust Cell Growth

D. Bolon, Parul Mishra, Natalie W. Pursell, 2012, Eukaryotic Cell.

Bound for observation.

D. Bolon, 2012, Journal of molecular biology.

Hsp90 and client protein maturation.

D. Bolon, Parul Mishra, Daniel N. A. Bolon, 2011, Methods in molecular biology.

Fitness analyses of all possible point mutations for regions of genes in yeast

Benjamin P. Roscoe, D. Bolon, Ryan T. Hietpas, 2012, Nature Protocols.

In Vitro Resistance Development of Oseltamivir Evolution of the Influenza A Virus Genome

Daniel R. Caffrey, C. Schiffer, D. Bolon, 2014 .

Constrained mutational sampling of amino acids in HIV-1 protease evolution

C. Schiffer, D. Bolon, T. Whitfield, 2018, bioRxiv.

Mapping the growth effect of previously hidden ubiquitin alleles using an overexpression based mutational scan

D. Bolon, Parul Mishra, David Mavor, 2019, bioRxiv.

Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance

Kyle A. Barlow, Wesley M. Marin, Gabriel K. Reder, 2018, Biology Open.

Research Advance: Extending chemical perturbations of the Ubiquitin fitness landscape in a classroom setting

Kyle A. Barlow, Wesley M. Marin, J. Derisi, 2017, bioRxiv.

Asymmetric Interactions of ATP with the AAA+ ClpX6 Unfoldase: Allosteric Control of a Protein Machine

Tania A. Baker, Robert T. Sauer, Greg L. Hersch, 2005, Cell.

Mutations in the hydrophobic core of ubiquitin differentially affect its recognition by receptor proteins.

D. Bolon, R. Deshaies, D. Fushman, 2008, Journal of molecular biology.

Resistance to vemurafenib resulting from a novel mutation in the BRAFV600E kinase domain

Michael R. Green, Benjamin P. Roscoe, D. Bolon, 2014, Pigment cell & melanoma research.

A complete allosteric map of a GTPase switch in its native cellular network.

Christopher J. P. Mathy, D. Bolon, T. Kortemme, 2023, Cell systems.

Prudent modeling of core polar residues in computational protein design.

Stephen L Mayo, S. L. Mayo, S. A. Ross, 2003, Journal of molecular biology.

Alanine scan of core positions in ubiquitin reveals links between dynamics, stability, and function.

D. Bolon, D. Fushman, C. Castañeda, 2014, Journal of molecular biology.

Sequence dependencies and biophysical features both govern cleavage of diverse cut-sites by HIV protease

D. Bolon, G. Nachum, Neha Samant, 2022, bioRxiv.

Altered Tethering of the SspB Adaptor to the ClpXP Protease Causes Changes in Substrate Delivery*

T. Baker, R. Sauer, D. Bolon, 2007, Journal of Biological Chemistry.

Nucleotide-dependent substrate handoff from the SspB adaptor to the AAA+ ClpXP protease.

T. Baker, R. Sauer, D. Bolon, 2004, Molecular cell.

Bivalent tethering of SspB to ClpXP is required for efficient substrate delivery: a protein-design study.

Robert T Sauer, Tania A Baker, Greg L. Hersch, 2004, Molecular cell.

Flexible linkers leash the substrate binding domain of SspB to a peptide module that stabilizes delivery complexes with the AAA+ ClpXP protease.

T. Baker, R. Sauer, D. Bolon, 2003, Molecular cell.

Dimerization of Hsp90 Is Required for in Vivo Function

D. Bolon, Daniel N. A. Bolon, Natalie Wayne, 2007, Journal of Biological Chemistry.

An experimental evaluation of drug-induced mutational meltdown as an antiviral treatment strategy

Ping Liu, D. Bolon, J. Jensen, 2016, bioRxiv.

Positive Selection Drives Preferred Segment Combinations during Influenza Virus Reassortment.

Daniel R. Caffrey, C. Schiffer, D. Bolon, 2015, Molecular biology and evolution.

Comprehensive fitness landscape of SARS-CoV-2 Mpro reveals insights into viral resistance mechanisms

C. Schiffer, D. Bolon, J. Flynn, 2022, bioRxiv.

A synthetic biology approach to probing nucleosome symmetry

N. Friedman, N. Kelleher, D. Bolon, 2017, bioRxiv.

Mechanistic Asymmetry in Hsp90 Dimers.

D. Bolon, J. Flynn, Parul Mishra, 2015, Journal of molecular biology.

Enforced N-domain Proximity Stimulates Hsp90 ATPase Activity and Is Compatible with Function in Vivo*

D. Bolon, Daniel N. A. Bolon, L. Pullen, 2011, The Journal of Biological Chemistry.

Charge-rich regions modulate the anti-aggregation activity of Hsp90.

D. Bolon, Daniel N. A. Bolon, Natalie Wayne, 2010, Journal of molecular biology.

Modular Control of Cross-oligomerization

D. Bolon, Yushuan Lai, Natalie Wayne, 2009, The Journal of Biological Chemistry.

Specificity versus stability in computational protein design.

T. Baker, R. Sauer, D. Bolon, 2005, Proceedings of the National Academy of Sciences of the United States of America.

De novo design of biocatalysts.

Christopher A. Voigt, Christopher A Voigt, Stephen L Mayo, 2002, Current opinion in chemical biology.

Hydrophobic core flexibility modulates enzyme activity in HIV-1 protease.

Celia A Schiffer, Yufeng Cai, C. Schiffer, 2012, Journal of the American Chemical Society.

Mutational fitness landscape and drug resistance.

D. Bolon, J. Flynn, Gily Schneider-Nachum, 2023, Current opinion in structural biology.

A bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: uncovering the potential for adaptive walks in challenging environments.

A. Wong, D. Bolon, J. Jensen, 2014, Genetics.

Investigating the influence of environment on the evolution of Investigating the influence of environment on the evolution of Hsp90 using comprehensive fitness maps [preprint] Hsp90 using comprehensive fitness maps [preprint] how document benefits you.

D. Bolon, J. Flynn, David Mavor, 2022 .

Molecular determinants of epistasis in HIV-1 protease: Elucidating the interdependence of L89V and L90M mutations in resistance.

C. Schiffer, D. Bolon, T. Whitfield, 2019, Biochemistry.

Analyses of HIV proteases variants at the threshold of viability reveals relationships between processing efficiency and fitness

C. Schiffer, D. Bolon, J. Flynn, 2021, Virus evolution.