John Straub, PhD
Boston University College of Arts and Sciences
Dept of Chemistry

PhD, Columbia University
MPhil, Columbia University
MA, Columbia University

John Straub explores protein dynamics and thermodynamics using theoretical and computational methods, with a particular focus on elucidating pathways for conformational change associated with protein energy transfer, signaling, folding, and aggregation.

The Straub Group investigates fundamental aspects of protein dynamics and thermodynamics underlying the formation of protein structure, through folding and aggregation, and enabling protein function, through pathways of energy flow and signaling. Student and postdoctoral research scientists in the Straub Group work to develop and employ state-of-the-art computational methods while working in collaboration with leading experimental research groups.

Kinetic and thermodynamic properties defining protein aggregation are elucidated through pioneering computational studies of the earliest stages of amyloid protein aggregation, including the formation of small oligomers (dimers through hexamers) from monomeric protein, and the production of monomeric protein from amyloid precursor proteins.

Novel computational algorithms for enhanced sampling of conformational ensembles in complex biomolecular systems include effective approaches for global optimization and enhanced conformational sampling, in complex molecular systems, and novel coarse-grained models of proteins, for use in protein structure prediction.

Novel computational approaches for the exploration of reaction dynamics allow for direct simulation of both ultrafast (quantum) and long-time (classical) dynamical events that translate how protein structure supports dynamical energy flow associated with protein function.

Pathways and mechanism for energy and signal flow in proteins are explored using classical and quantum dynamical simulations. This includes fundamental aspects of energy transfer associated with ligand binding and redox events in a variety of heme protein systems, with the ultimate goal of relating protein dynamics to function. Professor Straub’s book, “Proteins: Energy, Heat and Signal Flow,” co-edited with David Leitner, captures the state-of-the-art in theoretical studies of protein dynamics and signaling.

2016 Boston University: United Methodist Church Scholar/Teacher of the Year
2013 Nagoya University: JSPS Invitation Fellow
2006 Montana State University: Visiting Professor
2005 Boston University: Metcalf Award for Excellence in Teaching
1998 Institute for Advanced Studies, Hebrew University: Fellow
1995-1997 Alfred P. Sloan Research Fellow

Probing the roles of membrane and cholesterol on Aß biogenesis and prion protein interactions
06/01/2019 - 02/28/2023 (PI)
NIH/National Institute of General Medical Sciences

Probing the role of membrane domains and interfaces in protein assembly and function
07/01/2019 - 06/30/2022 (PI)
National Science Foundation

Probing the Role of Membrane and Cholesterol on APP-C99 Structure and Dynamics
03/01/2015 - 05/31/2019 (PI)
NIH/National Institute of General Medical Sciences

Complex Role of Solvationin Protein Structure and Dynamics in Micelles and Membranes
08/01/2014 - 07/31/2017 (PI)
National Science Foundation

06/15/2011 - 05/31/2015 (PI)
National Science Foundation

Faculty for the Future Fellowship (Schlumberger)
05/15/2012 - 04/30/2014 (PI)
Schlumberger Foundation, Inc.

01/01/2012 - 12/31/2012 (Subcontract PI)
AstraZeneca AstraZeneca

Scientific Communication and Professional Networking and Chemistry Education Opportunities
06/02/2011 - 08/31/2012 (PI)
Vertex Pharmaceuticals Incorporated


Yr Title Project-Sub Proj Pubs
2021 Probing the roles of membrane and cholesterol on A? biogenesis and prion protein interactions 5R01GM107703-07 13
2020 Probing the roles of membrane and cholesterol on A? biogenesis and prion protein interactions 5R01GM107703-06 13
2020 Probing the roles of membrane and cholesterol on A? biogenesis and prion protein interactions 5R01GM107703-06 13
2019 Probing the roles of membrane and cholesterol on A? biogenesis and prion protein interactions 2R01GM107703-05 13
2018 Probing the role of membrane and cholesterol on APP-C99 structure and dynamics 5R01GM107703-04 13
2017 Probing the role of membrane and cholesterol on APP-C99 structure and dynamics 5R01GM107703-03 13
2016 Probing the role of membrane and cholesterol on APP-C99 structure and dynamics 5R01GM107703-02 13
2015 Probing the role of membrane and cholesterol on APP-C99 structure and dynamics 1R01GM107703-01A1 13
2009 Probing the Principles Governing Protein Aggregation 5R01GM076688-08 31
2008 Probing the Principles Governing Protein Aggregation 5R01GM076688-07 31
Showing 10 of 17 results. Show All Results

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

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  1. Kumar A, Chakraborty D, Mugnai ML, Straub JE, Thirumalai D. Sequence Determines the Switch in the Fibril Forming Regions in the Low-Complexity FUS Protein and Its Variants. J Phys Chem Lett. 2021 Sep 23; 12(37):9026-9032. PMID: 34516126
  2. An X, Majumder A, McNeely J, Yang J, Puri T, He Z, Liang T, Snyder JK, Straub JE, Reinhard BM. Interfacial hydration determines orientational and functional dimorphism of sterol-derived Raman tags in lipid-coated nanoparticles. Proc Natl Acad Sci U S A. 2021 Aug 17; 118(33).View Related Profiles. PMID: 34389679; PMCID: PMC8379971; DOI: 10.1073/pnas.2105913118;
  3. Harris JJ, Pantelopulos GA, Straub JE. Finite-Size Effects and Optimal System Sizes in Simulations of Surfactant Micelle Self-Assembly. J Phys Chem B. 2021 05 20; 125(19):5068-5077. PMID: 33961427
  4. Majumder A, Straub JE. Addressing the Excessive Aggregation of Membrane Proteins in the MARTINI Model. J Chem Theory Comput. 2021 Apr 13; 17(4):2513-2521. PMID: 33720709
  5. Elkins MR, Bandara A, Pantelopulos GA, Straub JE, Hong M. Direct Observation of Cholesterol Dimers and Tetramers in Lipid Bilayers. J Phys Chem B. 2021 02 25; 125(7):1825-1837. PMID: 33560844
  6. Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, Chiricotto M, Ganguly P, McCarty J, Li MS, Hall C, Wang Y, Miller Y, Melchionna S, Habenstein B, Timr S, Chen J, Hnath B, Strodel B, Kayed R, Lesné S, Wei G, Sterpone F, Doig AJ, Derreumaux P. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chem Rev. 2021 02 24; 121(4):2545-2647. PMID: 33543942
  7. Straub JE. New and notable: A multiscale coarse-grained model of the SARS-CoV-2 virion. Biophys J. 2021 03 16; 120(6):975-976. PMID: 33577762; PMCID: PMC7837621; DOI: 10.1016/j.bpj.2020.12.032;
  8. Pantelopulos GA, Panahi A, Straub JE. Impact of Cholesterol Concentration and Lipid Phase on Structure and Fluctuation of Amyloid Precursor Protein. J Phys Chem B. 2020 11 12; 124(45):10173-10185. PMID: 33135883; PMCID: PMC7958706; DOI: 10.1021/acs.jpcb.0c07615;
  9. Ediger MD, Jensen L, Manolopoulos DE, Martinez TJ, Michaelides A, Reichman DR, Sherrill CD, Shi Q, Straub JE, Vega C, Wang LS, Brigham EC, Lian T. JCP Emerging Investigator Special Collection 2019. J Chem Phys. 2020 Sep 21; 153(11):110402. PMID: 32962387
  10. Chakraborty D, Straub JE, Thirumalai D. Differences in the free energies between the excited states of Aß40 and Aß42 monomers encode their aggregation propensities. Proc Natl Acad Sci U S A. 2020 08 18; 117(33):19926-19937. PMID: 32732434; PMCID: PMC7443889; DOI: 10.1073/pnas.2002570117;
Showing 10 of 118 results. Show More

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 118 publications over 27 distinct years, with a maximum of 14 publications in 2009


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