John Straub, PhD
Professor
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.


Probing the role of membrane domains and interfaces in protein assembly and function
07/01/2019 - 06/30/2023 (PI)
National Science Foundation
CHE-1900416

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
5R01GM107703-08

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
5R01GM107703-04

Complex Role of Solvationin Protein Structure and Dynamics in Micelles and Membranes
08/01/2014 - 07/31/2017 (PI)
National Science Foundation
CHE-1362524

ALGORITHMS FOR THE SIMULATION OF STRONG PHASE CHANGES IN COMPLEX MOLECULAR SYSTEMS
06/15/2011 - 05/31/2015 (PI)
National Science Foundation
CHE-1114676

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


ASTRAZENECA GRADUATE FELLOWSHIP IN ORGANIC CHEMISTRY
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




Title


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
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
2007 Probing the Principles Governing Protein Aggregation 5R01GM076688-06 31
Showing 10 of 16 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.

iCite Analysis       Copy PMIDs To Clipboard

  1. Majumder A, Kwon S, Straub JE. On Computing Equilibrium Binding Constants for Protein-Protein Association in Membranes. J Chem Theory Comput. 2022 May 17. PMID: 35580264
     
  2. Ceriotti M, Jensen L, Manolopoulos DE, Martinez TJ, Michaelides A, Ogilvie JP, Reichman DR, Shi Q, Straub JE, Vega C, Wang LS, Weiss E, Zhu X, Stein JL, Lian T. 2020 JCP Emerging Investigator Special Collection. J Chem Phys. 2021 12 21; 155(23):230401. PMID: 34937385
     
  3. Baiz CR, Blasiak B, Bredenbeck J, Cho M, Choi JH, Corcelli SA, Dijkstra AG, Feng CJ, Garrett-Roe S, Ge NH, Hanson-Heine MWD, Hirst JD, Jansen TLC, Kwac K, Kubarych KJ, Londergan CH, Maekawa H, Reppert M, Saito S, Roy S, Skinner JL, Stock G, Straub JE, Thielges MC, Tominaga K, Tokmakoff A, Torii H, Wang L, Webb LJ, Zanni MT. Correction to Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction. Chem Rev. 2021 Nov 10; 121(21):13698. PMID: 34709802
     
  4. 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; PMCID: PMC8826754; DOI: 10.1021/acs.jpclett.1c02310;
     
  5. 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 08 17; 118(33).View Related Profiles. PMID: 34389679; PMCID: PMC8379971; DOI: 10.1073/pnas.2105913118;
     
  6. 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
     
  7. 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; PMCID: PMC8829890; DOI: 10.1021/acs.jctc.0c01253;
     
  8. 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; PMCID: PMC8820947; DOI: 10.1021/acs.jpcb.0c10631;
     
  9. 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; PMCID: PMC8836097; DOI: 10.1021/acs.chemrev.0c01122;
     
  10. 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;
     
Showing 10 of 121 results. Show More

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

Bar chart showing 121 publications over 28 distinct years, with a maximum of 14 publications in 2009

YearPublications
19901
19933
19962
19971
19981
19993
20014
20023
20033
20045
20052
20066
20074
20084
200914
20105
20116
20123
20134
20149
20151
20166
20173
20187
20195
20206
20219
20221


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
Contact for Mentoring:

590 Commonwealth Ave
Boston MA 02215
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(617) 353-6466 (fax)

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