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

PhD, Columbia University
MPhil, Columbia University
MA, Columbia University
BS, University of Maryland



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.


En route to amyloid formation: Protein and hydration-water dynamics under liquid-liquid phase separation
07/01/2024 - 06/30/2027 (PI)
National Science Foundation
PHY-2423884

Probing the role of membrane domains and interfaces in protein assembly and function
07/01/2019 - 06/30/2024 (PI)
National Science Foundation
CHE-1900416

Probing the roles of membrane and cholesterol on Aß biogenesis and prion protein interactions
06/01/2019 - 02/29/2024 (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
2022 Probing the roles of membrane and cholesterol on Aß biogenesis and prion protein interactions 5R01GM107703-08
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
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.

iCite Analysis       Copy PMIDs To Clipboard

  1. Kwon S, Majumder A, Straub JE. Exploring Free Energy Landscapes for Protein Partitioning into Membrane Domains in All-Atom and Coarse-Grained Simulations. J Chem Theory Comput. 2024 Nov 01. PMID: 39484915
     
  2. Pantelopulos GA, Abraham CB, Straub JE. Cholesterol and Lipid Rafts in the Biogenesis of Amyloid-ß Protein and Alzheimer's Disease. Annu Rev Biophys. 2024 Jul; 53(1):455-486. PMID: 38382114
     
  3. Majumder A, Straub JE. Machine Learning Derived Collective Variables for the Study of Protein Homodimerization in Membrane. J Chem Theory Comput. 2024 Jul 09; 20(13):5774-5783. PMID: 38918177
     
  4. Majumder A, Straub JE. The role of structural heterogeneity in the homodimerization of transmembrane proteins. J Chem Phys. 2023 Oct 07; 159(13). PMID: 37782254; PMCID: PMC10547497; DOI: 10.1063/5.0159801;
     
  5. Abraham CB, Xu L, Pantelopulos GA, Straub JE. Characterizing the transmembrane domains of ADAM10 and BACE1 and the impact of membrane composition. Biophys J. 2023 Oct 03; 122(19):3999-4010. PMID: 37658602; PMCID: PMC10560698; DOI: 10.1016/j.bpj.2023.08.025;
     
  6. Majumder A, Vuksanovic N, Ray LC, Bernstein HM, Allen KN, Imperiali B, Straub JE. Synergistic computational and experimental studies of a phosphoglycosyl transferase membrane/ligand ensemble. J Biol Chem. 2023 Oct; 299(10):105194.View Related Profiles. PMID: 37633332; PMCID: PMC10519829; DOI: 10.1016/j.jbc.2023.105194;
     
  7. Thirumalai D, Kumar A, Chakraborty D, Straub JE, Mugnai ML. Conformational fluctuations and phases in fused in sarcoma (FUS) low-complexity domain. Biopolymers. 2024 Mar; 115(2):e23558. PMID: 37399327; PMCID: PMC10831756; DOI: 10.1002/bip.23558;
     
  8. Chakraborty D, Straub JE, Thirumalai D. Energy landscapes of Aß monomers are sculpted in accordance with Ostwald's rule of stages. Sci Adv. 2023 Mar 22; 9(12):eadd6921. PMID: 36947617; PMCID: PMC10032606; DOI: 10.1126/sciadv.add6921;
     
  9. Chakraborty D, Straub JE, Thirumalai D. Energy landscapes of Aß monomers are sculpted in accordance with Ostwald's rule of stages. Sci Adv. 2023 Mar 22; 9(12):eadd6921. PMID: 36947617; PMCID: PMC10032606; DOI: 10.1126/sciadv.add6921;
     
  10. Thirumalai D, Kumar A, Chakraborty D, Straub JE, Mugnai ML. Conformational Fluctuations and Phases in Fused in Sarcoma (FUS) Low-Complexity Domain. ArXiv. 2023 Mar 07. PMID: 36945688; PMCID: PMC10029050
     
Showing 10 of 135 results. Show More

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

Bar chart showing 133 publications over 30 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
202110
20223
20236
20243


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
Google Map

(617) 353-6466 (fax)

Straub's Networks
Click the "See All" links for more information and interactive visualizations
Concepts
_
Co-Authors
_
Similar People
_
Same Department