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.

Probing the Role of Membrane and Cholesterol on APP-C99 Structure and Dynamics
03/01/2015 - 02/28/2019 (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.

AstraZeneca Graduate Fellowship in Organic Chemistry
01/01/2012 - 12/31/2012 (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
2018 Probing the role of membrane and cholesterol on APP-C99 structure and dynamics 5R01GM107703-04 1
2017 Probing the role of membrane and cholesterol on APP-C99 structure and dynamics 5R01GM107703-03 1
2015 Probing the role of membrane and cholesterol on APP-C99 structure and dynamics 1R01GM107703-01A1 1
2009 Probing the Principles Governing Protein Aggregation 5R01GM076688-08 27
2008 Probing the Principles Governing Protein Aggregation 5R01GM076688-07 27
2007 Probing the Principles Governing Protein Aggregation 5R01GM076688-06 27
2006 Probing the Principles Governing Protein Aggregation 9R01GM076688-05A1 27
2004 Probling the Principles of Amyloid Formation 5R01NS041356-04 16
2003 Probling the Principles of Amyloid Formation 5R01NS041356-03 16
2002 Probling the Principles of Amyloid Formation 5R01NS041356-02 16
Showing 10 of 11 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.

  1. Pantelopulos GA, Straub JE, Thirumalai D, Sugita Y. Structure of APP-C991-99 and implications for role of extra-membrane domains in function and oligomerization. Biochim Biophys Acta. 2018 Apr 24. PMID: 29702072.
  2. Pantelopulos GA, Nagai T, Bandara A, Panahi A, Straub JE. Critical size dependence of domain formation observed in coarse-grained simulations of bilayers composed of ternary lipid mixtures. J Chem Phys. 2017 Sep 07; 147(9):095101. PMID: 28886648.
  3. Bove-Fenderson E, Urano R, Straub JE, Harris DA. Cellular prion protein targets amyloid-ß fibril ends via its C-terminal domain to prevent elongation. J Biol Chem. 2017 Oct 13; 292(41):16858-16871.View Related Profiles. PMID: 28842494.
  4. Aguayo-Ortiz R, Chávez-García C, Straub JE, Dominguez L. Characterizing the structural ensemble of ?-secretase using a multiscale molecular dynamics approach. Chem Sci. 2017 Aug 01; 8(8):5576-5584. PMID: 28970936.
  5. Bandara A, Panahi A, Pantelopulos GA, Straub JE. Exploring the structure and stability of cholesterol dimer formation in multicomponent lipid bilayers. J Comput Chem. 2017 Jun 15; 38(16):1479-1488. PMID: 27761918; DOI: 10.1002/jcc.24516;.
  6. Panahi A, Bandara A, Pantelopulos GA, Dominguez L, Straub JE. Specific Binding of Cholesterol to C99 Domain of Amyloid Precursor Protein Depends Critically on Charge State of Protein. J Phys Chem Lett. 2016 Sep 15; 7(18):3535-41. PMID: 27525349; DOI: 10.1021/acs.jpclett.6b01624;.
  7. Dominguez L, Foster L, Straub JE, Thirumalai D. Impact of membrane lipid composition on the structure and stability of the transmembrane domain of amyloid precursor protein. Proc Natl Acad Sci U S A. 2016 09 06; 113(36):E5281-7. PMID: 27559086; PMCID: PMC5018773; DOI: 10.1073/pnas.1606482113;.
  8. Nagai T, Pantelopulos GA, Takahashi T, Straub JE. On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics. J Comput Chem. 2016 Aug 05; 37(21):2017-28. PMID: 27338239; DOI: 10.1002/jcc.24430;.
  9. Chin SL, Lu Q, Dane EL, Dominguez L, McKnight CJ, Straub JE, Grinstaff MW. Combined Molecular Dynamics Simulations and Experimental Studies of the Structure and Dynamics of Poly-Amido-Saccharides. J Am Chem Soc. 2016 05 25; 138(20):6532-40.View Related Profiles. PMID: 27119983; DOI: 10.1021/jacs.6b01837;.
  10. Lu Q, Straub JE. Freezing Transitions of Nanoconfined Coarse-Grained Water Show Subtle Dependence on Confining Environment. J Phys Chem B. 2016 Mar 10; 120(9):2517-25. PMID: 26906259; DOI: 10.1021/acs.jpcb.5b10481;.
Showing 10 of 94 results. Show More

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

Bar chart showing 94 publications over 24 distinct years, with a maximum of 14 publications in 2009

Contact for Mentoring:

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

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