Michael H. Peters, Ph.D. profile photo

Michael H. Peters, Ph.D.

Professor, Department of Chemical and Life Science Engineering

Engineering West Hall, Room 408, Richmond, VA, US

(804) 828-7790 mpeters@vcu.edu

Professor Peters conducts experimental and theoretical research in the field of protein engineering.

Publications

Documents

Photos

Audio

Video

Social

Industry Expertise

  • Chemicals
  • Education/Learning
  • Health and Wellness
  • Writing and Editing

Areas of Expertise

Peptidyl-Biomimetics Inhibitors for Breast Cancer TargetsOpenContact: A Simple Static Protein-Protein Mapping AlgorithmExtended Liouville Equation for Open SystemsNeuronal Stem Cell Delivery SystemsProtein EngineeringSmall Molecule Drug Design for Cancer TherapeuticsComputational Biomolecular EngineeringStatistical Mechanics

Accomplishments

University Teaching Award | professional

2004 Awarded by the Florida State University

Elected Fellow of the American Physical Society | professional

Awarded by the American Physical Society

2001-01-01

Elvin J. Dantin Professorship | professional

Awarded by the Florida State University

2000-01-01

University Teaching Incentive Award | professional

Awarded by the Florida State University

1995-01-01

Education

Ohio State University

Ph.D., Chemical Engineering

1981

Ohio State University

M.S., Chemical Engineering

1979

University of Dayton

B.S., Chemical Engineering

1977

Affiliations

  • Gross and Developmental Anatomy faculty VCU School of Medicine
  • Associate member VCU Massey Cancer Center
  • Senior fellow Center for the Study of Biological Complexity

Selected Articles

A Simple Contact Mapping Algorithm for Identifying Potential Peptide Mimetics in Protein-Protein Interaction Partners | Structure Function and Bioinformatics

2014

A simple, static contact mapping algorithm has been developed as a first step at identifying potential peptide biomimetics from protein interaction partner structure files. This rapid and simple mapping algorithm, “OpenContact” provides screened or parsed protein interaction files based on specified criteria for interatomic separation distances and interatomic potential interactions. The algorithm, which uses all-atom Amber03 force field models, was blindly tested on several unrelated cases from the literature where potential peptide mimetics have been experimentally developed to varying degrees of success. In all cases, the screening algorithm efficiently predicted proposed or potential peptide biomimetics, or close variations thereof, and provided complete atom-atom interaction data necessary for further detailed analysis and drug development. In addition, we used the static parsing/mapping method to develop a peptide mimetic to the cancer protein target, epidermal growth factor receptor. In this case, secondary, loop structure for the peptide was indicated from the intra-protein mapping, and the peptide was subsequently synthesized and shown to exhibit successful binding to the target protein. The case studies, which all involved experimental peptide drug advancement, illustrate many of the challenges associated with the development of peptide biomimetics, in general.

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Langevin dynamics for the transport of flexible biological macromolecules in confined geometries | The Journal of Chemical Physics

2015

The transport of flexible biological macromolecules in confined geometries is found in a variety of important biophysical systems including biomolecular movements through pores in cell walls, vesicle walls, and synthetic nanopores for sequencing methods. In this study, we extend our previous analysis of the Fokker–Planck and Langevin dynamics for describing the coupled translational and rotational motions of single structuredmacromolecules near structured external surfaces or walls to the problem of many interacting macromolecules in the presence of structured external surfaces representing the confining geometry. Overall macromolecular flexibility is modeled through specified interaction potentials between the structured Brownian subunits (B-particles), as already demonstrated for protein and DNA molecules briefly reviewed here. We derive the Fokker–Planck equation using a formal multiple time scale perturbation expansion of the Liouville equation for the entire system, i.e., solvent,macromolecules, and external surface. A configurational–orientational Langevin displacement equation is also obtained for use in Brownian dynamics applications. We demonstrate important effects of the external surface on implicit solvent forces through formal descriptions of the grand frictiontensor and equilibrium average force of the solvent on the B-particles. The formal analysis provides both transparency of all terms of the Langevin displacement equation as well as a prescription for their determination. As an example, application of the methods developed, the real-time movement of an α-helix protein through a carbon nanotube is simulated.

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Completing Irving and Kirkwood’s Molecular Theory of Transport Phenomena: Nonequilibrium Entropy Conservation | Industrial and Engineering Chemistry Research

2009

Following Irving and Kirkwood’s classical approach to the statistical mechanics of transport processes and the conservation equations for mass, momentum, and energy, we introduce a particular dynamical variable for entropy and derive the general nonequilibrium entropy conservation equation. This particular formalism is shown to encompass both Boltzmann’s and Gibbs’ entropy definitions as special cases. Entropy generation is shown to follow from phase-space dimensionality loss and truncations or approximations in higher-order space, the latter of which is consistent with the thesis of Jaynes. The general approach to entropy conservation given here not only completes Irving and Kirkwood’s treatment of the transport equations but also allows for a consistent analysis of all transport equations for any given system. Following standard perturbation expansion methods about local equilibrium states, we derive the closed form of the entropy conservation equation for isolated systems, which is shown to be in agreement with well-known phenomenological results and the principles of irreversible thermodynamics. In addition, the generalized nonequilibrium entropy developed here is fully consistent with its equilibrium counterpart. As an example, our formalism allows the analysis of entropy changes in dense gases and liquids through the introduction of a nonequilibrium Green’s entropy. This study provides a firm molecular basis of entropy conservation by consistent methods across the transport equations, allowing ready extensions to complex systems. Such foundations are of contemporary importance in designing energy-efficient or minimum entropy generating engineering systems.

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