Electronic structure, dielectric response, and surface charge distribution of RGD (1FUV) peptide

Puja Adhikari; Amy M Wen; Roger H French; V Adrian Parsegian; Nicole F Steinmetz; Rudolf Podgornik; Wai-Yim Ching

doi:10.1038/srep05605

Electronic structure, dielectric response, and surface charge distribution of RGD (1FUV) peptide

Sci Rep. 2014 Jul 8:4:5605. doi: 10.1038/srep05605.

Authors

Puja Adhikari¹, Amy M Wen², Roger H French³, V Adrian Parsegian⁴, Nicole F Steinmetz⁵, Rudolf Podgornik⁶, Wai-Yim Ching¹

Affiliations

¹ Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO, 64110, USA.
² Department of Biomedical Engineering, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
³ 1] Department of Materials Science and Engineering, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA [2] Department of Physics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA [3] Department of Radiology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
⁴ Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003, USA.
⁵ 1] Department of Biomedical Engineering, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA [2] Department of Materials Science and Engineering, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA [3] Department of Radiology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA [4] Department of Macromolecular Science and Engineering, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
⁶ 1] Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003, USA [2] Department of Theoretical Physics, J. Stefan Institute, SI-1000 Ljubljana, Slovenia [3] Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia.

Abstract

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Binding Sites
Computer Simulation
Electric Impedance
Integrins / chemistry*
Integrins / ultrastructure*
Models, Chemical*
Molecular Docking Simulation / methods*
Oligopeptides / chemistry*
Protein Binding
Protein Conformation
Quantum Theory*
Static Electricity
Stress, Mechanical
Surface Properties

Substances

Integrins
Oligopeptides
arginyl-glycyl-aspartic acid

Grants and funding

T32 EB007509/EB/NIBIB NIH HHS/United States