title: Electronic structure, dielectric response, and surface charge distribution of RGD (1FUV) peptide.
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.
authors.affiliation: Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO, 64110, USA.
authors.forename: Puja
authors.initials: P
authors.lastname: Adhikari
authors.affiliation: Department of Biomedical Engineering, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
authors.forename: Amy M
authors.initials: AM
authors.lastname: Wen
authors.affiliation: 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.
authors.forename: Roger H
authors.initials: RH
authors.lastname: French
authors.affiliation: Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003, USA.
authors.forename: V Adrian
authors.initials: VA
authors.lastname: Parsegian
authors.affiliation: 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.
authors.forename: Nicole F
authors.initials: NF
authors.lastname: Steinmetz
authors.affiliation: 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.
authors.forename: Rudolf
authors.initials: R
authors.lastname: Podgornik
authors.affiliation: Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO, 64110, USA.
authors.forename: Wai-Yim
authors.initials: WY
authors.lastname: Ching
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D017097:Electric Impedance; D016023:Integrins / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D062105:Molecular Docking Simulation / Q000379:methods*; D009842:Oligopeptides / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D011789:Quantum Theory; D055672:Static Electricity; D013314:Stress, Mechanical; D013499:Surface Properties
chemical_list: D016023:Integrins; D009842:Oligopeptides; C047981:arginyl-glycyl-aspartic acid