Study of atomic force microscopy force-distance curves by simulation using the Connolly surface for proteins

A simulation of the interaction between atomic force microscope tips and protein surfaces employing the concept of the Connolly molecular surface with a carbon probe has been investigated. A methodology has been developed to allow the computation of the Connolly surface for a protein, where numerous atoms are simultaneously interacting with each other. The van der Waals and electrostatic interactions between the probe and the relevant Connolly surface elements are integrated to obtain the total interaction, resulting in precise theoretical accounts for a variety of interaction components.

[1]  Douglas C. Neckers,et al.  AFM Force−Distance Curve Methods for Measuring the Kinetics of Silicon Chemical Etching and Reactions between Silylating Agents and a Silicon Surface , 1999 .

[2]  A. Olson,et al.  Approximation and characterization of molecular surfaces , 1993, Biopolymers.

[3]  C. Daniel Frisbie,et al.  Direct Force Measurements at Polymer Brush Surfaces by Atomic Force Microscopy , 1998 .

[4]  S. Vansteenkiste,et al.  Direct measurement of protein adhesion at biomaterial surfaces by scanning force microscopy. , 2000 .

[5]  T. Matsuda,et al.  Adhesion Forces of the Blood Plasma Proteins on Self-Assembled Monolayer Surfaces of Alkanethiolates with Different Functional Groups Measured by an Atomic Force Microscope , 1999 .

[6]  Jan Greve,et al.  Reconstruction of the TIP-Surface Interaction Potential by Analysis of the Brownian Motion of an Atomic Force Microscope Tip , 2000 .

[7]  L. Krippahl,et al.  BiGGER: A new (soft) docking algorithm for predicting protein interactions , 2000, Proteins.

[8]  Jill E. Gready,et al.  Numerical calculation of molecular surface area. I. Assessment of errors , 1996 .

[9]  Raj Rajagopalan,et al.  Interaction between a Grafted Polymer Chain and an AFM Tip: Scaling Laws, Forces, and Evidence of Conformational Transition , 1998 .

[10]  Jill E. Gready,et al.  Numerical calculation of molecular surface area. II. Speed of calculation , 1996 .

[11]  L. T. Ten Eyck,et al.  Protein docking using continuum electrostatics and geometric fit. , 2001, Protein engineering.

[12]  Ying-Jie Zhu,et al.  Loading-rate dependence of individual ligand-receptor bond-rupture forces studied by atomic force microscopy , 2001 .

[13]  Ruth Nussinov,et al.  A Method for Biomolecular Structural Recognition and Docking Allowing Conformational Flexibility , 1998, J. Comput. Biol..

[14]  M. L. Connolly.  Solvent-accessible surfaces of proteins and nucleic acids. , 1983, Science.

[15]  M. L. Connolly.  Analytical molecular surface calculation , 1983 .

[16]  F. Ferrè,et al.  Protein surface similarities: a survey of methods to describe and compare protein surfaces , 2000, Cellular and Molecular Life Sciences CMLS.

[17]  M. L. Connolly.  Measurement of protein surface shape by solid angles , 1986 .

[18]  B. D. de Grooth,et al.  A physical approach to reduce nonspecific adhesion in molecular recognition atomic force microscopy. , 1999, Biophysical journal.

[19]  Jill E. Gready,et al.  Simple method for locating possible ligand binding sites on protein surfaces , 1999 .

[20]  S. L. Mayo,et al.  DREIDING: A generic force field for molecular simulations , 1990 .

[21]  D Fischer,et al.  Molecular surface representations by sparse critical points , 1994, Proteins.

[22]  H. Wolfson,et al.  Examination of shape complementarity in docking of Unbound proteins , 1999, Proteins.