The minimal molecular surface

TL;DR

The paper introduces the minimal molecular surface (MMS), a new model for biomolecule-solvent interfaces that minimizes surface free energy and can indicate DNA-binding specificity.

Contribution

It presents a novel concept of MMS, an iterative algorithm for its computation, and demonstrates its application in biomolecular modeling and DNA-binding analysis.

Findings

MMS effectively models biomolecule-solvent interfaces.

The algorithm accurately computes MMS in various examples.

MMS indicates DNA-binding specificity.

Abstract

We introduce a novel concept, the minimal molecular surface (MMS), as a new paradigm for the theoretical modeling of biomolecule-solvent interfaces. When a less polar macromolecule is immersed in a polar environment, the surface free energy minimization occurs naturally to stabilizes the system, and leads to an MMS separating the macromolecule from the solvent. For a given set of atomic constraints (as obstacles), the MMS is defined as one whose mean curvature vanishes away from the obstacles. An iterative procedure is proposed to compute the MMS. Extensive examples are given to validate the proposed algorithm and illustrate the new concept. We show that the MMS provides an indication to DNA-binding specificity. The proposed algorithm represents a major step forward in minimal surface generation.