Topic
Accessible surface area
About: Accessible surface area is a research topic. Over the lifetime, 616 publications have been published within this topic receiving 41622 citations.
Papers published on a yearly basis
Papers
TL;DR: The accessibility of atoms in the twenty common amino acids in model tripeptides of the type Ala-X-Ala are given for defined conformation and the larger non-polar amino acids tend to be more “buried” in the native form of all three proteins.
6,086 citations
TL;DR: In this paper, a computer algorithm is presented for calculating the part of the van der Waals surface of a molecule that is accessible to solvent, where the solvent molecule is modeled by a sphere and a sphere is, in effect, rolled over the molecule to generate a smooth outer surface contour.
Abstract: A computer algorithm is presented for calculating the part of the van der Waals surface of molecule that is accessible to solvent. The solvent molecule is modeled by a sphere. This sphere is, in effect, rolled over the molecule to generate a smooth outer-surface contour. This surface contour is made up of pieces of spheres and tori that join at circular arcs. The spheres, tori and arcs are defined by analytical expressions in terms of the atomic coordinates, van der Waals radii and the probe radius. The area of each surface piece may be calculated analytically and the surface may be displayed on either vector or raster computer-graphics systems. These methods are useful for studying the structure and interactions of proteins and nucleic acids.
2,607 citations
TL;DR: Denaturant m values, the dependence of the free energy of unfolding on denaturant concentration, have been collected for a large set of proteins and correlate very strongly with the amount of protein surface exposed to solvent upon unfolding.
Abstract: Denaturant m values, the dependence of the free energy of unfolding on denaturant concentration, have been collected for a large set of proteins. The m value correlates very strongly with the amount of protein surface exposed to solvent upon unfolding, with linear correlation coefficients of R = 0.84 for urea and R = 0.87 for guanidine hydrochloride. These correlations improve to R = 0.90 when the effect of disulfide bonds on the accessible area of the unfolded protein is included. A similar dependence on accessible surface area has been found previously for the heat capacity change (delta Cp), which is confirmed here for our set of proteins. Denaturant m values and heat capacity changes also correlate well with each other. For proteins that undergo a simple two-state unfolding mechanism, the amount of surface exposed to solvent upon unfolding is a main structural determinant for both m values and delta Cp.
1,790 citations
TL;DR: The accessible surface areas have been calculated for the individual residues in 12 proteins, and for the extended chains, the secondary structures and tertiary structure of six proteins and it is shown that the accessible surface area of folded proteins is simply proportional to the two-thirds power of their molecular weight.
1,235 citations
TL;DR: In this article, a new method for exact analytical calculation of the accessible surface areas and their gradients with respect to atomic coordinates is described, which finds solvent-exposed vertices of intersecting atoms, and thereby avoids calculating buried vertices which are not needed to determine the surface area by the Gauss)Bonnet theorem.
Abstract: A new method for exact analytical calculation of the accessible surface areas and their gradients with respect to atomic coordinates is described. The new surface routine, GETAREA, finds solvent-exposed vertices of intersecting atoms, and thereby avoids calculating buried vertices which are not needed to determine the accessible surface area by the Gauss)Bonnet theorem. The surface routine was implemented in FANTOM, a program for energy minimization and Monte Carlo simulation, and tested for accuracy and efficiency in extensive energy minimizations of Met-enkephalin, the a-amylase inhibitor . tendamistat, and avian pancreatic polypeptide APP . The CPU time for the exact calculation of the accessible surface areas and their gradients has been . . reduced by factors of 2.2 Met-enkephalin and 3.2 tendamistat compared with our previous approach. The efficiency of our exact method is similar to the recently described approximate methods MSEED and SASAD. The performance of several atomic solvation parameter sets was tested in searches for low energy conformations of APP among conformations near the native X-ray crystal structure and highly distorted structures. The protein solvation parameters from w . x
1,127 citations
Related Topics (5)
Performance Metrics
| Year | Papers |
|---|---|
| 2025 | 2 |
| 2024 | 5 |
| 2023 | 5 |
| 2022 | 16 |
| 2021 | 19 |
| 2020 | 20 |