Search results for "Accessible surface area"

Polymorphism, Metastable Species and Interconversion

2014

Abstract The natively unfolded peptide hormone glucagon forms fibrillar structures with amyloid properties. Here, we summarize past advances in glucagon fibrillation and combine them with recent new unpublished data to provide some more general conclusions on how glucagon fibrillation adapts to different physicochemical conditions such as high temperature, pressure, mechanical and chemical stress. Factors such as peptide concentration, accessible surface area, surface hydration of the glucagon molecular state, contact surface, temperature and ionic strength all contribute to fibrillar structure and stability. In addition to fundamental changes in secondary structure, glucagon fibril morphol…

New dimension indices for the characterization of the solvent-accessible surface

2001

The solvent-excluding surface as a descriptor of ionic channels: Gramicidin-A

1998

Abstract We have set out a methodology for checking the performance of the methods used to compute the Solvent-Excluding Surface. The method consists of computing the area of the Solvent-Excluding Surface of a model of channel, with a fixed pore size, for several values of the solvent radius. The graphical representation of the value of the area versus the radius of the solvent sphere shows a sharp change just at the radius of the pore. With this model we may analyze the ability of each method to describe small changes of the surface. We made the study with GEPOL93, older versions of GEPOL and MSDOT. The study is applied to a natural protein channel, as is Gramicidin-A, showing that this ty…

GEPOL: An improved description of molecular surfaces. III. A new algorithm for the computation of a solvent-excluding surface

1994

To understand and calculate the interactions of a solute with a solvent, a good method of computing the molecular surface is needed. Three kinds of surfaces may be used: the van der Waals Surface, the Accessible Surface, and the Molecular Surface. The latter is redefined in this article as the Solvent-Excluding Surface. The new algorithm for computing the Solvent-Excluding Surface included in the GEPOL93 program is described. GEPOL93 follows the same concept as former versions of GEPOL but with a full new algorithm. Thus, it computes the Solvent-Excluding Surface by filling the spaces not accessible to the solvent with a set of new spheres. The computation is controlled by three parameters:…

Novel metal–organic frameworks based on 5-bromonicotinic acid: Multifunctional materials with H2 purification capabilities

2012

Two new metal–organic frameworks based on 5-bromonicotinic acid complexes [Cd(5-BrNic)2]n (1) and [Co(5-BrNic)2(H2O)]n (2) have been synthesized by hydrothermal reactions of this ligand with cadmium and cobalt metallic(II) salts in the presence of water. Compound 1 displays intense photoluminescence properties in the solid state at room temperature, while 2 exhibits an antiferromagnetic interaction between Co(II) ions with a J value of −4.1 cm−1. Experimental studies, backed up by Monte Carlo simulations about adsorption, pore size distribution and accessible surface area reveal the capability of 2 for H2 purification applications.

String kernels and high-quality data set for improved prediction of kinked helices in α-helical membrane proteins.

2011

The reasons for distortions from optimal α-helical geometry are widely unknown, but their influences on structural changes of proteins are significant. Hence, their prediction is a crucial problem in structural bioinformatics. For the particular case of kink prediction, we generated a data set of 132 membrane proteins containing 1014 manually labeled helices and examined the environment of kinks. Our sequence analysis confirms the great relevance of proline and reveals disproportionately high occurrences of glycine and serine at kink positions. The structural analysis shows significantly different solvent accessible surface area mean values for kinked and nonkinked helices. More important, …

Interacting induced dipoles polarization model for molecular polarizabilities: application to benzothiazole (A)-benzobisthiazole (B) oligomers AB13A

1998

Abstract We have outlined a method for the calculation of atomic net charges and molecular dipole-dipole,  α , dipole-quadrupole,  A , and quadrupole-quadrupole,  C , polarizabilities which we have successfully applied to benzothiazole (A)-benzobisthiazole (B) oligomers in the series AB1A to AB13A, and the results have been extrapolated to give predictions for polybenzobisthiazole. The calculation of  α ,  A and  C has been carried out by the interacting induced dipoles polarization model that calculates tensor effective anisotropic point polarizabilities (method of Applequist). The mean effective atomic αeffpolarizabilities for the monomeric unit are of the same order of magnitud…

2021

Amino acids with small side chains and motifs of small residues in a distance of four are rather abundant in human single-span transmembrane helices. While interaction of such helices appears to be common, the role of the small residues in mediating and/or stabilizing transmembrane helix oligomers remains mostly elusive. Yet, the mere existence of (small)xxx(small) motifs in transmembrane helices is frequently used to model dimeric TM helix structures. The single transmembrane helix of the human carbonic anhydrases XII contains a large number of amino acids with small side chains, and critical involvement of these small amino acids in dimerization of the transmembrane domain has been sugges…

Theoretical characterization of iron and manganese porphyrins for catalyzed saturated alkane hydroxylations

1997

Abstract The theoretical characterization of porphin (H2Por), iron and manganese porphyrins MIII(Por) and their chlorine derivatives MIII(Por)Cl has been carried out. This work represents a first step for modelling catalyzed saturated alkane hydroxylations. The chlorine atom is responsible for the existence of a dipole moment of 1.2–2.0 D in the MIII(Por)Cl molecules and for a negative value of the mean quadrupole moment (−16–(−14)DA). The charge of the metal atom (1.8–2.2 e) is rather varied (to 2.1–2.6 e) and the effective polarizability (2.8–2.9 A3) is increased (to 3.5–3.6 A3) by the addition of the chlorine atom. Starting from the porphin molecule, the presence of the metal atom decrea…