Search results for "conformation"
showing 10 items of 1414 documents
Intra-Helical Salt Bridge Contribution to Membrane Protein Insertion.
2021
ABSTRACTSalt bridges between negatively (D, E) and positively charged (K, R, H) amino acids play an important role in protein stabilization. This has a more prevalent effect in membrane proteins where polar amino acids are exposed to a very hydrophobic environment. In transmembrane (TM) helices the presence of charged residues can hinder the insertion of the helices into the membrane. This can sometimes be avoided by TM region rearrangements after insertion, but it is also possible that the formation of salt bridges could decrease the cost of membrane integration. However, the presence of intra-helical salt bridges in TM domains and their effect on insertion has not been properly studied ye…
Counterion-mediated attraction and kinks on loops of semiflexible polyelectrolyte bundles.
2006
The formation of kinks in a loop of bundled polyelectrolyte filaments is analyzed in terms of the thermal fluctuations of charge density due to polyvalent counterions adsorbed on the polyelectrolyte filaments. It is found that the counterion-mediated attraction energy of filaments depends on their bending. By consideration of curvature elasticity energy and counterion-mediated attraction between polyelectrolyte filaments, the characteristic width of the kink and the number of kinks per loop is found to be in reasonable agreement with existing experimental data for rings of bundled actin filaments.
Unexpectedly normal phase behavior of single homopolymer chains
2006
Employing Monte Carlo simulations, we show that the topology of the phase diagram of a single flexible homopolymer chain changes in dependence on the range of an attractive square well interaction between the monomers. For a range of attraction larger than a critical value, the equilibrium phase diagram of the single polymer chain and the corresponding polymer solution phase diagram exhibit vapor (swollen coil, dilute solution), liquid (collapsed globule, dense solution), and solid phases. Otherwise, the liquid-vapor transition vanishes from the equilibrium phase diagram for both the single chain and the polymer solution. This change in topology of the phase diagram resembles the behavior k…
Influence of chain stiffness on knottedness in single polymers.
2013
In the present article, we investigate and review the influence of chain stiffness on self-entanglements and knots in a single polymer chain with Monte Carlo simulations spanning good solvent, theta and globular phases. The last-named are of particular importance as a model system for DNA in viral capsids. Intriguingly, the dependence of knot occurrence and complexity with increasing stiffness is non-trivial, but can be understood with a few simple concepts outlined in the present article.
Biomolecular-solvent stereodynamic coupling probed by deuteration.
1983
Thermodynamic interpretation of experiments with isotopically perturbed solvent supports the view that solvent stereodynamics is directly relevant to thermodynamic stability of biomolecules. According with the current understanding of the structure of the aqueous solvent, in any stereodynamic configuration of the latter, connectivity pathways are identifiable for their topologic and order properties. Perturbing the solvent by isotopic substitution or, e.g., by addition of co-solvents, can therefore be viewed as reinforcing or otherwise perturbing these topologic structures. This microscopic model readily visualizes thermodynamic interpretation. In conclusion, the topologic stereodynamic str…
Conformational investigation of α, β-dehydropeptides
2009
The crystal structure of Ac-Pro-delta Val-NHCH3 was examined to determine the influence of the alpha,beta-dehydrovaline residue on the nature of peptide conformation. The peptide crystallizes from methanol-diethyl ether solution at 4 degrees in needle-shaped form in orthorhombic space group P2(1)2(1)2(1) with a = 11.384(2) A, b = 13.277(2) A, c = 9.942(1) A, V = 1502.7(4) A3, Z = 4, Dm = 1.17 g.cm-3 and Dc = 1.18 g.cm-3. The structure was solved by direct methods using SHELXS-86 and refined to an R value of 0.057 for 1922 observed reflections. The peptide is found to adopt a beta-bend between the type I and the type III conformation with phi 1 = -68.3(4) degrees, psi 1 = -20.1(4) degrees, p…
Coupling of the guanosine glycosidic bond conformation and the ribonucleotide cleavage reaction: implications for barnase catalysis.
2007
To examine the possible relationship of guanine-dependent GpA conformations with ribonucleotide cleavage, two potential of mean force (PMF) calculations were performed in aqueous solution. In the first calculation, the guanosine glycosidic (Gχ) angle was used as the reaction coordinate, and computations were performed on two GpA ionic species: protonated (neutral) or deprotonated (negatively charged) guanosine ribose O2 ′. Similar energetic profiles featuring two minima corresponding to the anti and syn Gχ regions were obtained for both ionic forms. For both forms the anti conformation was more stable than the syn, and barriers of ∼4 kcal/mol were obtained for the anti → syn transition. Str…
Internal rotation of 1,2-dichloroethane in haloalkane dehalogenase. A test case for analyzing electrostatic effects in enzymes
2003
1,2-Dichoroethane (DCE) is a prototypical molecule for studying electrostatic solvent effects on molecular conformation as far as rotation around the carbon−carbon bond notably changes the electric...
Asymmetrically substituted calix[4]arenes; A two-dimensional 1H NMR study of a tetraester derivative in the cone-conformation
1991
Abstract Several new chiral calix[4]arenes with three or four different substituents in the p-position have been prepared by fragment condensation. Standard derivatization procedures always led to the formation of mixtures of various conformational isomers from which the derivative in the cone-conformation could be isolated only by preparative HPLC. For a tetraester derivative it was shown by two-dimensional 1H NMR spectroscopy, that due to the different substituents the cone-conformation is strongly distorted. The sodium complex of this tetraester, however, assumes a regular cone-conformation again.
Restricted rotation in unbridged sandwich complexes: rotational behavior of closo-[Co(eta 5-NC4H4)(C2B9H11)] derivatives.
2005
Rotation about the centroid/ metal/centroid axis in ferrocene is facile; the activation energy is 1-5 kcal mol - 1 . The structurally similar sandwich complexes derived from closo-[3-Co(η 5 -NC 4 H 4 )-1,2-C 2 B 9 H 1 1 ] (1) have a different rotational habit. In 1, the cis rotamer in which the pyrrolyl nitrogen atom bisects the carboranyl cluster atoms is 3.5 kcal mol - 1 more stable in energy than the rotamer that is second lowest in energy. This cis rotamer is wide, spanning 216°, and may be split into three rotamers of almost equal energy by substituting the N and the carboranyl carbon atoms adequately. To support this statement, closo-[3-Co(η 5 -NC 4 H 4 )-1,2-(CH 3 ) 2 -1,2-C 2 B 9 H …