Influence Of Local Interactions Research Articles

Toward Closing the Gap: Quantum Mechanical Calculations and Experimentally Measured Chemical Shifts of a Microcrystalline Lectin.

NMR chemical shifts are exquisitely sensitive probes for conformation and dynamics in molecules and supramolecular assemblies. Although isotropic chemical shifts are easily measured with high accuracy and precision in conventional NMR experiments, they remain challenging to calculate quantum mechanically, particularly in inherently dynamic biological systems. Using a model benchmark protein, the 133-residue agglutinin from Oscillatoria agardhii (OAA), which has been extensively characterized by us previously, we have explored the integration of X-ray crystallography, solution NMR, MAS NMR, and quantum mechanics/molecular mechanics (QM/MM) calculations for analysis of 13Cα and 15NH isotropic chemical shifts. The influence of local interactions, quaternary contacts, and dynamics on the accuracy of calculated chemical shifts is analyzed. Our approach is broadly applicable and expected to be beneficial in chemical shift analysis and chemical-shift-based structure refinement for proteins and protein assemblies.

Local Interactions in Pitcher Plant Communities Scale-Up to Regional Patterns in Distribution and Abundance

We used the aquatic communities living in the purple pitcher plant (Sarracenia purpurea L., Sarraceniaceae) to determine if patterns produced by trophic interactions at the local scale can be detected at larger spatial scales. Mosquitoes (Wyeomyia smithii Coq., Diptera: Culicidae) are known to have a negative effect on the aquatic microfauna within leaves. We compared the abundance of two microfaunal taxa, Bodo (Kinetoplastea: Bodonidae) and Habrotrocha rosa Donner (Rotifera: Bdelloidea), in bogs with and without pitcher plant mosquitoes. Bogs containing pitcher plant mosquitoes had lower densities of bacteria through the study period. However, within these bogs, leaves with mosquitoes did not have lower bacterial densities. We found that the pattern for Bodo was similar at the leaf and bog spatial scales. Abundance of Bodo was closely linked to bacterial densities and the presence of mosquitoes strengthened that relationship, because of greater predator impacts when bacteria were scarce. In contrast, different patterns emerged at the two scales for H. rosa. At the leaf scale, a predator effect was seen only for low bacterial densities (as for Bodo), but at the bog scale, H. rosa was less abundant in mosquito bogs, and abundance was not associated with bacterial levels. We suggest that differences in life history characteristics (population growth rate and average abundance) may influence the relative influence of local interactions and regional processes such as colonization.

Confined phonons in glasses. A study by nuclear inelastic absorption and Raman scattering.

We have applied nuclear inelastic absorption (NIA) to the molecular glass former dibutyl phthalate/ferrocene, both in bulk and in nanoporous matrices having pore sizes of 50 and 25 A. The quantity g(E)/E(2), where g(E) is the vibrational density of states (VDOS) of the iron atoms, exhibits a pronounced maximum around 2 meV. Confinement in pores leads to a suppression of the VDOS below 1.5 meV, independent of the pore size. The influence of local interactions at the pore wall was assessed using Raman scattering. Our observations are discussed in the light of experimental and theoretical results on nanoparticles and for the Boson peak.

Prediction of protein backbone conformation based on seven structure assignments: Influence of local interactions

A method is developed to compute backbone tertiary folds from the amino acid sequence. In this method, the number of degrees of freedom is drastically reduced by neglecting side-chain flexibility, and by describing backbone conformations as combinations of only seven structural states. These are characterized by single values of the dihedral angles φ, ψ and ω, representing allowed conformations of the isolated dipeptide. We show that this restrictive model is none the less capable of describing native backbones to within acceptable deviations. Using our backbone description, potentials of mean force are derived from a database of known protein structures, based on statistical influences of single residues and residue pairs on the conformational states in their vicinity along the chain. This yields the force-field component due to local interactions, which is then used to predict lowest-energy conformations from any given amino acid sequence. The prediction algorithm does not require searching conformational space andis therefore extremely fast. Another important asset of our method is that it is able to compute not only the minimum energy conformation, but any number of lowest energy structures, whose relative preferences can be determined from the corresponding computed energy values. The performance of our procedure is tested on short peptides that are likely to be stabilized by local interactions. These include several helical structures and a hexapeptide with a β-bend conformation, corresponding to peptides shown to have relatively well-defined conformations in aqueous solution, and to protein segments believed to adopt their native conformation early during folding. In addition, several flexible peptides are analysed. Except for the problems encountered in predicting observed disulphide bridges in two of the flexible peptides, and in a somewhat larger fragment comprising residues 30 to 51 of bovine trypsin inhibitor, prediction results compare very favourably with experimental data. Potential applications of our procedure to protein modelling and its extension to protein folding are discussed.

Photophysical Properties of Hematoporphyrin and Dihematoporphyrin Ether (Ester)in Homogeneous and Microheterogeneous Environments

Abstract Excitation wavelength effects on hematoporphyrin (HP) and hematoporphyrin derivative (HPD, Photofrin II) fluorescence spectra, quantum yields and decays were comparatively studied in homo­ geneous (at different pH and substrate concentrations) and microheterogeneous (Triton X 100 micelles and Bovine serum albumin) aqueous environments, in which the porphyrins are expected to be present in different monomer/aggregate equilibria. The observed wavelength dependences of the fluorescence yield and of short lived contributions to the total fluorescence do not correlate to the porphyrin aggregation state obtained from absorption spectra. In micro-heterogeneous environ­ ment the influence of local interactions between the porphyrin and hydrophobic sites of the cosolutes on HP and HPD photophysics is demonstrated.

Structural information from OH-stretching vibrations—XIV. The influence of local interactions on the OH-stretching frequency in alcohols with an α-triple bond

The effect on the OH-stretching vibration of changes in the π-character of alcohols with an α-triple bond has been studied by means of the i.r. absorption band. It is demonstrated that in the investigated alcohols the OH … π interaction causes an increase of the OH-frequency as a result of the position of the OH-group with respect to that of the triple bond. Changes in the charge on the triple bond are reflected in the frequency: the larger the negative charge the higher the OH-frequency. Compared to saturated tertiary alcohols the accessibility of the hydroxyl for solvent molecules and hence the OH … solvent interaction is increased due to the absence of two (shielding) β-H-atoms. It turns out that the raising of the frequency caused by the triple bond is overruled by the lowering effect of the solvent.

Influence of local interactions on protein structure. II. Conformational energy studies of N‐acetyl‐N′‐methylamides of Ala‐X and X‐Ala dipeptides

AbstractConformational energy calculations using an empirical conformational energy program for peptides (ECEPP) were carried out on 17 N‐acetyl‐N′‐methylamides of Ala‐X and X‐Ala dipeptides, Where X = Ala, Asn, Asp, Gly, Phe, Ser, Tyr, Val, and Pro. Each dipeptide was found to have many low‐energly minima, some of which corresponded to bend structures. The stability of bends was found to depend on the amino acid composition and sequence, with the Ala‐X dipeptide generally favoring bends more than the X‐Ala dipeptide for a particular X. In bends and nonbends alike, intraresidue interactions dominate over interresidue interactions in determining conformational propeties. The calcutions were shown to be in good agreement with available experimental data.

Influence of local interactions on protein structure. III. Conformational energy studies of N‐acety‐N′‐methylamides of Gly‐X and X‐Gly dipeptides

AbstractConformational energy calculations using an empirical conformational energy program for peptides (ECEPP) were carried out on 20 N‐acetyl‐ N′‐methylamides of Gly‐X and X‐Gly depeptides, where X = Ala, Asn, Asp, Gly, Phe, Ser, Thr, Tyr, Val, and Pro, and also of Leu‐Gly. Each depeptde was found to have 25 or more low‐energy minima, except Gly‐Thr, which had only 11 low‐energy minima because of the stable side chian‐backbone hydrogen present in all low‐energy conformation. As a group, the stble chain‐backbone hydrogen bonds present in all low‐energy conformations. As a group, the Gly‐containing dipeptides were calculated in all low‐energy prpensity for formation of bends than the Ala‐containing depeptides. The X‐ Gly dipeptides were calculated to favor bends more than the Gly‐X dipeptides, primarlly because of the high stability of the type II bend in X‐Gly dipeptides. These results are in agreement with obseved occurrences of bends in the x‐ray structures of globular proteins. The calculated conformation properties were found to be in good agreement with experimental results.

Influence of local interactions on protein structure. I. Conformational energy studies of N‐acetyl‐N′‐methylamides of pro‐X and X‐pro dipeptides

Influence of local interactions on protein structure. I. Conformational energy studies of <i>N</i>‐acetyl‐<i>N</i>′‐methylamides of pro‐X and X‐pro dipeptides

Influence of local interactions on protein structure. I. Conformational energy studies of N-acetyl-N'-methylamides of Pro-X and X-Pro dipeptides.

AbstractConformational energy calculations using an Empirical Conformational Energy Program for Peptides (ECEPP) were carried out on the N‐acetyl‐N′‐methylamides of Pro‐X, where X = Ala, Asn, Asp, Gly, Leu, Phe, Ser, and Val, and of X‐Pro, where X = Ala, Asn, Gly, and Pro. The conformational energy was minimized from starting conformations which included all combinations of low‐energy single‐residue minima and several standard bend structures. It was found that almost all resulting minima are combinations of low‐energy single‐residue minima, suggesting that intra residue interactions predominate in determining conformation. The calculations also indicate, however, that inter residue interactions can be important. In addition, librational entropy was found to influence the relative stabilities of some minima. Because of the existence of 10–100 low‐energy minima for each dipeptide, the normalized statistical weight of an individual minimum rarely exceeds 0.3, suggesting that these dipeptides have considerable conformational flexibility and exist as statistical ensembles of low‐energy structures. The propensity of each dipeptide to form bend conformations was calculated, and the results were compared with available experimental data. It was found that bends are favored in Pro‐X dipeptides because ϕPro is fixed by the pyrrolidine ring in a conformation which is frequently found in bends, but that bends are not favored in X‐Pro dipeptides because interactions between the X residue and the pyrrolidine ring restrict the X residue to conformations which are not usually found in bends.