Conformations of 2-phenyl-3-pyridylpropenoic acid (alpha-phenyl pyridylcinnamic acid) dimers – A computational study

Motivation. Cinnamic acid analogs are not only important parts of the shikimic acid metabolic pathway of higher plants but it is possible to assemble, particularly from those containing oxygen or nitrogen heteroatoms, various patterned structures kept together with CH...O or CH...N hydrogen bonds. The fundamental unit of these structures is the acid dimer, e.g., the dimer of E and Z–2–phenyl–3–pyridylpropenoic acids of this study, which may exist in many conformations. As a preparation for a detailed conformational analysis of the patterned structures, it was decided to study the conformational behavior of these acid dimers, containing the N heteroatom in all possible positions of the aromatic ring. The conformational behavior of any cinnamic acid analogs in the dimeric form has not been studied before. Method. The conformational search module of the HyperChem package was used for the conformational analysis of the acid dimers with the PM3 semiempirical method. Calculations were performed for isolated dimers, i.e., without solvent. Results. The conformational search identified many conformers of the acid dimers. Although their numbers amounted to hundreds, they were found to fill the conformational space unevenly, in a highly symmetric nature. The distribution patterns were typical for the stereoisomers, but resembled to each other irrespective to the position of the nitrogen atom. Conclusions. It was proved to be possible to study the conformational behavior of cinnamic acid analogs in their dimeric forms for the first time. Large number of conformers was identified and they were found the fill the conformational space in a patterned way

Side-chain conformational changes upon protein-protein association

Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational changes in the side chains. The results indicate that short and long side chains have different propensities for the conformational changes. Long side chains with three or more dihedral angles are often subject to large conformational transition. Shorter residues with one or two dihedral angles typically undergo local conformational changes not leading to a conformational transition. The relationship between the local readjustments and the equilibrium fluctuations of a side chain around its unbound conformation is suggested. Most of the side chains undergo larger changes in the dihedral angle most distant from the backbone. The amino acids with symmetric aromatic (Phe and Tyr) and charged (Asp and Glu) groups show the opposite trend where the near-backbone dihedral angles change the most. The frequencies of the core-to-surface interface transitions of six nonpolar residues and Tyr exceed the frequencies of the opposite, surface-to-core transitions. The binding increases both polar and nonpolar interface areas. However, the increase of the nonpolar area is larger for all considered classes of protein complexes. The results suggest that the protein association perturbs the unbound interfaces to increase the hydrophobic forces. The results facilitate better understanding of the conformational changes in proteins and suggest directions for efficient conformational sampling in docking protocols.Comment: 21 pages, 6 figure

Dogs Never Gets Prion Diseases. The Entropic Landscape Analysis of Prion Proteins Answers Why.

The Entropic Landscape Analysis was applied to the prion protein sequences of various mammals in order to detect potential sites of variants that would be responsible for the susceptibility of prion disease infection. Among familiar mammals, canines including dogs have been demonstrating strong resistance to prion diseases. Among the canine specifc substitutions the entropic landscape analysis pinpoints the substitutions Asn104Gly and Ser107Asn having the biggest impact to the conformational transition and stability. Although they must be further corroborated by experiments in vivo et vitro, the results are demonstrating that the entropic landscape analysis is useful enough to screen substitutions and polymorphisms potentially relevant to conformational stability and transition because the calculation time for the analysis is as long as a few seconds, and the analysis can be done without knowing the 3D structures

Conformational analysis of olefin-carbene ruthenium metathesis catalysts

We settle a long-standing disagreement of DFT with experiment (both solution and gas phase) for the phosphine dissociation process in Grubbs metathesis catalysis. Our findings with the M06 functional provide further support to gas-phase experimental work, concluding that for the ring-closing metathesis of norbornene, the resting state is the alkylidene−olefin complex and the rate-determining step is the loss of norbornene as a ligand and generation of the 14-electron activated species. Comparing to recent solution NMR data on olefin−carbene Ru complexes relevant to olefin metathesis, we find that the M06 density functional leads to accurate predictions for the stability of conformers, ~0.5 kcal/mol better than is found by B3LYP. Using this methodology, we suggest that Piers and co-workers observed the cis-dichloro “down” isomer exclusively following the ring opening of acenaphthalene

A user-friendly Matlab program and GUI for the pseudorotation analysis of saturated five-membered ring systems based on scalar coupling constants

Background: The advent of combinatorial chemistry has revived the interest in five-membered heterocyclic rings as scaffolds in pharmaceutical research. They are also the target of modifications in nucleic acid chemistry. Hence, the characterization of their conformational features is of considerable interest. This can be accomplished from the analysis of the (3)J(HH) scalar coupling constants. Results: A freely available program including an easy-to-use graphical user interface (GUI) has been developed for the calculation of five-membered ring conformations from scalar coupling constant data. A variety of operational modes and parameterizations can be selected by the user, and the coupling constants and electronegativity parameters can be defined interactively. Furthermore, the possibility of generating high-quality graphical output of the conformational space accessible to the molecule under study facilitates the interpretation of the results. These features are illustrated via the conformational analysis of two 4'-thio-2'-deoxynucleoside analogs. Results are discussed and compared with those obtained using the original PSEUROT program. Conclusion: A user-friendly Matlab interface has been developed and tested. This should considerably improve the accessibility of this kind of calculations to the chemical community

Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis

Aim: Molecular dynamics simulations and normal mode analysis are well-established approaches to generate receptor conformational ensembles (RCEs) for ligand docking and virtual screening. Here, we report new fast molecular dynamics-based and normal mode analysis-based protocols combined with conformational pocket classifications to efficiently generate RCEs. Materials \& methods: We assessed our protocols on two well-characterized protein targets showing local active site flexibility, dihydrofolate reductase and large collective movements, CDK2. The performance of the RCEs was validated by distinguishing known ligands of dihydrofolate reductase and CDK2 among a dataset of diverse chemical decoys. Results \& discussion: Our results show that different simulation protocols can be efficient for generation of RCEs depending on different kind of protein flexibility