Conformational effects of one glycine residue on the other glycine residues in the Ac-Gly-Gly-Gly-NHMe tripeptide motif: an ab initio exploratory study

Ab initio molecular computations were carried out on the tripeptide model, Ac-Gly-Gly-Gly-NHMe at the RHF/3-21G ab initio level of theory. Two of the glycine residues were chosen at a time to be in the fully extended, or beta (C-5) conformation, in order to monitor the effects on the third residue with varying the backbone conformation. The topologies of each of the three Ramachandran type conformational potential energy surfaces were analyzed and five minima (beta, gamma(L), gamma(D), delta(L), delta(D).) associated with each one of the three glycine residues, were located for each surface. (C) 2002 Elsevier Science B.V. All rights reserved

N-acetyl-l-aspartic acid-N'-methylamide with side-chain orientation capable of external hydrogen bonding

In this study, we generated and analyzed the side-chain conformational potential energy hyper-surfaces for each of the nine possible backbone conformers for N-acetyl-L-aspartic acid-N' methylamide. We found a total of 27 out of the 81 possible conformers optimized at the B3LYP/6-31G(d) level of theory. The relative energies, as well as the stabilization energies exerted by the side-chain on the backbone, have been calculated for each of the 27 optimized conformers at this level of theory. Various backbone-backbone (N-(HO)-O-...=C) and backbone-side-chain (N-(HO)-O-...=C; N-(HOH)-O-...) hydrogen bonds were analyzed. The appearance of the notoriously absent epsilon(L) backbone conformer may be attributed to such side-chain-backbone (SC/BB) and backbone-backbone (BB/BB) hydrogen bonds

Can NO2+ exist in bent or cyclic forms?

Calculations of NO2+ at HF, CBS-4, CASSCF, MBPT(2), MBPT(3), and MBPT(4) theory levels, using 3-21G and 6-31G(d) basis sets, found two C-2V structures along with the linear geometry. Computations using MBPT(2) and CCSD(T) approaches and the aug-cc-pvtz basis set confirmed these results. Harmonic vibrational frequency calculations, performed with MBPT(2) and CCSD(T) theories, indicated that the linear structure was the global minimum while one of the bent structures (angle ONO = 80 degrees) was a higher energy local minimum. The second C-2V structure (angle ONO = 45 degrees) exhibited a large imaginary vibrational frequency along the asymmetric stretching (B-2) mode, indicating its saddle point nature. (C) 2001 Elsevier Science B.V. All rights reserved

Characteristics of Ramachandran maps of L-alanine diamides as computed by various molecular mechanics, semiempirical and ab initio MO methods. A search for primary standard of peptide conformational stability

The optimized geometries and relative energies obtained by four force field and two semi-empirical methods were compared with ab initio results computed for formyl-L-alaninamide. Not all methods yielded the same number of minimum energy conformers. Furthermore, while the optimized geometries of the conformers found were comparable, the computed relative energies varied substantially. Also, the force field calculations produced Ramachandran maps that did not even have the appearance of the ab initio Ramachandran map. Correlating the ab initio relative energies (Delta E) or free energy (Delta G) with the log of relative populations, In(p(x)/p(gamma L)), led to linear relationships from which four conformers deviated; two of them (alpha(L) and epsilon(L)) were overly destabilized and two of them (gamma(L) and gamma(D)) were over-stabilized. It is suggested that, after such deviations are corrected, a primary standard may be obtained that might be useful in further investigations related to force-field parametrization as well as protein folding. (C) 1998 Elsevier Science B.V. All rights reserved

Magyar Tanítóképző 44 (1931) 4

Magyar Tanítóképző A Tanítóképző-intézeti Tanárok Országos Egyesületének folyóirata 44. évfolyam, 4. szám Budapest, 1931. máju

Prospects in computational molecular medicine: a millennial mega-project on peptide folding

During the second half of the 20th century, Molecular Computations have reached to a level that can revolutionize chemistry. The next target will be structural biology, which will be followed soon by Molecular Medicine. The present paper outlines where we are at, in this field, at the end of the 20th century, and in what direction the development may take in the new millennium. In view of the gigantic nature of the problem, it is suggested that a suitably designed cooperative Millennial Mega-project might accelerate our schedule. (C) 2000 Elsevier Science B.V. All rights reserved

Peptide Models - XXIV: An ab Initio Study on N-formyl-l-prolinamide With Trans Peptide Bond. The Existence or Non-existence of Alpha(l) And Epsilon(l) Conformations

N-formyl-L-prolinamide was subjected to geometry optimization at three levels of theory: HF/3-21G, HF/6-31G (d) and B3LYP/6-31G (d). At all three levels of computation the global minimum was gamma(L) (inverse gamma-Turn) backbone conformation with two ring-puckered forms "UP" and "DOWN". At HF/3-21G level of theory three backbone conformations were found gamma(L), epsilon(L), and alpha(L). At higher levels of theory the epsilon(L), and alpha(L) conformations disappeared. The ''UP'' and ''DOWN'' ring-puckered forms, in the gamma(L) backbone conformation, led to practically identical vibrational spectra at the B3LYP/6-31G (d) level of theory

Phenylalanine Ammonia-Lyase-Catalyzed Deamination of an Acyclic Amino Acid: Enzyme Mechanistic Studies Aided by a Novel Microreactor Filled with Magnetic Nanoparticles

Phenylalanine ammonia-lyase (PAL), found in many organisms, catalyzes the deamination of l-phenylalanine (Phe) to (E)-cinnamate by the aid of its MIO prosthetic group. By using PAL immobilized on magnetic nanoparticles and fixed in a microfluidic reactor with an in-line UV detector, we demonstrated that PAL can catalyze ammonia elimination from the acyclic propargylglycine (PG) to yield (E)-pent-2-ene-4-ynoate. This highlights new opportunities to extend MIO enzymes towards acyclic substrates. As PG is acyclic, its deamination cannot involve a Friedel–Crafts-type attack at an aromatic ring. The reversibility of the PAL reaction, demonstrated by the ammonia addition to (E)-pent-2-ene-4-ynoate yielding enantiopure l-PG, contradicts the proposed highly exothermic single-step mechanism. Computations with the QM/MM models of the N-MIO intermediates from l-PG and l-Phe in PAL show similar arrangements within the active site, thus supporting a mechanism via the N-MIO intermediate

Helix compactness and stability: Electron structure calculations of conformer dependent thermodynamic functions

Structure, stability, cooperativity and molecular packing of two major backbone forms: 310-helix and β-strand are investigated. Long models HCO-(Xxx)n-NH2 Xxx = Gly and (l-)Ala, n ⩽ 34, are studied at two levels of theory including the effect of dispersion forces. Structure and folding preferences are established, the length modulated cooperativity and side-chain determined fold compactness is quantified. By monitoring ΔG°β→α rather than the electronic energy, ΔEβ→α, it appears that Ala is a much better helix forming residue than Gly. The achiral Gly forms a more compact 310-helix than any chiral amino acid residue probed here for l-Ala