Dihedral angle
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Recent advances in polarizable force fields have revealed that major reparameterization is necessary when the polarization energy is treated explicitly. This study is focused on the torsional parameters, which are crucial for the accurate description of conformational equilibria in biomolecules. In particular, attention is paid to the influence of polarization on the (i) transferability of dihedral terms between molecules, (ii) transferability between different environments, and (iii) additivity of dihedral energies. To this end, three polarizable force fields based on the induced point dipole model designed for use in AMBER are tested, including two recent ff02 reparameterizations. Attention is paid to the contributions due to short range interactions (1-2, 1-3, and 1-4) within the four atoms defining the dihedral angle. The results show that when short range 1-2 and 1-3 polarization interactions are omitted, as for instance in ff02, the 1-4 polarization contribution is rather small and unlikely to improve the description of the torsional energy. Conversely, when screened 1-2 and 1-3 interactions are included, the polarization contribution is sizeable and shows potential to improve the transferability of parameters between different molecules and environments as well as the additivity of dihedral terms. However, to reproduce intramolecular polarization effects accurately, further fine-tuning of the short range damping of polarization is necessary.
The molecule of 2,2-dinitroethene-1,1-diamine (FOX-7) is one of the most interesting molecules with multiple redox centres stabilized by push-pull effect. To reveal the detailed mechanism of its electrochemical process radical intermediates formed in the course of its electrochemical reduction in organic aprotic media have been studied by in situ simultaneous electrochemical ESR measurements (SEESR). The radical generated on the second reduction step possesses an alternating line-width (AL) effect in the ESR spectra as a result of intramolecular dynamic processes in the timescale of ESR splitting constants. The spectra measured at different temperatures (230-335 K) were analysed with the help of a fitting program which includes a molecular dynamics. Observed dynamics describes well an asymmetric 2-site exchange model for the whole temperature range. With help of the optimized parameters and quantum chemical calculations this radical has been identified as 2,2-dinitroethane-1-amine-1-imine radical dianion, [(H2N)(HN)C=C(NO2)2]2-. The dynamic process responsible for the AL effect consists of mutual turning (changing of dihedral angle) of the both nitro groups, resulting in an intramolecular spin-density (electron) transfer. The dynamic parameters of the process have been established.
- Publikační typ
- časopisecké články MeSH
The infrared (IR), vibrational circular dichroism (VCD), and electronic circular dichroism (ECD) spectra of short cationic sequential peptides (L-Lys-L-Ala-L-Ala)(n) (n = 1, 2, and 3) were measured over a range of temperatures (20-90 degrees C) in aqueous solution at near-neutral pH values in order to investigate their solution conformations and thermally induced conformational changes. VCD spectra of all three oligopeptides measured in the amide I' region indicate the presence of extended helical polyproline II (PPII)-like conformation at room temperature. UV-ECD spectra confirmed this conclusion. Thus, the oligopeptides adopt a PPII-like conformation, independent of the length of the peptide chain. However, the optimized dihedral angles phi and psi are within the range -82 to -107 degrees and 143-154 degrees , respectively, and differ from the canonical PPII values. At elevated temperatures, the observed intensity and bandshape variations in the VCD and ECD spectra show that the PPII-like conformation of the Lys-Ala-Ala sequence is still preferred, being in equilibrium with an unordered conformer at near-neutral pH values within the range of temperatures from 20 to 90 degrees C. This finding was obtained from analysis of the temperature-dependent spectra using the singular value decomposition method. The study presents KAA-containing oligopeptides as conformationally stable models of biologically important cationic peptides and proteins.
The N-terminus of the B-chain of insulin may adopt two alternative conformations designated as the T- and R-states. Despite the recent structural insight into insulin-insulin receptor (IR) complexes, the physiological relevance of the T/R transition is still unclear. Hence, this study focused on the rational design, synthesis, and characterization of human insulin analogues structurally locked in expected R- or T-states. Sites B3, B5, and B8, capable of affecting the conformation of the N-terminus of the B-chain, were subjects of rational substitutions with amino acids with specific allowed and disallowed dihedral φ and ψ main-chain angles. α-Aminoisobutyric acid was systematically incorporated into positions B3, B5, and B8 for stabilization of the R-state, and N-methylalanine and d-proline amino acids were introduced at position B8 for stabilization of the T-state. IR affinities of the analogues were compared and correlated with their T/R transition ability and analyzed against their crystal and nuclear magnetic resonance structures. Our data revealed that (i) the T-like state is indeed important for the folding efficiency of (pro)insulin, (ii) the R-state is most probably incompatible with an active form of insulin, (iii) the R-state cannot be induced or stabilized by a single substitution at a specific site, and (iv) the B1-B8 segment is capable of folding into a variety of low-affinity T-like states. Therefore, we conclude that the active conformation of the N-terminus of the B-chain must be different from the "classical" T-state and that a substantial flexibility of the B1-B8 segment, where GlyB8 plays a key role, is a crucial prerequisite for an efficient insulin-IR interaction.
- MeSH
- cirkulární dichroismus MeSH
- inzulin analogy a deriváty chemie MeSH
- krystalografie rentgenová MeSH
- kyseliny aminoisomáselné chemie MeSH
- lidé MeSH
- molekulární modely MeSH
- molekulární struktura MeSH
- nukleární magnetická rezonance biomolekulární MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
... and orthogonality properties 245 -- 6.4 SOME FINITE GROUPS 247 -- 6.4.1 Cyclic groups 247 -- 6.4.2 Dihedral ... ... FORWARD PROBLEMS 1154 -- 17.1.1 CD formulations for parallel-beam SPECT 1155 -- 17.1.2 Equally spaced angles ...
Wiley series in pure and applied optics
[1st ed.] xli, 1540 s. : il.
