1,722,012 research outputs found
Folding of an Ala-Ala-Ala Tripeptide into a β-Turn via Hydrophobic Encapsulation
No full textAn Ac-Ala-Ala-Ala-NH2 tripeptide was folded into a β-turn structure even in water through hydrophobic binding by a self-assembled porphyrin cage. The turn conformation of the bound peptide was fully assigned from NOESY measurements and was strongly supported by molecular dynamics simulation. Single mutation experiments and molecular modeling also suggested that CH−π interactions between methyl groups of Ala residues and porphyrin ligands were important for the stabilization of the turn conformation. Furthermore, we observed the induction of a β-hairpin structure by encapsulation of a heptapeptide, Ac-Gly-Gly-Ala-Ala-Ala-Gly-Gly-NH2, possessing Ala-Ala-Ala sequence at the middle
Relative energies of the three helical structures of Ac-Ala-Ala-Ala-NHMe by MP2/6–311(1d,1p) quantum calculations <i>in vacuo</i>.
No full text<p>Relative energies of the three helical structures of Ac-Ala-Ala-Ala-NHMe by MP2/6–311(1d,1p) quantum calculations <i>in vacuo</i>.</p
Location of the two energy mimima-like positions on the potential energy surfaces of Ac-Ala-Ala-Ala-NHMe based on methodology.
No full text<p>Location of the two energy mimima-like positions on the potential energy surfaces of Ac-Ala-Ala-Ala-NHMe based on methodology.</p
Complexation of poly(Lys-Ala) and poly(Lys-Ala-Ala-Ala) with pectins and potassium oligogalacturonates
No full textThe selected model polypeptides poly(Lys-Ala) and poly(Lys-Ala-Ala-Ala) underwent a helix-forming interaction with potassium pectates and pectinates of various esterification degree (E) and with some potassium oligogalacturonates (n = 2-5, 9, 13). Formation of the complex quantitatively monitored by a circular dichroic measurement showed that the specific band distribution of charged side chains of lysine units at the surface of helical structure does not constitute grounds for the local mode of interaction. Potassium pectinate of esterification degree E 57%, corresponding to polypeptides by charge density, does not reveal enhanced complexation values. The complex-forming efficacy continuously decreases with the increase of the esterification degree of pectin. Saturation of charges of the polypeptide was achieved predominantly by the spatial action of the superhelical structure of D-galacturonate chains.</jats:p
Formation of the poly(Lys-Ala-Ala) complex with pectin of various esterification degree
No full textThe helix-forming interaction of poly(Lys-Ala-Ala) with potassium pectinates of various esterification degree (E 0-87%) was quantitatively investigated by circular dichroism spectra. The helix-forming effect of pectinates is significant even at a low density of carboxyl anions in the molecule at a high esterification degree. The mutual complementarity of linear charge density of both interacting polyions plays a decisive role. The charge densities of unesterified pectate and helical poly(Lys-Ala-Ala) are very close. Orientation of the potassium pectate macromolecule (E0%) in the proposed spatial model is parallel to the axis of poly(Lys-Ala-Ala) α-helix. Saturation of the polypeptide charge with pectinates of an esterification degree E > 0% is achieved through formation of a superhelical structure of the pectinate with a turn density corresponding to the equivalence of charge densities of both interacting components in the complex.</jats:p
Understanding CH-Stretching Raman Optical Activity in Ala–Ala Dipeptides
No full textRaman optical activity (ROA) becomes a standard method to monitor
peptide conformation. However, the signal in the CH-stretching region
is particularly difficult to measure and interpret. In order to understand
the structural information contained in this part of the spectrum,
data obtained on a custom-made ROA spectrometer have been analyzed
for the model Ala–Ala molecule, with the help of molecular
dynamics (MD) and density functional theory computations. The Ala–Ala
enantiomers provided the “mirror image” spectra, which
proves that the signal can be reliably measured, in spite of a rather
low ROA/Raman intensity ratio (∼2 × 10–5). The theoretical modeling indicated that the most intense ROA bands
can be attributed to locally asymmetric CH3 and αCH vibrations, whereas symmetric methyl CH-stretching modes contribute
less. A simplified model made it possible to estimate the contribution
of local chirality of the two alanine residues to the resultant ROA
pattern. In spite of a significant frequency shift (over 100 cm–1) because of the anharmonic corrections, the harmonic
level was able to explain the main spectral features. The anharmonic
corrections were treated by second-order perturbation and limited
vibrational configuration interaction procedures. This allowed for
assignment of some weaker spectral features because of the combination
and overtone vibrations. The results show that the peptide CH-stretching
ROA signal contains rich structural information, reflecting also the
peptide environment. The experimental data, however, need to be deciphered
by relatively complex and time-consuming spectral simulations
The Ala/Ala genotype of PPARY Pro12 Ala polymorphism is associated with late onset of multiple sclerosis
Get PDFThe function of peroxisome proliferator-activated receptor gamma (PPAR gamma) in immune regulation, as well as in anti-inflammatory and anti-proliferative actions towards T lymphocytes, has been reported. A potential role of PPARs in multiple sclerosis (MS) was suggested. The aim of this study was to investigate if there is an association of PPAR gamma-2 Pro12Ala polymorphism with MS in 361 patients from Serbia. The genotype and allele frequencies of Pro12Ala polymorphism were not significantly different between controls and patients, or between females and males. In contrast to controls, we detected a rare Ala/Ala genotype in patients with MS. We found that there is a significant association of Ala/Ala genotype with older age at onset (ANOVA, p=0.07; LSD post-hoc, Ala/Ala vs. Pro/Ala, p=0.03, Ala/Ala vs. Pro/Pro p=0.02). It would be useful to validate our results in other populations, as well as to perform follow-up of the disease progression in regard to PPAR gamma genotypes
The Ala/Ala genotype of PPARY Pro12 Ala polymorphism is associated with late onset of multiple sclerosis
No full textThe function of peroxisome proliferator-activated receptor γ (PPARγ) in immune regulation, as well as in antiinflammatory and anti-proliferative actions towards T lymphocytes, has been reported. A potential role of PPARs in multiple sclerosis (MS) was suggested. The aim of this study was to investigate if there is an association of PPARγ-2 Pro12Ala polymorphism with MS in 361 patients from Serbia. The genotype and allele frequencies of Pro12Ala polymorphism were not significantly different between controls and patients, or between females and males. In contrast to controls, we detected a rare Ala/Ala genotype in patients with MS. We found that there is a significant association of Ala/Ala genotype with older age at onset (ANOVA, p=0.07; LSD post-hoc, Ala/Ala vs. Pro/Ala, p=0.03, Ala/Ala vs. Pro/Pro p=0.02). It would be useful to validate our results in other populations, as well as to perform follow-up of the disease progression in regard to PPARγ genotypes. [Projekat Ministarstva nauke Republike Srbije, br. 175085
Synthesis of a modified peptide fragment analog Val-Tyr (P)-Val-Ala-Ala-OH of cAMP protein kinase regulatory sub unit type II employing Fmoc chemistry
No full textThe synthesis of new peptide fragment analog (Val-Tyr(P)-Val-Ala-Ala-OH) incorporating Tyr into the phosphorylation site of the cAMP protein kinase regulatory sub unit type II in place of Ser (Val-SCr(P)-Val-Ala-Ala-OH) has been described. The phosphopentapeptide fragment is prepared by Fmoc chemistry employing the global phosphorylation method. The yield (68) as well as purity of the final peptide is satisfactory. The peptide is fully characterized by HPLC, NMR and mass spectral data
Formation of the poly(Lys-Ala-Ala) complex with potassium oligogalacturonates
No full textThe helix-forming interaction of poly(Lys-Ala-Ala) with potassium oligogalacturonates of various polymerization degree (n = 1-9) was investigated by the circular dichroism spectra. The complex-forming effect of these oligomers is considerably lower than that of the polymeric D-galacturonan. The highest efficiency was observed at n = 4 and 6, where the chain lengths of oligogalacturonates approximate to the distance of the most nearly located -NH3(+) groups of the α-helical polypeptide conformation.</jats:p
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