451 research outputs found
Investigation of The Role of Aromatic-Backbone Amide Interactions in Peptide and Protein Structure
No full textThe delicate balance of noncovalent interactions determines the three dimensional structure of peptides and proteins. These interactions include hydrogen bonds, salt bridges, weakly polar interactions and the hydrophobic effect. Weakly polar interaction can be between aromatic side chains of amino acids and amides of the polypeptide backbone (Ar-HN). Although, it is known that Ar-HN interactions can be responsible for the formation of local structures in polypeptides, the detailed understanding of their role and significance in peptide and protein structure remains unclear.
In the present study Ar-HN interactions in model peptides and proteins are investigated. Protein database survey of Ar-HN interactions found that Ar(i)-HN(i+l, i+2 and i+3) interactions are more common (7.10%, 2.08% and 0.54%, respectively) than are Ar(i)-HN(i-l, i-2 and i-3) interactions (0.66%, <0.1% and 0.18%, respectively). Ar- HN interactions constrain the x' torsion angle of the aromatic residue. Analyses of the secondary structures of the protein fragments containing Ar-HN interactions showed that Ar-HN interactions were in all types of secondary structures. Search results suggest that Ar-HN interactions have a stabilizing effect on all types of secondary structures.
Interactions between the side chain aromatic rings and hydrogens of backbone amides and CHn of aliphatic groups (tt-CH) were found to constrain individual conformations of the Pro-Xaa (where Xaa is either Phe, Tyr or Trp) and Xaa-Pro fragments. These local structures were found to be independent of the secondary structure of the polypeptide chains in which the fragments were located. This suggests,that weakly polar interactions, like Ar-HN and rr-CH, are weak separately, but in combination, they can have significant influence on the stability of polypeptide structure.
The interaction between the aromatic side chain of the z'th residue and the backbone amide group of the i+2 residue was studied in the tripeptide acetyl-Phe-Gly- Gly-N-methyl amide. It is an ideal model peptide to study such interactions, since side chains in positions i+1 and i+2 do not interfere with the formation of Ar-HN interaction. Simulated annealing studies with and without implicit solvation model using three different force fields (Amber 5.0, CHARMM22 and OPLSAA) found that lowest energy structures of the model peptide contained Ar-HN interaction. Molecular dynamics (MD) simulations revealed, that Ar(i)-HN(i+l) interactions were four times more frequent than were Ar(i)-HN(i+2) interactions in acetyl-Phe-Gly-Gly-N-methyl amide, and that half of the conformations with Ar(i)-HN(i+2) interactions also contained an Ar(i)-HN(i+l) interaction. The solvent access surface area of the Phel side-chain and of the amide groups of Phel, Gly2 and Gly3 involved in Ar-HN interactions was significantly smaller than in residues not involved in such interactions. The number of hydrogen bonds between the solvent and Phel, Gly2 and Gly3 amide groups was also lower in conformations with Ar-HN interactions. Thus, the attractive force between the backbone amide and the side chain aromatic ring is strong enough to outweigh any free energy losses due to solvation of the backbone and entropic costs of backbone and side chain stabilization.
The interaction between the aromatic side chain of Tyr and the a-helical backbone was investigated by studying a-helix stability in Ala based model peptides, with Tyr replacement in the N-terminal and inner helical positions, using circular dichroism, ’H-NMR and molecular dynamics simulations (MD). Interaction between the aromatic ring and the backbone highly depended on the orientation of the aromatic ring to the helical backbone since aromatic-backbone amide, -carbonyl and -aCH interactions were observed in MD. Solvent screening by the aromatic side chain decreased the solvent accessible surface area of some polar backbone groups by more than 80%. The fractional helical content, determined by NMR, suggested that Tyr in inner helical positions destabilized the helix in the peptides, while in N-terminal positions Tyr had the same helix stabilizing effect as had Ala.ProQuest Traditional Publishing Optionxvii, 540 leave
TOX3_TOX4_TOX5 generated data
No full textThe TOX3, TOX4 and TOX5 datasets are QSAR ones published by Gramatica et al. In their paper the experimental EC50 values (growth inhibition with respect to algea species Pseudokirchneriella subcapitata) of 35 triazole or benzo-triazole derivatives were used as training set. In the original article three linear QSAR models were developed using these 35 compounds (models A, B and C). Thereafter, the models were used on further 369 compounds, but for these no experimental data were available. In our calculation three datasets were formed. Each set contained the merged set of cases with altogether 404 molecules and the corresponding descriptor values of the given model. The response values were calculated in a quasi-independent way. For example, the response values for set TOX3 were defined as the averages of the response values calculated according to models B and C. For TOX4 the average responses of models A and C and for TOX5 the average responses of A and B were used. All responses were calculated in this way. We know that the generation procedure of TOX3-TOX5 datasets regularized the responses and probably eliminated the outliers. The original data were downloaded from the qsardb repository.
P. Gramatica, S. Cassani, P.P. Roy, S. Kovarich, C.W. Yap, E. Papa, QSAR Modeling is not “Push a Button and Find a Correlation”: A Case Study of Toxicity of (Benzo-)triazoles on Algae, Mol. Inform. 31 (2012) 817-835. http://dx.doi.org/10.1002/minf.201200075
V. Ruusmann, S. Sild, U. Maran, QSAR DataBank repository: open and linked qualitative and quantitative structure–activity relationship models. J. Cheminf. 7 (2015) 32. https://doi.org/10.1186/s13321-015-0082-6, http://www.qsardb.org
TOX3 multivariate linear regression R2 on total set
404 cases 3 descriptors 1 response 0.75
TOX4 multivariate linear regression
404 cases 3 descriptors 1 response 0.80
TOX5 multivariate linear regression
404 cases 3 descriptors 1 response 0.8
Csomapupa Pall-Gergely
No full textGenus Csomapupa Páll-Gergely, n. gen. Type species. Pomatias grandis Godwin-Austen, 1876. Diagnosis. Shell large, turriform/spindle-shaped, regularly ribbed, ribs very low and weak; shallow "scoring" or groove above the suture; aperture oval with very smooth columellar-parietal and parietal-palatal transitions; peristome very much widened; operculum thin. Differential diagnosis. Differs from Vargapupa n. gen. and Nodopomatias by the absence of a basal keel, and from Pseudopomatias by the presence of a shallow groove above the suture. Csomapupa n. gen. species have conspicuously widened peristome margin, which is wider than in any species of Pseudopomatias. The parietalpalatal transition of the aperture is not angled in Cs. luyorensis, but very slightly angled in Cs. grandis. In Pseudopomatias this transition is usually much more conspicuous. Etymology. The new genus Csomapupa (gender feminine) is dedicated to Sándor Kőrösi Csoma (1784?– 1842), also known as Alexander Csoma de Kőrös (approximate pronunciation is “choma”), Hungarian- Szekler (Székely) philologist and orientalist, author of the first Tibetan-English dictionary and grammar book. The name Csomapupa is the combination of the family name Csoma and Pupa. Content. Cs. grandis (Godwin-Austen, 1876), Cs. luyorensis (Godwin-Austen, 1917). Distribution (Fig. 7): The two species of Csomapupa n. gen. were reported from the Dafla and Abor Hills (north-eastern India) (see also Fig. 2).Published as part of Páll-Gergely, Barna, Fehér, Zoltán, Hunyadi, András & Asami, Takahiro, 2015, Revision of the genus Pseudopomatias and its relatives (Gastropoda: Cyclophoroidea: Pupinidae), pp. 1-49 in Zootaxa 3937 (1) on page 16, DOI: 10.11646/zootaxa.3937.1.1, http://zenodo.org/record/23713
Armament and Society in the Mirror of the Avar Archaelogy The Transdanubia-Phenomenon Revisited
No full textOne of the most significant problems of the A var archaeology is the question of
Germanic (mainly Gepidic) continuity in Transdanubia. In my paper I would like to
make some comments on the so-called Transdanubia-phenomenon of the Early A var
Carpathian Basin based on the analysis of weapon-combinations found in six
cemeteries of Eastern Transdanubia. I intend to answer the following questions: I.
How far the weapon-combinations of the East-Transdanubian cemeteries of the early
Avar Period (568-650) are identical or similar to the general picture of Avar armament
drawn by contemporary cemeteries? 2. Are the weapon-combinations or armament of
these cemeteries similar to that of the earlier Gepidic and Langobardic sites from the
early 6th centuries or to the contemporary Germanic (Alemannic, Frank or Bavarian)
cemeteries of the present-day Germany?
As a result, the early A var cemeteries of Transdanubia are characterized by the
relatively high number of close-combat weapons compared to other sites of the Avar
Khaganate. However, comparing to Merovingian sites the burials containing only
close-combat weapons are very low and in most of the cases the weapon-combinations
characteristic to this culture is missing
Pseudopomatias reischuetzi Pall-Gergely, n. sp.
No full textPseudopomatias reischuetzi Páll-Gergely, n. sp. Fig. 10 H Diagnosis. A small to medium sized, glossy, rather spindle-shaped species with almost smooth neck region, rather triangular aperture (strongly angled parietal-palatal transition) and weak peristome margin. Description. Shell greyish-yellowish, glossy, spindle shaped, widest at the penultimate whorl; the 7.25–8 (n= 4) bulging whorls are separated by deep suture; protoconch consists of 1.5 whorls, the first half is very finely granulated, the remaining part is very finely, regularly ribbed; teleoconch also regularly, very finely ribbed; ribs low, not sharp; on the last half whorl the ribbed surface turns into a rather smooth surface having irregular growth lines; shell surface without spiral lines; aperture rather triangular, with smoothly angled columellar-parietal transition and sharply angled parietal-palatal transition; apertural rim slightly thickened and very slightly reflexed, consists of two circles; the inner circle is sharp in front and conspicuously protruding; the outer one being wider; parietal callus normally developed; there are 2–3 inner palatal plicae visible above the umbilicus through the translucent shell. Measurements (in mm). H: 7.3–8.9, D: 3.3–3.7 (n= 3). Differential diagnosis. P. reischuetzi n. sp. differs from P. harli n. sp. and P. pleurophorus by the presence of plicae inside the last whorl, the more slender, spindle-shaped shell, the triangular aperture and the absence of spiral sculpture. P. h i m al ay a e is smaller, has much stronger and sharper ribs, especially on the neck region, it has a rounded aperture and also lacks the plicae. See also under P. si yomensis. Material. Lhota Naga, Godwin-Austen coll., NHMUK 1903.7.1.1549/ 1 (holotype), NHMUK 1903.7.1.1549/ 2–4 (3 paratypes). Type locality. Lhota Naga. Etymology. The new species is dedicated to and named after Alexander Reischütz, Austrian malacologist, the friend of the first author. Distribution. Only the type series is known, which was collected in "Lhota Naga", Naga Hills. See also Fig. 2 and Table 3. Remarks. There may be more, deeper situated plicae within the last whorl that are visible only by breaking the shells (see Notes on useful shell characters).Published as part of Páll-Gergely, Barna, Fehér, Zoltán, Hunyadi, András & Asami, Takahiro, 2015, Revision of the genus Pseudopomatias and its relatives (Gastropoda: Cyclophoroidea: Pupinidae), pp. 1-49 in Zootaxa 3937 (1) on pages 27-28, DOI: 10.11646/zootaxa.3937.1.1, http://zenodo.org/record/23713
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