Exploration of the forbidden regions of the Ramachandran plot (ϕ-ψ) with QTAIM

2017 ◽  
Vol 19 (38) ◽  
pp. 26423-26434 ◽  
Author(s):  
Roya Momen ◽  
Alireza Azizi ◽  
Lingling Wang ◽  
Yang Ping ◽  
Tianlv Xu ◽  
...  
Keyword(s):  
Amino Acids ◽  
Peptide Structure ◽  
Ramachandran Plot ◽  
Left Response ◽  
Forbidden Regions ◽  
Dark Green ◽  
Ramachandran Plots ◽  
Pale Green

Left: Response β is defined as: β = arccos(e̲2·y̲) with β* = arccos(e̲1·y̲). Right: QTAIM interpreted Ramachandran plots {(βϕ,βϕ*)-(βψ,βψ*)} ‘-’ is a hyphen and not a subtraction sign. Pale green and dark green crosses indicate the glycine, pink and red pluses represent the remaining amino acids (a.a.) in the magainin peptide structure.

Investigation of Optimum Conformations and Structure Analysis of RL and LR Nests using Ramachandran Plot

2015 ◽  
pp. 209-224
Author(s):  
Sumukh Deshpande ◽  
Saikat Kumar Basu ◽  
Pooja Purohit
Keyword(s):  
Amino Acids ◽  
Ring Structure ◽  
Ramachandran Plot ◽  
Binding Motifs ◽  
Automated Algorithm ◽  
Automation And Control ◽  
The Common ◽  
And Control ◽  
Common Anion ◽  
Unique Application

We have surveyed polypeptides with the optimal conformations of nests which are the common anion-binding motifs comprising 8% of the amino acids which are characterized by a structural depression or a hole. Using automated bioinformatics algorithm, novel ring structure of the nest has been found. Using automated algorithm, models of polypeptides were made in-silico (computationally) and oxygen atoms are inserted along the extension of the NH groups. These sophisticated algorithms allow insertion of atoms along the NH group at the correct distance which causes extension of the group thus forming hydrogen bond. Optimal conformations of these structures are found from these customized models. This study chapter provides a demonstration of an important discovery of optimum conformations of RL and LR nests by the use of sophisticated bioinformatics automation pipeline and a unique application of automation and control in bioinformatics.

scholarly journals Stapled Peptides—A Useful Improvement for Peptide-Based Drugs

Molecules ◽  
2019 ◽  
Vol 24 (20) ◽  
pp. 3654 ◽  
Author(s):  
Mattia Moiola ◽  
Misal G. Memeo ◽  
Paolo Quadrelli
Keyword(s):  
Amino Acids ◽  
Scientific Community ◽  
Peptide Structure ◽  
Peptide Drug ◽  
Cross Link ◽  
Stapled Peptides ◽  
New Techniques ◽  
Low Degree ◽  
Drug Synthesis ◽  
The Right

Peptide-based drugs, despite being relegated as niche pharmaceuticals for years, are now capturing more and more attention from the scientific community. The main problem for these kinds of pharmacological compounds was the low degree of cellular uptake, which relegates the application of peptide-drugs to extracellular targets. In recent years, many new techniques have been developed in order to bypass the intrinsic problem of this kind of pharmaceuticals. One of these features is the use of stapled peptides. Stapled peptides consist of peptide chains that bring an external brace that force the peptide structure into an α -helical one. The cross-link is obtained by the linkage of the side chains of opportune-modified amino acids posed at the right distance inside the peptide chain. In this account, we report the main stapling methodologies currently employed or under development and the synthetic pathways involved in the amino acid modifications. Moreover, we report the results of two comparative studies upon different kinds of stapled-peptides, evaluating the properties given from each typology of staple to the target peptide and discussing the best choices for the use of this feature in peptide-drug synthesis.

Inclusions and wall deposits in cells of plants infected with oat necrotic mottle virus

1974 ◽  
Vol 52 (3) ◽  
pp. 621-626 ◽  
Author(s):  
C. C. Gill
Keyword(s):  
Cell Wall ◽  
Avena Sativa ◽  
Inclusion Bodies ◽  
Mottle Virus ◽  
Mesophyll Cells ◽  
Virus Like Particles ◽  
Green Tissue ◽  
Dark Green ◽  
Pale Green ◽  
In Cells

Virus-like particles and two types of inclusion bodies were found in cells of leaves of oats, Avena sativa L., and Canada bluegrass, Poa compressa L., infected with oat necrotic mottle virus. The particles and inclusion bodies were seen in pale green tissue and in most samples of dark green tissue of mottled, mature oat leaves, but were seen only in the pale green tissue of immature leaves. There was also evidence of infection in oat roots.Tubules and (or) vesicles occurred between the cell wall and the plasmalemma (boundary formation) in many mesophyll cells of infected, mature bluegrass and oat leaves. Three types of abnormal deposits, localized, extensive, and fibrillar, also occurred between the wall and the plasmalemma in many of these cells. The extensive and fibrillar deposits were more common in bluegrass than in oats.

scholarly journals Fluoro-aluminoleakeite, NaNa2(Mg2Al2Li)Si8O22F2, a new mineral of the amphibole group from Norra Kärr, Sweden: description and crystal structure

2009 ◽  
Vol 73 (5) ◽  
pp. 817-824 ◽  
Author(s):  
R. Oberti ◽  
F. Cámaraite ◽  
F. C. Hawthorne ◽  
N. A. Ball
Keyword(s):  
Crystal Structure ◽  
Structure Refinement ◽  
Polarized Light ◽  
Crystal Structure Analysis ◽  
New Mineral ◽  
Monoclinic Space Group ◽  
Calculated Density ◽  
Greenish Blue ◽  
Dark Green ◽  
Pale Green

AbstractFluoro-aluminoleakeite, ideally , is a new mineral of the amphibole group from Norra Kärr, Sweden (IMA-CNMMNC 2009-012). It occurs in a proterozoic alkaline intrusion that mainly comprises a fine-grained schistose agpaitic nepheline-syenite (grennaite). Fluoro- aluminoleakeite occurs as isolated prismatic crystals 0.10–2 mm long in a syenitic matrix. Crystals are light greenish-blue with a greenish-blue streak. It is brittle, has a Mohs hardness of 6 and a splintery fracture; it is non-fluorescent with perfect {110} cleavage, no observable parting, and has a calculated density of 3.14 g cm–3. In plane-polarized light, it is pleochroic, X = pale green, Y = dark green, Z = pale green; X ^ a = 62.9° (in β obtuse), Y || b. Fluoro-aluminoleakeite is biaxial negative, α = 1.632(1), β = 1.638(1), γ = 1.643(1); 2Vobs. = 98.0(4)°, 2Vcalc. = 95.5°.MFluoro-aluminoleakeite is monoclinic, space group C2/m, a = 9.7043(5) Å, b = 17.7341(8) Å, c = 5.2833(3) Å, β = 104.067(4)°, V = 882.0(2) Å3, Z = 2. The eight strongest X-ray diffraction lines in the powder-diffraction pattern are [d in Å, (I), (hkl)]: 2.687, (100), (31, 151); 4.435, (80), (021, 040); 3.377, (80), (131); 2.527, (60), (02); 8.342, (50), (110); 3.096, (40), (310); 2.259, (40), (71, 12) and 2.557, (30), (002, 061). Analysis, by a combination of electron microprobe and crystal-structure refinement, gives SiO2 58.61, Al2O3 7.06, TiO2 0.32, FeO 3.27, Fe2O3 6.05, MgO 8.61, MnO 0.73, ZnO 0.43, CaO 0.05, Na2O 9.90, K2O 2.43, Li2O 1.62, F 3.37, H2Ocalc. 0.50, sum 101.08 wt.%. The formula unit, calculated on the basis of 24 (O,OH,F,Cl) p.f.u. with (OH) + F = 2 a.p.f.u., is A(Na0.65 O22W(F1.47OH0.53)Σ=2.00. Crystal-structure analysis shows CLi to be completely ordered at the M(3) site, and provided reliable site populations. Fluoro-aluminoleakeite is related to the end-member leakeite, , by the substitutions CFe3+ → CAl and WF → W(OH).

Fmoc-protected tropane-based amino acids for peptide structure-function studies

1997 ◽  
Vol 38 (16) ◽  
pp. 2907-2910 ◽  
Author(s):  
Philip E. Thompson ◽  
Milton T.W. Hearn
Keyword(s):  
Amino Acids ◽  
Structure Function ◽  
Peptide Structure

δ-Peptides and δ-Amino Acids as Tools for Peptide Structure DesignA Theoretical Study

2004 ◽  
Vol 69 (19) ◽  
pp. 6214-6220 ◽  
Author(s):  
Carsten Baldauf ◽  
Robert Günther ◽  
Hans-Jörg Hofmann
Keyword(s):  
Amino Acids ◽  
Theoretical Study ◽  
Peptide Structure

scholarly journals DESCRIPTION OF THE PREPARATORY STAGES OF NEONYMPHA AREOLATUS, Smith–Abbot

1882 ◽  
Vol 14 (9) ◽  
pp. 163-166
Author(s):  
W. H. Edwards
Keyword(s):  
Low Power ◽  
Body Segment ◽  
Single Hair ◽  
Dark Green ◽  
Pale Green ◽  
Dorsal Stripe ◽  
Base Duration

Egg—Nearly globular; the surface smooth under a low power, but under a high one, thickly covered with shallow depressions, which are irregular in size and also in form, being pentagonal, rounded or oval; color pale green. Duration of this stage about 6 days.Young Larva.—Length .12 inch; cylindrical, nearly even, tapering a little posteriorly, the last segment bluntly forked; color delicate green; over the surface many white hairs, and among these are black clubbed hairs disposed in longitudinal rows, four on the dorsum of each segment, two in front, two in rear; feet and legs green; head large, about twice as broad as any body segment, sub-globose, a little depressed at top; on each vertex a short semi-ovoid appendage, at the top giving out two divergent black hairs; just below vertex, on the front, is a similar smaller appendage with single hair, and on the side half way down is a second; color black. Towards the end of this stage the color of body changes to decided green, and several longitudinal stripes appear; on either side of a dark green medio-dorsal stripe is a whitish one, a similar one on middle of side and another along base. Duration of this stage about 8 days, but depending on the weather.

Utilization of tyrosine dipeptides and acetyltyrosine in normal and uremic humans

1991 ◽  
Vol 260 (2) ◽  
pp. E280-E285 ◽  
Author(s):  
W. Druml ◽  
H. Lochs ◽  
E. Roth ◽  
W. Hubl ◽  
P. Balcke ◽  
...  
Keyword(s):  
Amino Acids ◽  
Renal Failure ◽  
Parenteral Nutrition ◽  
Whole Body ◽  
Peptide Structure ◽  
Healthy Controls ◽  
The Impact ◽  
Hydrolysis Of ◽  
Regular Hemodialysis ◽  
Body Clearance

The impact of renal failure on the elimination and hydrolysis of three sources of tyrosine for parenteral nutrition, the dipeptides alanyltyrosine (Ala-Tyr), glycyltyrosine (Gly-Tyr), and N-acetyltyrosine (NAc-Tyr) was investigated in eight patients on regular hemodialysis therapy (HD) and seven healthy controls (CON). In CON, whole body clearance (Ctot) of Ala-Tyr (3,169 +/- 198 ml/min) was higher than Gly-Tyr (1,781 +/- 184, P less than 0.001), and both exceeded NAc-Tyr (284 +/- 24, P less than 0.001). In HD, Ctot of Ala-Tyr was not different from CON, but Ctot of Gly-Tyr (858 +/- 73, P less than 0.001) and NAc-Tyr (129 +/- 30, P less than 0.02) was decreased. The rise in plasma levels of constituent amino acids was higher in Ala-Tyr vs. Gly-Tyr (P less than 0.01). In HD, the pattern was similar, although the increase in Tyr was less than in CON. Plasma Tyr did not increase with NAc-Tyr in either group. Urinary loss of peptides was neglible, but 60% of NAc-Tyr infused was excreted by CON. The half-life of peptides incubated in CON and HD plasma was unchanged for Ala-Tyr (12.3 +/- 0.9 vs. 14.6 +/- 1.9 min) and prolonged for Gly-Tyr in HD (101.7 +/- 4.9 vs. 131.3 +/- 12, P less than 0.05). Thus renal failure does not impair Ala-Tyr disposal and delays Gly-Tyr utilization. These differential effects on peptide assimilation underscore the importance of peptide structure on metabolism. Both peptides, but not NAc-Tyr, may serve as a nutritional substrate in renal failure patients.

Olivenite and cornwallite from the Podlipa copper deposit near Ľubietová, Slovakia

2021 ◽  
Vol 29 (2) ◽  
pp. 189-196
Author(s):  
Martin Števko ◽  
Jiří Sejkora ◽  
Zdeněk Dolníček
Keyword(s):  
Copper Deposit ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Chemical Zoning ◽  
Cell Parameters ◽  
P Content ◽  
Dark Green ◽  
Pale Green

An interesting occurrence of olivenite and cornwallite was recently discovered in cavities of quartz at the Podlipa copper deposit near Ľubietová, Slovakia. Olivenite occurs as olive to pale green sprays or radial aggregates consisting of individual acicular crystals up to 5 mm long. Its refined unit-cell parameters (for the monoclinic space group P21/n) are: a 8.6192(13) Å, b 8.2300(11) Å, c 5.9349(8) Å, α 90.055(12)° and V 420.99(7) Å3. Studied olivenite shows intense chemical zoning caused by strong variation of As and P contents. Most of the zones are corresponding to olivenite (with P content ranging between 0.02 to 0.39 apfu), but darker zones or domains of As-rich libethenite (with As content ranging between 0.18 to 0.24 apfu) were occasionally observed. Cornwallite forms dark green massive fillings between olivenite crystals or microcrystalline botryoidal crusts. The refined unit-cell parameters (for the monoclinic space group P21/c) of botryoidal cornwallite from the Podlipa deposit are: a 4.6112(2) Å, b 5.7698(3) Å, c 17.4167(11) Å, β 92.009(5)° and V 463.10(3) Å3. The two compositional types of cornwallite were distinguished. The first type is represented by relatively homogenous aggregates with only minor contents of P (from 0.04 to 0.22 apfu). The second type occurs as polycrystalline fillings with strong chemical zoning and has much more significant variation of As and P contents, representing solid-solution series between P-rich cornwallite (with 1.41 apfu of As and 0.59 apfu of P) and As-rich pseudomalachite (with 1.37 apfu of P and 0.63 apfu of As).

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