scholarly journals Dynamics of Serine-8 Side-Chain in Amyloid-β Fibrils and Fluorenylmethyloxycarbonyl Serine Amino Acid, Investigated by Solid-State Deuteron NMR

2020 ◽  
Vol 124 (23) ◽  
pp. 4723-4731
Author(s):  
Liliya Vugmeyster ◽  
Dan Fai Au ◽  
Dmitry Ostrovsky ◽  
Dillon Ray Lee Rickertsen ◽  
Scott M. Reed
Keyword(s):  
Amino Acid ◽  
Solid State ◽  
Amyloid Β ◽  
Side Chain ◽  
Deuteron Nmr

scholarly journals Solid-State and Solution-Phase Conformations of Pseudoproline-Containing Dipeptides

2009 ◽  
Vol 62 (7) ◽  
pp. 711 ◽  
Author(s):  
Jack K. Clegg ◽  
James R. Cochrane ◽  
Nima Sayyadi ◽  
Danielle Skropeta ◽  
Peter Turner ◽  
...  
Keyword(s):  
Amino Acid ◽  
Solid State ◽  
Crystal Packing ◽  
Amide Bond ◽  
Side Chain ◽  
Trans Conformation ◽  
N Terminus ◽  
Structural Differences ◽  
Terminal Amino ◽  
Packing Interactions

The conformations of 14 threonine-derived pseudoproline-containing dipeptides (including four d-allo-Thr derivatives) have been investigated by NMR. In solution, the major conformer observed for all dipeptides is that in which the amide bond between the pseudoproline and the preceding amino acid is cis. For dipeptides in which the N-terminus is protected, the ratio of cis- to trans-conformers does not depend significantly on the side chain of the N-terminal amino acid, or the stereochemistry of the Thr residue. However, for dipeptides bearing a free N-terminus, there are significant differences in the ratios of cis- to trans-conformers depending on the side chain present. Three dipeptides were crystallized and their X-ray structures determined. In two cases, (benzyloxycarbonyl (Cbz)-Val-Thr(ΨMe,Mepro)-OMe and Cbz-Val-Thr(ΨMe,Mepro)-OH), the dipeptides adopt a trans-conformation in the solid state, in contrast to the structures observed in solution. In the third case, (9-fluorenylmethoxycarbonyl (Fmoc)-Val-d-allo-Thr(ΨMe,Mepro)-OH), a cis-amide geometry is observed. These structural differences are attributed to crystal-packing interactions.

Polypeptides Folding: Rules for the Calculation of the Backbone Dihedral Angles φ starting from the Amino Acid Sequence

2020 ◽  
Author(s):  
Michele Larocca
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Theoretical Approach ◽  
Polypeptide Chain ◽  
Hydrophobic Effect ◽  
Side Chain ◽  
Dihedral Angles ◽  
Mechanical Forces ◽  
Specific Chemical

<p>Protein folding is strictly related to the determination of the backbone dihedral angles and depends on the information contained in the amino acid sequence as well as on the hydrophobic effect. To date, the type of information embedded in the amino acid sequence has not yet been revealed. The present study deals with these problematics and aims to furnish a possible explanation of the information contained in the amino acid sequence, showing and reporting rules to calculate the backbone dihedral angles φ. The study is based on the development of mechanical forces once specific chemical interactions are established among the side chain of the residues in a polypeptide chain. It aims to furnish a theoretical approach to predict backbone dihedral angles which, in the future, may be applied to computational developments focused on the prediction of polypeptide structures.</p>

Schistosomal Sulfotransferase Interaction with Oxamniquine Involves Hybrid Mechanism of Induced-fit and Conformational Selection

2020 ◽  
Vol 16 (4) ◽  
pp. 451-459 ◽  
Author(s):  
Fortunatus C. Ezebuo ◽  
Ikemefuna C. Uzochukwu
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Binding Energy ◽  
Binding Site ◽  
Conformational Dynamics ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Conformational Selection ◽  
Hybrid Mechanism ◽  
Dynamics Simulations

Background: Sulfotransferase family comprises key enzymes involved in drug metabolism. Oxamniquine is a pro-drug converted into its active form by schistosomal sulfotransferase. The conformational dynamics of side-chain amino acid residues at the binding site of schistosomal sulfotransferase towards activation of oxamniquine has not received attention. Objective: The study investigated the conformational dynamics of binding site residues in free and oxamniquine bound schistosomal sulfotransferase systems and their contribution to the mechanism of oxamniquine activation by schistosomal sulfotransferase using molecular dynamics simulations and binding energy calculations. Methods: Schistosomal sulfotransferase was obtained from Protein Data Bank and both the free and oxamniquine bound forms were subjected to molecular dynamics simulations using GROMACS-4.5.5 after modeling it’s missing amino acid residues with SWISS-MODEL. Amino acid residues at its binding site for oxamniquine was determined and used for Principal Component Analysis and calculations of side-chain dihedrals. In addition, binding energy of the oxamniquine bound system was calculated using g_MMPBSA. Results: The results showed that binding site amino acid residues in free and oxamniquine bound sulfotransferase sampled different conformational space involving several rotameric states. Importantly, Phe45, Ile145 and Leu241 generated newly induced conformations, whereas Phe41 exhibited shift in equilibrium of its conformational distribution. In addition, the result showed binding energy of -130.091 ± 8.800 KJ/mol and Phe45 contributed -9.8576 KJ/mol. Conclusion: The results showed that schistosomal sulfotransferase binds oxamniquine by relying on hybrid mechanism of induced fit and conformational selection models. The findings offer new insight into sulfotransferase engineering and design of new drugs that target sulfotransferase.

Synthesis and conformation of sequential basic polypeptides with branched and linear side chains

1985 ◽  
Vol 50 (12) ◽  
pp. 2925-2936 ◽  
Author(s):  
Štěpánka Štokrová ◽  
Jan Pospíšek ◽  
Jaroslav Šponar ◽  
Karel Bláha
Keyword(s):  
Amino Acid ◽  
Salt Concentration ◽  
Salt Solution ◽  
Theoretical Work ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Cd Spectra ◽  
Low Salt ◽  
Conformational Freedom ◽  
Basic Polypeptides

Polypeptides (Lys-X-Ala)n and (Lys-X-Gly)n in which X represents residues of isoleucine and norleucine, respectively, and polypeptide (Tle-Lys-Ala)n, were synthesized via polymerization of 1-hydroxysuccinimidyl esters of the appropriate tripeptides to complete previously studied series. Circular dichroism (CD) spectra of the respective polymers were measured as a function of pH and salt concentration of the medium. The results were correlated with those obtained previously with the same series containing different amino acid residues at the X-position. The helix forming ability of the polypeptides (Lys-X-Ala)n with linear X side chain was found to be independent of the length. In the series (Lys-X-Gly)n the unordered conformation was the most probable one except (Lys-Ile-Gly)n. This polymer assumed the β conformation even in low salt solution at neutral pH. An agreement with some theoretical work concerned with the restriction of conformational freedom of amino acid residue branching at Cβ atom with our experimental results is evident.

Comparison of the Potency of 8-L-Arginine, 8-D-Arginine and 8-D-Homoarginine Vasopressin Analogs with Substituted Phenylalanine in Position 2

1994 ◽  
Vol 59 (6) ◽  
pp. 1439-1450 ◽  
Author(s):  
Miroslava Žertová ◽  
Jiřina Slaninová ◽  
Zdenko Procházka
Keyword(s):  
Amino Acid ◽  
Solid Phase Synthesis ◽  
Solid Phase ◽  
Basic Amino Acid ◽  
The Other ◽  
Side Chain ◽  
Inhibitory Potency ◽  
Phase Synthesis ◽  
Other Hand ◽  
Order Of Magnitude

An analysis of the uterotonic potencies of all analogs having substituted L- or D-tyrosine or -phenylalanine in position 2 and L-arginine, D-arginine or D-homoarginine in position 8 was made. The series of analogs already published was completed by the solid phase synthesis of ten new analogs having L- or D-Phe, L- or D-Phe(2-Et), L- or D-Phe(2,4,6-triMe) or D-Tyr(Me) in position 2 and either L- or D-arginine in position 8. All newly synthesized analogs were found to be uterotonic inhibitors. Deamination increases both the agonistic and antagonistic potency. In the case of phenylalanine analogs the change of configuration from L to D in position 2 enhances the uterotonic inhibition for more than 1 order of magnitude. The L to D change in position 8 enhances the inhibitory potency negligibly. Prolongation of the side chain of the D-basic amino acid in position 8 seems to decrease slightly the inhibitory potency if there is L-substituted amino acid in position 2. On the other hand there is a tendency to the increase of the inhibitory potency if there is D-substituted amino acid in position 2.

Analogues of the cholecystokinin octapeptide modified in the central part of the molecule

1991 ◽  
Vol 56 (9) ◽  
pp. 1963-1970 ◽  
Author(s):  
Jan Hlaváček ◽  
Václav Čeřovský ◽  
Jana Pírková ◽  
Pavel Majer ◽  
Lenka Maletínská ◽  
...  
Keyword(s):  
Amino Acid ◽  
Biological Activities ◽  
Point Of View ◽  
Biologically Active ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Cholecystokinin Octapeptide ◽  
Biological Tests ◽  
Biological Potency ◽  
Biologically Active Conformation

In a series of analogues of the cholecystokinin octapeptide (CCK-8) the amino acid residues were gradually modified by substituting Gly by Pro in position 4, Trp by His in position 5, Met by Cle in position 6, or the Gly residue was inserted between Tyr and Met in positions 2 and 3 of the peptide chain, and in the case of the cholecystokinin heptapeptide (CCK-7) the Met residues were substituted by Nle or Aib. These peptides were investigated from the point of view of their biological potency in the peripheral and central region. From the results of the biological tests it follows that the modifications carried out in these analogues and in their Nα-Boc derivatives mean a suppression of the investigated biological activities by 2-3 orders of magnitude (at a maximum dose of the tested substance of 2 . 10-2 mg per animal).This means that a disturbance of the assumed biologically active conformation of CCK-8, connected with a considerable decrease of the biological potency of the molecule, takes place not only after introduction of the side chain into its centre (substitution of Gly4), but also after the modification of the side chains of the amino acids or by extension of the backbone in further positions around this central amino acid.

scholarly journals Interaction Profiles of Amino Acid Side-Chain Analog Pairs within Membrane Environments

2014 ◽  
Vol 106 (2) ◽  
pp. 499a
Author(s):  
Vahid Mirjalili ◽  
Michael Feig
Keyword(s):  
Amino Acid ◽  
Side Chain ◽  
Amino Acid Side Chain

scholarly journals Effects of 18F-fluorinated neopentyl glycol side-chain on the biological characteristics of stilbene amyloid-β PET ligands

2021 ◽  
Vol 94-95 ◽  
pp. 38-45
Author(s):  
Tetsuro Tago ◽  
Jun Toyohara ◽  
Ryo Fujimaki ◽  
Maho Tatsuta ◽  
Ruichong Song ◽  
...  
Keyword(s):  
Amyloid Β ◽  
Biological Characteristics ◽  
Side Chain ◽  
Neopentyl Glycol

scholarly journals Effect of roasting temperature on lipid and protein oxidation and amino acid residue side chain modification of beef patties

RSC Advances ◽  
2021 ◽  
Vol 11 (35) ◽  
pp. 21629-21641
Author(s):  
Chao Xia ◽  
Pingping Wen ◽  
Yaming Yuan ◽  
Xiaofan Yu ◽  
Yijing Chen ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Residue ◽  
Protein Oxidation ◽  
Relative Number ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Beef Patties ◽  
Lipid And Protein Oxidation ◽  
Roasting Temperature

The relative number of peptides modified by the amino acid residues of actin from raw beef patties and those cooked at different roasting temperatures.

scholarly journals CLAC binds to amyloid β peptides through the positively charged amino acid cluster within the collagenous domain 1 and inhibits formation of amyloid fibrils. Vol. 280 (2005) 8596–8605

2005 ◽  
Vol 280 (15) ◽  
pp. 15484
Author(s):  
Yoshihide Osada ◽  
Tadafumi Hashimoto ◽  
Akiko Nishimura ◽  
Yuko Matsuo ◽  
Tomoko Wakabayashi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amyloid Fibrils ◽  
Amyloid Β ◽  
Collagenous Domain ◽  
Amino Acid Cluster ◽  
Positively Charged
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