Structures and stabilities of ternary copper(II) complexes containing an acidic and a basic amino acid. Evidence for arginine side chain involvement in intermolecular interactions and its biological implication

1993 ◽  
Vol 32 (7) ◽  
pp. 1111-1118 ◽  
Author(s):  
Hideki Masuda ◽  
Akira Odani ◽  
Takayasu Yamazaki ◽  
Tatsuo Yajima ◽  
Osamu Yamauchi
Keyword(s):  
Amino Acid ◽  
Intermolecular Interactions ◽  
Basic Amino Acid ◽  
Side Chain ◽  
Biological Implication ◽  
Arginine Side Chain

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.

Tryptic splitting of vasopressin analogues containing homologues of lysine or arginine in position 8

1979 ◽  
Vol 44 (8) ◽  
pp. 2451-2454
Author(s):  
Anastasia Dimeli ◽  
Tomislav Barth
Keyword(s):  
Amino Acid ◽  
Arginine Vasopressin ◽  
Basic Amino Acid ◽  
Peptide Bond ◽  
Peptide Chain ◽  
Side Chain ◽  
Lysine Vasopressin ◽  
Vasopressin Analogues

Vasopressin analogues containing an amino acid with a shorter side chain in position 8 of the peptide chain were more resistant to tryptic splitting of the peptide bond formed by the basic amino acid and terminal glycine amide. In the lysine vasopressin series, analogues with ornithine or lower homologues of lysine in position 8 were not hydrolyzed. In the arginine vasopressin series, the analogue containing 3-guanidino-2-aminopropionic acid in position 8 was completely resistant to the action of trypsin. The vasopressin analogue with norarginine in position 8 was split at a lower rate than natural arginine vasopressin.

scholarly journals Arginine off-kilter: guanidinium is not as planar as restraints denote

2020 ◽  
Vol 76 (12) ◽  
pp. 1159-1166
Author(s):  
Nigel W. Moriarty ◽  
Dorothee Liebschner ◽  
Dale E. Tronrud ◽  
Paul D. Adams
Keyword(s):  
Amino Acid ◽  
Software Package ◽  
Structural Chemistry ◽  
The Other ◽  
Side Chain ◽  
Torsion Angles ◽  
Bond Lengths ◽  
Arginine Side Chain ◽  
Parameter Ratio ◽  
The Asymmetry

Crystallographic refinement of macromolecular structures relies on stereochemical restraints to mitigate the typically poor data-to-parameter ratio. For proteins, each amino acid has a unique set of geometry restraints which represent stereochemical information such as bond lengths, valence angles, torsion angles, dihedrals and planes. It has been shown that the geometry in refined structures can differ significantly from that present in libraries; for example, it was recently reported that the guanidinium moiety in arginine is not symmetric. In this work, the asymmetry of the N∊—Cζ—Nη1 and N∊—Cζ—Nη2 valence angles in the guanidinium moiety is confirmed. In addition, it was found that the Cδ atom can deviate significantly (more than 20°) from the guanidinium plane. This requires the relaxation of the planar restraint for the Cδ atom, as it otherwise causes the other atoms in the group to compensate by distorting the guanidinium core plane. A new set of restraints for the arginine side chain have therefore been formulated, and are available in the software package Phenix, that take into account the asymmetry of the group and the planar deviation of the Cδ atom. This is an example of the need to regularly revisit the geometric restraint libraries used in macromolecular refinement so that they reflect the best knowledge of the structural chemistry of their components available at the time.

Effect of the basic amino-acid side chain length and the penultimate residue on the hydrolysis of benzoyldipeptides by carboxypeptidase B

1978 ◽  
Vol 56 (5) ◽  
pp. 315-318 ◽  
Author(s):  
Graham J. Moore ◽  
N. Leo Benoiton
Keyword(s):  
Amino Acid ◽  
Chain Length ◽  
Basic Amino Acid ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Carboxypeptidase B ◽  
Side Chain Length ◽  
C Terminus ◽  
Guanidino Group ◽  
Hydrolysis Of

The kinetic parameters Km and kcat/Km have been determined for the carboxypeptidase B (CPB, EC 3.4.12.3) catalyzed hydrolysis of benzoylglycyl-DL-homolysine and benzoylglycyl-L-homoarginine. Plots of these data and those for Bz-Gly-Orn and Bz-Gly-Arg (Wolff, E. C., Schirmer, E. W. &Folk, J. E. (1962) J. Biol. Chem. 237, 3094–3099) and Bz-Gly-Lys versus the length of the side chain of the basic amino acid indicate that unlike trypsin (EC 3.4.21.4) (Seely, J. H. &Benoiton, N. L. (1970) Can. J. Biochem. 48, 1122–1131) CPB has a higher binding affinity for a guanidino group than for an amino group at the side chain of the substrate C-terminus. On the other hand, CPB is similar to trypsin (ibid) in that the best substrate would have a side chain length between those of lysine and arginine.Studies with Bz-MeGly-Lys and Bz-Ala-Lys showed that the former is very slowly hydrolyzed by CPB but that the latter is a good substrate, with a high affinity for the enzyme, indicative of considerable participation of the Cα-methyl group of alanine in the binding of the substrate to the enzyme.

On the Nature of Intermolecular Interactions in Nucleic Acid Base−Amino Acid Side-Chain Complexes

2009 ◽  
Vol 113 (33) ◽  
pp. 11511-11520 ◽  
Author(s):  
Ż. Czyżnikowska ◽  
P. Lipkowski ◽  
R. W. Góra ◽  
R. Zaleśny ◽  
A. C. Cheng
Keyword(s):  
Amino Acid ◽  
Nucleic Acid ◽  
Intermolecular Interactions ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Acid Base ◽  
Chain Complexes ◽  
Nucleic Acid Base

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>

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