scholarly journals Genetic Code Evolution Reconstructed with Aligned Metrics

2020 ◽  
Author(s):  
Brian K. Davis
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Functional Difference ◽  
Polar Cluster ◽  
Path Distance ◽  
Residue Frequency ◽  
Trna Species ◽  
Aspartate Family

AbstractSequence homology in pre-divergence tRNA species revealed cofactor/adaptors cognate for 16 amino acids derived from oxaloacetate, pyruvate, phosphoglycerate, or phosphoenolpyruvate were related. Synthesis path-distances of these amino acids correlated with phylogenetic depth, reflecting relative residue frequency in pre-divergence sequences. Both metrics were thus aligned in the four sub-families of the Aspartate family, and misaligned in the small Glutamate family; a functional difference was noted and seen to parallel synthetase duality. Amino acid synthetic order, based on path-distances, indicate NH4+ fixer amino acids, Asp1, Asn2, and homologues, Glu1, Gln2, formed the first code. Together with a termination signal, they acquired all four triplet 4-sets in the XAN column (X, 5’ coding site; N, any 3’-base). An invariant mid-A conformed with pre-code translation on a poly(A) template by a ratchet-equipped ribosome resulting in random, polyanionic polypeptides. Code expansion occurred in a compact (mutation minimizing) columnwise pattern, (XAN) ➔ XCN ➔ XGN ➔ XUN; with increasing mean path-distance, (1.5) ➔ 4 ➔ 5 ➔ 7 steps; amino acid side-chain hydrophobicity, (+6.6) ➔ −0.8 ➔ −1.5 ➔ −3.2 kcal/ mol; codon:anticodon H bond enthalpy (selection for bond-strength), (−12.5) ➔ −17.5 ➔ −15.5 ➔ −14.5 kcal/ mol; and precursorspecific 5’-base, A, oxaloacetate, G, pyruvate/oxaloacetate, U, phosphoglycerate/oxaloacetate, C, oxoglutarate, forming horizontal code domains. Codon bias evidence corroborated the XCN ➔ XGN step in expansion, and revealed row GNN coevolved with ANN, on correction for overprinting. Extended surfaceattachment (Fajan-Paneth principle) by pro-Fd[5] and bilayer partitioning by H+ ATPase proteolipid-h1 subunit implicated expansion phase proteins in driving increases in side-chain hydrophobicity during code expansion. 3’-Base recruitment in pre-assigned codon boxes added six long (9-to 14-step) path amino acid, bearing a basic, or cyclic, side-chain; 3 of 4 polar, post-expansion amino acids acquired polar cluster NAN codons and 2 of 3 non-polar (Ile7 included) acquired non-polar cluster NUN codons, yieldng a split-box pair homology of p = 5.4×10-3. All eight overprinted codon boxes (GAYR for Asp1, Glu1 included) exhibit weak codon:anticodon H-bond enthalpy, −14 kcal/mol or higher, in three of six distinct code enthalpy states.

scholarly journals DLPacker: Deep Learning for Prediction of Amino Acid Side Chain Conformations in Proteins

2021 ◽  
Author(s):  
Mikita Misiura ◽  
Raghav Shroff ◽  
Ross Thyer ◽  
Anatoly Kolomeisky
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Protein Design ◽  
Structure Prediction ◽  
Deep Neural Networks ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Image Transformation ◽  
Hydrophobic Amino Acids ◽  
Chain Conformations

Prediction of side chain conformations of amino acids in proteins (also termed 'packing') is an important and challenging part of protein structure prediction with many interesting applications in protein design. A variety of methods for packing have been developed but more accurate ones are still needed. Machine learning (ML) methods have recently become a powerful tool for solving various problems in diverse areas of science, including structural biology. In this work we evaluate the potential of Deep Neural Networks (DNNs) for prediction of amino acid side chain conformations. We formulate the problem as image-to-image transformation and train a U-net style DNN to solve the problem. We show that our method outperforms other physics-based methods by a significant margin: reconstruction RMSDs for most amino acids are about 20% smaller compared to SCWRL4 and Rosetta Packer with RMSDs for bulky hydrophobic amino acids Phe, Tyr and Trp being up to 50% smaller.

scholarly journals Poly(ester amide)s based on (L)-lactic acid oligomers and α-amino acids: influence of the α-amino acid side chain in the poly(ester amide)s properties

2013 ◽  
Vol 24 (12) ◽  
pp. 1391-1409 ◽  
Author(s):  
Ana C. Fonseca ◽  
Jorge F.J. Coelho ◽  
Joana F.A. Valente ◽  
Tiago R. Correia ◽  
Ilídio J. Correia ◽  
...  
Keyword(s):  
Amino Acids ◽  
Lactic Acid ◽  
Amino Acid ◽  
Side Chain ◽  
Amino Acid Side Chain

Carbobenzoxy amino acids: structural requirements for cholecystokinin receptor antagonist activity

1985 ◽  
Vol 248 (4) ◽  
pp. G479-G484 ◽  
Author(s):  
P. N. Maton ◽  
V. E. Sutliff ◽  
R. T. Jensen ◽  
J. D. Gardner
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Receptor Antagonist ◽  
Amino Acid Derivative ◽  
Side Chain ◽  
Amylase Secretion ◽  
Amino Acid Side Chain ◽  
Antagonist Activity ◽  
Cholecystokinin Receptor ◽  
Stimulation Of

We used dispersed acini prepared from guinea pig pancreas to examine 28 carbobenzoxy (CBZ) amino acids for their abilities to function as cholecystokinin receptor antagonists. All amino acid derivatives tested, except for CBZ-alanine, CBZ-glycine, and N alpha-CBZ-lysine, were able to inhibit the stimulation of amylase secretion caused by the C-terminal octapeptide of cholecystokinin. In general, there was a good correlation between the ability of a carbobenzoxy amino acid to inhibit stimulated amylase secretion and the ability of the amino acid derivative to inhibit binding of 125I-cholecystokinin. The inhibition of cholecystokinin-stimulated amylase secretion was competitive, fully reversible, and specific for those secretagogues that interact with the cholecystokinin receptor. The potencies with which the various carbobenzoxy amino acids inhibited the action of cholecystokinin varied 100-fold and CBZ-cystine was the most potent cholecystokinin receptor antagonist. This variation in potency was primarily but not exclusively a function of the hydrophobicity of the amino acid side chain.

scholarly journals The stimulating effect of fatty acids and amino acid derivatives on the labellar sugar receptor of the fleshfly.

1978 ◽  
Vol 71 (1) ◽  
pp. 19-36 ◽  
Author(s):  
I Shimada
Keyword(s):  
Amino Acids ◽  
Fatty Acids ◽  
Amino Acid ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Amino Groups ◽  
Neutral Ph ◽  
Sugar Receptor ◽  
Fatty Acid Derivatives ◽  
Effect Of Treatment

Seven D-amino acids, including D-valine, D-phenylalanine, D-leucine, D-isoleucine, D-tryptophan, D-methionine, and D-alpha-aminobutyric acid, are markedly less stimulative than the corresponding L-isomers that can stimulate the labellar sugar receptor of the fleshfly. A distinct effect of len;th of the amino acid side chain is clearly observed. Esterification and amidation of the alpha-carboxyl group, as well as substitution by hydroxyl and methyl groups, result in extremely decreased responses. Amino acids whose amino groups are located at a position other than the alpha are almost ineffective. With all these rigid stereospecificities of the sugar receptor for amino acids, certain replacement of the alpha-amino group with the hydroxyl or carbonyl group shows a slight increase of the response at neutral pH. Furthermore, certain fatty acids can stimulate the sugar receptor once the solutions are buffered at neutral pH. This observation was further supported by the presence of a remarkable similarity of stimulating effectiveness between amino acids that can stimulate the sugar receptor and those fatty acids. The similarity was shown by testing the response concentration relationships, the stimulating effect of fatty acid derivatives, the effect of treatment with p-chloromercuribenzoate, the behavioral response, and so on.

Molecular aggregation in crystalline 1:1 complexes of hydrophobic D- and L-amino acids. I. The L-isoleucine series

1999 ◽  
Vol 55 (3) ◽  
pp. 424-431 ◽  
Author(s):  
Bjørn Dalhus ◽  
Carl Henrik Görbitz
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Aminobutyric Acid ◽  
Side Chain ◽  
Side Chains ◽  
Amino Acid Side Chain ◽  
Molecular Aggregation ◽  
Plane Symmetry ◽  
Hydrogen Bond Pattern ◽  
Polar Parts

The amino acid L-isoleucine has been cocrystallized with seven selected D-amino acids including D-methionine [L-isoleucine–D-methionine (1/1), C6H13NO2.C5H11NO2S, amino-acid side chain R = —CH2—CH2—S—CH3] and a homologous series from D-alanine [L-isoleucine–D-alanine (1/1), C6H13NO2.C3H7NO2, R = —CH3] through D-α-aminobutyric acid [L-isoleucine–D-α-aminobutyric acid (1/1), C6H13NO2.C4H9NO2, R = —CH2—CH3] and D-norvaline [L-isoleucine–D-norvaline (1/1), C6H13NO2.C5H11NO2, R = —CH2—CH2—CH3] to D-norleucine [L-isoleucine–D-norleucine (1/1), C6H13NO2.C6H13NO2, R = —CH2—CH2—CH2—CH3] with linear side chains, and D-valine [L-isoleucine–D-valine (1/1), C6H13NO2.C5H11NO2, R = —CH—(CH3)2] and D-leucine [L-isoleucine–D-leucine (1/1), C6H13NO2.C6H13NO2, R = —CH2—CH—(CH3)2] with branched side chains. All the crystal structures are divided into distinct hydrophilic and hydrophobic layers. In the five complexes with amino acids with linear side chains the polar parts of the D- and L-amino acids are related by pseudo-glide-plane symmetry, and four of them have remarkably similar molecular arrangements. The D-valine and D-leucine complexes, on the other hand, are structurally quite different with the polar parts of the D- and L-amino acids related by pseudo-inversion. Differences in the hydrogen-bond pattern in the two molecular arrangements are discussed.

scholarly journals [60]Fullerenyl amino acids and peptides: a review of their synthesis and applications

RSC Advances ◽  
2014 ◽  
Vol 4 (86) ◽  
pp. 46383-46398 ◽  
Author(s):  
Sreenu Jennepalli ◽  
Stephen G. Pyne ◽  
Paul A. Keller
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Functional Types ◽  
Review Reports

This review reports on the latest progress in the synthesis of fullerenyl amino acids and related derivatives, and categorises the molecules into functional types for different uses: these include directly attached fullerenyl amino acids, fullerenyl N- and C-capping amino acids, and those amino acids in which the [60]fullerene group is attached to the amino acid side chain.

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