Residual Dipolar Couplings in Short Peptidic Foldamers: Combined Analyses of Backbone and Side-Chain Conformations and Evaluation of Structure Coordinates of Rigid Unnatural Amino Acids

ChemBioChem ◽  
2009 ◽  
Vol 10 (3) ◽  
pp. 440-444 ◽  
Author(s):  
Markus B. Schmid ◽  
Matthias Fleischmann ◽  
Valerio D'Elia ◽  
Oliver Reiser ◽  
Wolfram Gronwald ◽  
...  
Keyword(s):  
Amino Acids ◽  
Unnatural Amino Acids ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Side Chain ◽  
Chain Conformations

A Solid-Phase Synthetic Route to Unnatural Amino Acids with Diverse Side-Chain Substitutions

2002 ◽  
Vol 67 (9) ◽  
pp. 2960-2969 ◽  
Author(s):  
William L. Scott ◽  
Martin J. O'Donnell ◽  
Francisca Delgado ◽  
Jordi Alsina
Keyword(s):  
Amino Acids ◽  
Unnatural Amino Acids ◽  
Solid Phase ◽  
Side Chain ◽  
Synthetic Route

Residual Dipolar Couplings in Short Peptides Reveal Systematic Conformational Preferences of Individual Amino Acids

2006 ◽  
Vol 128 (41) ◽  
pp. 13508-13514 ◽  
Author(s):  
Sonja Alexandra Dames ◽  
Regula Aregger ◽  
Navratna Vajpai ◽  
Pau Bernado ◽  
Martin Blackledge ◽  
...  
Keyword(s):  
Amino Acids ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Short Peptides ◽  
Conformational Preferences

A New and Efficient Synthesis of Unnatural Amino Acids and Peptides by Selective 3,3-Dimethyldioxirane Side-Chain Oxidation

1999 ◽  
Vol 64 (23) ◽  
pp. 8468-8474 ◽  
Author(s):  
Raffaele Saladino ◽  
Maurizio Mezzetti ◽  
Enrico Mincione ◽  
Ines Torrini ◽  
Mario Paglialunga Paradisi ◽  
...  
Keyword(s):  
Amino Acids ◽  
Unnatural Amino Acids ◽  
Side Chain ◽  
Efficient Synthesis ◽  
Chain Oxidation

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.

A phase transition from monoclinicC2 withZ′ = 1 to triclinicP1 withZ′ = 4 for the quasiracemateL-2-aminobutyric acid–D-methionine (1/1)

2016 ◽  
Vol 72 (7) ◽  
pp. 536-543 ◽  
Author(s):  
Carl Henrik Görbitz ◽  
David S. Wragg ◽  
Ingrid Marie Bergh Bakke ◽  
Christian Fleischer ◽  
Gaute Grønnevik ◽  
...  
Keyword(s):  
Phase Transition ◽  
Amino Acids ◽  
Room Temperature ◽  
Aminobutyric Acid ◽  
Side Chain ◽  
Side Chains ◽  
Significant Difference ◽  
Hydrophobic Amino Acids ◽  
Chain Conformations ◽  
Triclinic Form

Racemates of hydrophobic amino acids with linear side chains are known to undergo a unique series of solid-state phase transitions that involve sliding of molecular bilayers upon heating or cooling. Recently, this behaviour was shown to extend also to quasiracemates of two different amino acids with opposite handedness [Görbitz & Karen (2015).J. Phys. Chem. B,119, 4975–4984]. Previous investigations are here extended to an L-2-aminobutyric acid–D-methionine (1/1) co-crystal, C4H9NO2·C5H11NO2S. The significant difference in size between the –CH2CH3and –CH2CH2SCH3side chains leads to extensive disorder at room temperature, which is essentially resolved after a phase transition at 229 K to an unprecedented triclinic form where all four D-methionine molecules in the asymmetric unit have different side-chain conformations and all three side-chain rotamers are used for the four partner L-2-aminobutyric acid molecules.

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