scholarly journals Rotamer libraries for the high-resolution design of beta-amino acid foldamers

2016 ◽  
Author(s):  
Andrew W Watkins ◽  
P. Douglas Renfrew ◽  
Timothy W Craven ◽  
Paramjit S Arora ◽  
Richard Bonneau
Keyword(s):  
Amino Acids ◽  
High Resolution ◽  
State Of The Art ◽  
Biologically Active ◽  
Side Chain ◽  
Model Refinement ◽  
Nonnatural Amino Acids ◽  
Conformational Preferences ◽  
Chain Conformations ◽  
Macromolecular Modeling

β-amino acids offer attractive opportunities to develop biologically active peptidomimetics, either employed alone or in conjunction with natural α-amino acids. Owing to their potential for unique conformational preferences that deviate considerably from α-peptide geometries, β-amino acids greatly expand the possible chemistries and physical properties available to polyamide foldamers. Complete in silico support for designing new molecules incorporating nonnatural amino acids typically requires representing their side chain conformations as sets of discrete rotamers for model refinement and sequence optimization. Such rotamer libraries are key components of several state of the art design frameworks. Here we report the development, incorporation in to the Rosetta macromolecular modeling suite, and validation of rotamer libraries for β3-amino acids.

scholarly journals Oxytocin analogues with amide groups substituted by tetrazole groups in position 4, 5 or 9.

2007 ◽  
Vol 54 (4) ◽  
pp. 805-811 ◽  
Author(s):  
Michał Manturewicz ◽  
Zbigniew Grzonka ◽  
Lenka Borovicková ◽  
Jirina Slaninová
Keyword(s):  
Amino Acids ◽  
Solid Phase ◽  
Biological Activities ◽  
Synthesis Method ◽  
Oxytocin Receptor ◽  
Amide Group ◽  
Biologically Active ◽  
Side Chain ◽  
Electronic Effects

Eleven oxytocin analogues substituted in position 4, 5 or 9 by tetrazole analogues of amino acids were prepared using solid-phase peptide synthesis method and tested for rat uterotonic in vitro and pressor activities, as well as for their affinity to human oxytocin receptor. The tetrazolic group has been used as a bioisosteric substitution of carboxylic, ester or amide groups in structure-activity relationship studies of biologically active compounds. Replacement of the amide groups of Gln(4) and Asn(5) in oxytocin by tetrazole analogues of aspartic, glutamic and alpha-aminoadipic acids containing the tetrazole moiety in the side chains leads to analogues with decreased biological activities. Oxytocin analogues in which the glycine amide residue in position 9 was substituted by tetrazole analogues of glycine had diminished activities as well. The analysis of differences in rat uterotonic activity and in the affinity to human oxytocin receptors of analogues containing either an acidic 5-substituted tetrazolic group or a neutral 1,5- or 2,5-tetrazole nucleus makes it possible to draw some new conclusions concerning the role of the amide group of amino acids in positions 4, 5 and 9 of oxytocin for its activity. The data suggest that the interaction of the side chain of Gln(4) with the oxytocin receptor is influenced mainly by electronic effects and the hydrogen bonding capacity of the amide group. Steric effects of the side chain are minor. Substitution of Asn(5) by its tetrazole derivative gave an analogue of very low activity. The result suggests that in the interaction between the amide group of Asn(5) and the binding sites of oxytocic receptor hydrogen bonds are of less importance than the spatial requirements for this group.

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.

NMR and molecular modeling study of active and inactive taxol analogues in aqueous and nonaqueous solution

1994 ◽  
Vol 72 (1) ◽  
pp. 252-260 ◽  
Author(s):  
Howard J. Williams ◽  
A. Ian Scott ◽  
Reiner A. Dieden ◽  
Charles S. Swindell ◽  
Lisa E. Chirlian ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Water Solution ◽  
Biologically Active ◽  
Side Chain ◽  
Coupling Constant ◽  
Solution Conformation ◽  
Solution Structures ◽  
H Nmr ◽  
Chain Conformations ◽  
Inactive Analog

The conformations of the biologically active taxol analogs Taxotere®, 3R, 4R, and 4S, and the biologically inactive analog 3S were evaluated in CDCl3 and DMSO–water solution using 1H NMR coupling constant and NOESY data and molecular modeling. The solution structures of Taxotere® were very similar to those detected previously for taxol. The A-ring side chain conformations of analogs 3 and 4 could not be defined with the same precision as had been possible for taxol, but the conformational possibilities could be significantly limited by the data. Analogs 3R, 4R, and 4S (but not 3S) can mimic the dominant conformation of taxol in chloroform, but no logical relationship between biological activity and aqueous solution conformation could be detected.

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