scholarly journals Understanding the physical basis for the side-chain conformational preferences of methionine

2016 ◽  
Vol 84 (7) ◽  
pp. 900-911 ◽  
Author(s):  
Alejandro Virrueta ◽  
Corey S. O'Hern ◽  
Lynne Regan
Keyword(s):  
Physical Basis ◽  
Side Chain ◽  
Conformational Preferences

A proton magnetie resonance and molecular orbital study of the conformational preferences of the vinylic fragment in some 2-vinylfurans and in 2-vinylthiophene

1976 ◽  
Vol 54 (20) ◽  
pp. 3216-3223 ◽  
Author(s):  
William J. E. Parr ◽  
Roderick E. Wasylishen ◽  
Ted Schaefer
Keyword(s):  
Molecular Orbital ◽  
Long Range ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Side Chain ◽  
Orbital Theory ◽  
Molecular Orbital Study ◽  
Conformational Preferences ◽  
Spin Coupling Constants ◽  
Spin Spin Coupling

The stereospecific spin–spin coupling constants over five bonds between the α-proton in the side chain and the protons in the heterocycle in 2-vinylfuran, in its β-nitro and β-aldehydic derivatives, and in 2-vinylthiophene are used to demonstrate the preponderance of the s-trans conformers in polar and nonpolar solutions. These conclusions are compared with predictions made by molecular orbital theory at the STO-3G, INDO, CNDO/2, and MINDO/3 levels. Long-range coupling constants between the protons in the side chain and protons in the heterocycle are calculated by CNDO/2 and INDO–MO–FPT and are compared with experiment. It is concluded that the five-bond couplings involving the α-proton are most sensitive to conformation and that they are transmitted mainly via a σ electron mechanism. The other long-range coupling constants are discussed in terms of σ and π electron mechanisms. The STO-3G calculations yield barriers to internal rotation of greater than 4.8 kcal/mol.

scholarly journals Glycine in Water Favors the Polyproline II State

Biomolecules ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1121 ◽  
Author(s):  
Brian Andrews ◽  
Shuting Zhang ◽  
Reinhard Schweitzer-Stenner ◽  
Brigita Urbanc
Keyword(s):  
Amino Acid ◽  
Spectroscopic Data ◽  
Heavy Atom ◽  
Conformational Space ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Glycine Residue ◽  
Polyproline Ii ◽  
Conformational Preferences ◽  
Central Residue

Conformational preferences of amino acid residues in water are determined by the backbone and side-chain properties. Alanine is known for its high polyproline II (pPII) propensity. The question of relative contributions of the backbone and side chain to the conformational preferences of alanine and other amino acid residues in water is not fully resolved. Because glycine lacks a heavy-atom side chain, glycine-based peptides can be used to examine to which extent the backbone properties affect the conformational space. Here, we use published spectroscopic data for the central glycine residue of cationic triglycine in water to demonstrate that its conformational space is dominated by the pPII state. We assess three commonly used molecular dynamics (MD) force fields with respect to their ability to capture the conformational preferences of the central glycine residue in triglycine. We show that pPII is the mesostate that enables the functional backbone groups of the central residue to form the most hydrogen bonds with water. Our results indicate that the pPII propensity of the central glycine in GGG is comparable to that of alanine in GAG, implying that the water-backbone hydrogen bonding is responsible for the high pPII content of these residues.

scholarly journals Side-Chain Conformational Preferences Govern Protein–Protein Interactions

2016 ◽  
Vol 138 (33) ◽  
pp. 10386-10389 ◽  
Author(s):  
Andrew M. Watkins ◽  
Richard Bonneau ◽  
Paramjit S. Arora
Keyword(s):  
Protein Interactions ◽  
Side Chain ◽  
Protein Protein Interactions ◽  
Conformational Preferences

scholarly journals Effects of charge states, charge sites and side chain interactions on conformational preferences of a series of model peptide ions

The Analyst ◽  
2015 ◽  
Vol 140 (20) ◽  
pp. 6933-6944 ◽  
Author(s):  
Chunying Xiao ◽  
Lisa M. Pérez ◽  
David H. Russell
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Gas Phase ◽  
Dynamics Simulation ◽  
Side Chain ◽  
Peptide Ions ◽  
Conformational Preference ◽  
Model Peptide ◽  
Factors Affecting ◽  
Conformational Preferences

The factors affecting conformational preference of gas phase peptide ions are investigated by IM-MS and molecular dynamics simulation.

Spin–spin coupling constants between side-chain and ring fluorine nuclei in some benzotrifluoride, benzal fluoride, and benzyl fluoride derivatives: coupling mechanisms

1979 ◽  
Vol 57 (7) ◽  
pp. 807-812 ◽  
Author(s):  
Ted Schaefer ◽  
Walter Niemczura ◽  
Chiu-Ming Wong ◽  
Kirk Marat
Keyword(s):  
Nmr Spectra ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Complete Analysis ◽  
Side Chain ◽  
Coupling Mechanism ◽  
Conformational Preferences ◽  
Spin Coupling Constants ◽  
Spin Spin Coupling ◽  
Coupling Mechanisms

A complete analysis of the 1H and 19F nmr spectra of 2,5- and 3,4-difluorobenzotrifluoride, together with multiple resonance experiments, yields the signs and magnitudes of the long-range 19F,19F and 1H,19F spin–spin coupling constants. The coupling mechanisms are discussed. In particular, the coupling over six bonds, [Formula: see text], whose sign is interpretable in terms of a σ–π mechanism, is too large in magnitude when compared to [Formula: see text], and [Formula: see text] in the analogous compounds. These latter three couplings are consistent in sign and magnitude with what is known about hyperfine interaction constants. The magnitudes of [Formula: see text] are reported for 4-fluorobenzotrifluoride, 3-amino-4-fluorobenzotrifluoride, 3-nitro-4-fluorobenzotrifluoride, as are 6JpF,F values for p-fluorobenzal fluoride and p-fluorobenzyl fluoride. In contrast to 6JpH,CH and 6JpF,CH it seems unlikely that, unless its coupling mechanism becomes more precisely understood, 6JpF,CF will be a reliable indicator of conformational preferences.

Conformational studies of hydantoin-5-acetic acid and orotic acid

2012 ◽  
Vol 68 (2) ◽  
pp. o92-o98 ◽  
Author(s):  
Valeska Gerhardt ◽  
Maya Tutughamiarso ◽  
Michael Bolte
Keyword(s):  
Hydrogen Bonding ◽  
Acetic Acid ◽  
Orotic Acid ◽  
Three Dimensional ◽  
Side Chain ◽  
Dimensional Network ◽  
Conformational Preferences ◽  
Donor Acceptor ◽  
Acid Function ◽  
Hydrogen Bonding Site

Hydantoin-5-acetic acid [2-(2,5-dioxoimidazolidin-4-yl)acetic acid] and orotic acid (2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid) each contain one rigid acceptor–donor–acceptor hydrogen-bonding site and a flexible side chain, which can adopt different conformations. Since both compounds may be used as coformers for supramolecular complexes, they have been crystallized in order to examine their conformational preferences, giving solvent-free hydantoin-5-acetic acid, C5H6N2O4, (I), and three crystals containing orotic acid, namely, orotic acid dimethyl sulfoxide monosolvate, C5H4N2O4·C2H6OS, (IIa), dimethylammonium orotate–orotic acid (1/1), C2H8N+·C5H3N2O4−·C5H4N2O4, (IIb), and dimethylammonium orotate–orotic acid (3/1), 3C2H8N+·3C5H3N2O4−·C5H4N2O4, (IIc). The crystal structure of (I) shows a three-dimensional network, with the acid function located perpendicular to the ring. Interestingly, the hydroxy O atom acts as an acceptor, even though the carbonyl O atom is not involved in any hydrogen bonds. However, in (IIa), (IIb) and (IIc), the acid functions are only slightly twisted out of the ring planes. All H atoms of the acidic functions are directed away from the rings and, with respect to the carbonyl O atoms, they show an antiperiplanar conformation in (I) and synperiplanar conformations in (IIa), (IIb) and (IIc). Furthermore, in (IIa), (IIb) and (IIc), different conformations of the acid O=C—C—N torsion angle are observed, leading to different hydrogen-bonding arrangements depending on their conformation and composition.

scholarly journals The Protein Geometry Database: exploring protein conformational features

2014 ◽  
Vol 70 (a1) ◽  
pp. C499-C499
Author(s):  
Dale Tronrud ◽  
P. Karplus
Keyword(s):  
Bond Angle ◽  
Side Chain ◽  
Peptide Fragments ◽  
Search Form ◽  
Conformational Preferences ◽  
Peptide Unit ◽  
Chain Conformations ◽  
Cis Peptides ◽  
Validation Tool

Have you ever seen a feature in your structure and asked, "I wonder how novel this is?" For instance a residue with a certain phi/psi angle, or an Asp residue followed by three further residues that make a tight turn centered on the side chain, or a peptide unit deviating 25° from planarity? If so, the Protein Geometry Database (PGD) is something you'll want to know about. The PGD web service (pgd.science.oregonstate.edu, Berkholz 2009a) manages access to a database containing the geometric details of 1.9 million amino acids. Working with the PGD involves two easy steps - using a search form to find a set of peptides matching your interests, and analyzing the geometric details of the set. The search form allows you to find examples of peptide fragments that have any specified combination of backbone conformations and sequence. Filtering can also be performed based on side chain conformations, or bond angles. You can also specify the quality of models included in the search. Once a set of peptides has been identified, their geometric properties can be analyzed on the web site. You can look at the averages and standard deviations for any bond length, bond angle, or conformational angle, or you can explore relationships between properties by displaying highly customizable plots. An option to export the search results allows you to perform any further analyses you might devise. We will show how the PGD has been used to develop a Conformation Dependent Library of main chain bond angle targets for crystallographic refinement (Berkholz 2009b), as well as to advance our understanding of peptide non-planarity, and of conformational preferences for pairs of residues and of cis-peptides. We will also describe how simple searches for outliers in bond lengths and angles are a powerful validation tool that can both uncovering errors in PDB models and can lead to the discovery of very interesting and real deviations from what is normally considered ideal geometry.

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