A Computational Study of Partially Modified Retro-Inverso Valine Dipeptides:  Effect of the Side Chain on the Conformational Preferences of Malonyl andgem-Diamino Residues

2001 ◽  
Vol 105 (4) ◽  
pp. 860-866 ◽  
Author(s):  
Carlos Alemán
Keyword(s):  
Computational Study ◽  
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 Steroid Hydroxylation by Basidiomycete Peroxygenases: a Combined Experimental and Computational Study

2015 ◽  
Vol 81 (12) ◽  
pp. 4130-4142 ◽  
Author(s):  
Esteban D. Babot ◽  
José C. del Río ◽  
Marina Cañellas ◽  
Ferran Sancho ◽  
Fátima Lucas ◽  
...  
Keyword(s):  
Computational Study ◽  
Biological Activities ◽  
Side Chain ◽  
Enzymatic Reactions ◽  
Fungal Enzymes ◽  
Content Type ◽  
Protein Energy ◽  
Esterified Sterols ◽  
Ligand Diffusion ◽  
Protein Energy Landscape

ABSTRACTThe goal of this study is the selective oxyfunctionalization of steroids under mild and environmentally friendly conditions using fungal enzymes. With this purpose, peroxygenases from three basidiomycete species were tested for the hydroxylation of a variety of steroidal compounds, using H2O2as the only cosubstrate. Two of them are wild-type enzymes fromAgrocybe aegeritaandMarasmius rotula, and the third one is a recombinant enzyme fromCoprinopsis cinerea. The enzymatic reactions on free and esterified sterols, steroid hydrocarbons, and ketones were monitored by gas chromatography, and the products were identified by mass spectrometry. Hydroxylation at the side chain over the steroidal rings was preferred, with the 25-hydroxyderivatives predominating. Interestingly, antiviral and other biological activities of 25-hydroxycholesterol have been reported recently (M. Blanc et al., Immunity 38:106–118, 2013,http://dx.doi.org/10.1016/j.immuni.2012.11.004). However, hydroxylation in the ring moiety and terminal hydroxylation at the side chain also was observed in some steroids, the former favored by the absence of oxygenated groups at C-3 and by the presence of conjugated double bonds in the rings. To understand the yield and selectivity differences between the different steroids, a computational study was performed using Protein Energy Landscape Exploration (PELE) software for dynamic ligand diffusion. These simulations showed that the active-site geometry and hydrophobicity favors the entrance of the steroid side chain, while the entrance of the ring is energetically penalized. Also, a direct correlation between the conversion rate and the side chain entrance ratio could be established that explains the various reaction yields observed.

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.

Computational study on the conformational preferences in nateglinide

2011 ◽  
Vol 25 (8) ◽  
pp. 649-657 ◽  
Author(s):  
Vaibhav Jain ◽  
Devendra Kumar Dhaked ◽  
Yoganjaneyulu Kasetti ◽  
P. V. Bharatam
Keyword(s):  
Computational Study ◽  
Conformational Preferences

Computational study of conformational preferences of thioamide-containing azaglycine peptides

2003 ◽  
Vol 25 (2) ◽  
pp. 169-178 ◽  
Author(s):  
Ho-Jin Lee ◽  
Jong Hyun Kim ◽  
Hee Jung Jung ◽  
Kun-Young Kim ◽  
Eun-Jung Kim ◽  
...  
Keyword(s):  
Computational Study ◽  
Conformational Preferences
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