Molecular Modeling of a Functionalized Aib-Based Octapeptide by Molecular Mechanics Calculations Restrained by NMR and Fluorescence Data in DMSO

1997 ◽  
Vol 30 (17) ◽  
pp. 4905-4910 ◽  
Author(s):  
B. Pispisa ◽  
A. Palleschi ◽  
M. E. Amato ◽  
A. L. Segre ◽  
M. Venanzi
Keyword(s):  
Molecular Modeling ◽  
Molecular Mechanics ◽  
Molecular Mechanics Calculations

scholarly journals Conformational Analysis in 18-Membered Macrolactones Based on Molecular Modeling

2011 ◽  
Vol 2011 ◽  
pp. 1-5 ◽  
Author(s):  
Salah Belaidi ◽  
Dalal Harkati
Keyword(s):  
Molecular Dynamics ◽  
Molecular Modeling ◽  
Conformational Analysis ◽  
Molecular Mechanics ◽  
Conformational Flexibility ◽  
Molecular Mechanics Calculations

Conformational analysis of 18-ring membered macrolactones has been carried out using molecular mechanics calculations and molecular dynamics. A high conformational flexibility of macrolactones was obtained, and an important stereoselectivity was observed for the complexed macrolides. For 18d macrolactone, which was presented by a most favored conformer with 20.1% without complex, it was populated with 50.1% in presence of Fe(CO)3.

Molecular Modeling of Slip Supposed to Occur in the Shock Initiation of Crystalline PETN

1992 ◽  
Vol 296 ◽  
Author(s):  
James P. Ritchie
Keyword(s):  
Shear Stress ◽  
Shear Strength ◽  
Molecular Modeling ◽  
Molecular Mechanics ◽  
Molecular Mechanics Calculations ◽  
Rigid Displacement ◽  
Shock Initiation ◽  
Flexible Molecules ◽  
Finite Lattices ◽  
Molecular Deformations

AbstractSome molecular modeling of slip using both rigid and flexible molecules of PETN in perfect, but finite, lattices has been performed. Studies of rigid displacement show slip on (001)<010> to be relatively unhindered. The shock orientation with a maximum resolved shear stress in this direction would, therefore, be expected to be insensitive. Molecular mechanics calculations have also been performed. The results show that it is likely that molecular deformations occur and have an important effect in determining the shear strength of crystalline PETN.

scholarly journals Inclusion Complexes of Sunscreen Agents withβ-Cyclodextrin: Spectroscopic and Molecular Modeling Studies

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Nathir A. F. Al-Rawashdeh ◽  
Khaled S. Al-Sadeh ◽  
Mohammad Bassam Al-Bitar
Keyword(s):  
Molecular Modeling ◽  
Molecular Mechanics ◽  
Inclusion Complexes ◽  
Dynamic Features ◽  
Scanning Calorimetry ◽  
Molecular Mechanics Calculations ◽  
Vis Spectroscopy ◽  
Nmr Techniques ◽  
Sunscreen Agents ◽  
C Nmr

The inclusion complexes of selected sunscreen agents, namely, oxybenzone (Oxy), octocrylene (Oct), and ethylhexyl-methoxycinnamate (Cin) withβ-cyclodextrin (β-CD) were studied by UV-Vis spectroscopy, differential scanning calorimetry (DSC),13C NMR techniques, and molecular mechanics (MM) calculations and modeling. Molecular modeling (MM) study of the entire process of the formation of 1 : 1 stoichiometry sunscreen agent/β-cyclodextrin structures has been used to contribute to the understanding and rationalization of the experimental results. Molecular mechanics calculations, together with13C NMR measurements, for the complex withβ-CD have been used to describe details of the structural, energetic, and dynamic features of host-guest complex. Accurate structures of CD inclusion complexes have been derived from molecular mechanics (MM) calculations and modeling. The photodegradation reaction of the sunscreen agents' molecules in lotion was explored using UV-Vis spectroscopy. It has been demonstrated that the photostability of these selected sunscreen agents has been enhanced upon forming inclusion complexes withβ-CD in lotion. The results of this study demonstrate thatβ-CD can be utilized as photostabilizer additive for enhancing the photostability of the selected sunscreen agents' molecules.

The conformational properties of calix[4]arenes 1h NMR and molecular mechanics calculations

1989 ◽  
Vol 86 ◽  
pp. 945-954 ◽  
Author(s):  
F. Bayard ◽  
D. Decoret ◽  
D. Pattou ◽  
J. Royer ◽  
A. Satrallah ◽  
...  
Keyword(s):  
Molecular Mechanics ◽  
1H Nmr ◽  
Molecular Mechanics Calculations ◽  
Conformational Properties

scholarly journals THU0017 ATTEMPTS TO LINK EXONIC GENE POLYMORPHISMS TO SYSTEMIC LUPUS ERYTHEMATOSUS (SLE)-ASSOCIATED PROTEIN MODIFIED FUNCTIONALITY: A STRUCTURAL BIOLOGY APPROACH

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 221.1-222
Author(s):  
E. Eliopoulos ◽  
G. Goulielmos ◽  
M. Matalliotakis ◽  
D. Vlachakis ◽  
T. Niewold ◽  
...  
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Protein Structure ◽  
Molecular Modeling ◽  
Nucleic Acid ◽  
Molecular Mechanics ◽  
Lupus Erythematosus ◽  
Gene Polymorphisms ◽  
Association Studies ◽  
Systemic Lupus ◽  
Molecular Graphics

Background:Gene association studies and genome wide association studies (GWAS) have played a primary role in depicting genetic contributions to systemic lupus erythematosus (SLE) development, while accommodating the exonic polymorphisms on the protein structure level, when available, enhances our understanding of protein function modification or depletion. Linking human genetics with therapeutic targets requires the biological function of the causal gene and variant to be known.Objectives:To investigate recently identified SLE-associated functional gene polymorphisms, such asPARP1,ITGAM, TNFAIP3, NCF1, PON1, IFIH1, SH2B3andTYK2[1-4] by correlation to protein structure and function.Methods:Three-dimensional (3D) homology modeling and molecular mechanics/dynamics studies were applied for the localization of the polymorphisms under study on the respective proteins. The mutants were constructed using molecular modeling with the program Maestro (Schrodinger, LLC), which was also used to analyze the conformational changes caused by the mutation. All figures depicting 3D models were created using the molecular graphics program PyMOL V.2.2 [5].Results:Modeling revealed that rs1136410 SNP encodes the less common polymorphism Val762Ala onPARP1that reduces enzymatic activity of Poly(ADP-ribose) polymerase 1 (Figure 1),ITGAMpolymorphism rs1143679 (Arg77His) on Integrin alpha M, component of the macrophage-1 antigen complex affects protein surface recognition,TNFAIP3rs2230926 polymorphism encodes Cys instead of Phe at residue 127 of the ubiquitin editing A20 protein, while rs201802880 polymorphism of the neutrophil cytosolic factor 1 (NCF1) gene modifies the function of the cytosolic subunit of neutrophil NADPH oxidase with the mutation Arg90His.PON1is involved in the oxidative stress process that cause tissue damage observed in SLE and anti-phospholipid syndrome (APS). ThePON1Gln192Arg mutation (rs662 SNP) affects shape and recognition of the ligand recognition site as part of the evolutionary process, whileIFIH1(rs35667974) helicase C domain1 mutant I923V is located on an essential RNA beta loop interacting directly with the nucleic acid (Figure 2). Finally, the rs3184504 SNP ofSH2B3gene generates mutant Arg262Trp on SH2 adapter protein 3, acting as a signaling pathway involved in autoimmune disorders, while inTYK2 gene, one of the Janus kinases, the rs35018800 producing mutant Ala928Val modifies the ADP binding site.Figure 1.Details of the Val762 interaction where V762A mutation occurs in PARP1protein.Figure 2.Nucleic acid interacting IFIH1 helicase beta-loop where I923V mutation occurs (in purple).Conclusion:Based on several examples, we have tried to define a rational link from SLE-associated gene polymorphisms to structure and to modified function, including metagenomic analysis of SNPs, protein crystallography, protein molecular modeling, molecular mechanics and dynamics. Locating, shaping and understanding the target protein interaction interface plays a decisive role in most cases and provides clues for further pharmacological or medical actions [6].References:[1]Hur JW et al (2006). Rheumatology 45:711-7[2]Maiti AK et al (2014). Hum Mol Genet 23:4161-76[3]Shimane K et al (2010). Arthritis Rheum. 62:574-9[4]Linge P et al (2019). Ann Rheum Dis. 2019 Nov 8. pii: annrheumdis-2019-215820[5]Schrödinger LLC: The PyMOL Molecular Graphics System 2016 version 2.2. Available from: pymol.org/2/support.html[6]Plenge RM et al (2013). Nat Rev Drug Discov 12:581–94Disclosure of Interests:None declared

Molecular Mechanics Calculations and the Metal Ion Selective Extraction of Lanthanoids

1998 ◽  
Vol 37 (13) ◽  
pp. 3310-3315 ◽  
Author(s):  
Peter Comba ◽  
Karsten Gloe ◽  
Katsutoshi Inoue ◽  
Torsten Krüger ◽  
Holger Stephan ◽  
...  
Keyword(s):  
Molecular Mechanics ◽  
Metal Ion ◽  
Selective Extraction ◽  
Molecular Mechanics Calculations
Sign in / Sign up

Export Citation Format

Share Document