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  • 1
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 108 (1986), S. 5732-5737 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 0948-5023
    Keywords: Keywords Major histocompatibility compound, Human leukocyte antigen, HLA complexes with peptides, Molecular modeling, Ligand docking
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The three-dimensional structure of human leukocyte antigens HLA-DR*0301 and HLA-DR*0302 have been calculated using the homology modeling approach. General structural features of our models are similar to those of related HLA molecules. The typical layout of segments of the secondary structure is well preserved. However polypeptide chains are less tightly bound, which causes slightly broader opening of the binding groove. It also results in the modified layout of pockets in the binding groove. Amino acids defining the restricted sequence diversity of studied proteins are easily available for interactions with ligands. A set of docking simulations was performed using modeled structures of both HLA molecules and various specific peptide ligands. The control docking of influenza hemagglutinin peptide into HLA-DR*0101 molecule gives the complex structure which is in good agreement with that from crystallographic studies. The extensive analysis of the structure of modeled complexes of HLA-DR*0301 and HLA-DR*0302 with various ligands indicates that sequence microvariation of both alleles is not directly controlling the binding specificity. Preferences for binding of specific ligands, as evaluated from interactions in modeled complexes, agree qualitatively with experimental observations. Thus the computer aided docking simulations can be successfully used to calculate the three-dimensional structure of HLA-ligand complexes. However detailed explanation of binding specificity can not be achieved using presently available modeling procedures.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 16 (1979), S. 293-298 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The role of some amino acids and metal ions in the catalytic activity of carbonic anhydrase (carbonate dehydratase EC 4.2.1.1) has been investigated. The additional stabilization of the transition state complex was used as the qualitative measure of the effect of molecular surrounding on CO2 hydration reaction calculated within the approximate CNDO/2 approach. The effect of the molecular environment has been simulated by inclusion into the SCF LCAO MO Hamiltonian, a term representing the interaction with a set of point charges and atomic dipoles centered on experimentally determined position of Zn2+ ion and all atoms of histidine 94, 96, 119 and threonine 199, 200 (or histidine 200 in the case of carbonic anhydrase B). The possible molecular mechanism of CO2 hydration inside the active site has been also discussed.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 666-672 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Electron correlation corrections have a considerable influence on the relative stabilities of lithium isocyanide (1), lithium cyanide (2), and the bridged form, 3. While Hartree-Fock theory finds 1 to be most stable and 3 not to be a minimum, MP2/6-31G* optimization indicates 3 to be the global minimum. At higher levels employing full fourth-order Møller-Plesset theory and a quadruply split valence and polarized basis set (MP4STDQ/6-311+G*), 2 is only about 2 kcal/mol less stable than 1 and 3, which are indicated to have nearly the same energy. LiNC thus is similar to C(Na)N and C(K)N, both of which are known to prefer T-shaped (bridged) structures in the gas phase. However, to an even greater extent than formerly realized, rotation of the lithium cation around the cyanide anion nucleus should be practically free. ΔHf298O (LiCN) = 32.8 kcal/mol is estimated from the calculated lithium cation affinity of 151.2 kcal/mol. In addition, we find at the MP4SDTQ/6-31+G*//MP2/6-31G* level that the bridged form of NaCN is favored by 2-3 kcal/mol over the corresponding linear forms, which have nearly the same energy.
    Additional Material: 6 Tab.
    Type of Medium: Electronic Resource
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