Search Results - (Author, Cooperation:R. Abagyan)

2015-01-24

American Association for the Advancement of Science (AAAS)

0036-8075

1095-9203

Biology

Chemistry and Pharmacology

Computer Science

Medicine

Natural Sciences in General

Physics

Amino Acid Sequence ; Chemokine CXCL12/chemistry ; Chemokines/*chemistry ; Crystallography, X-Ray ; Drug Design ; Humans ; Models, Chemical ; Molecular Sequence Data ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Receptors, CXCR4/agonists/antagonists & inhibitors/*chemistry ; Structural Homology, Protein

2011-06-24

Nature Publishing Group (NPG)

0028-0836

1476-4687

Biology

Chemistry and Pharmacology

Medicine

Natural Sciences in General

Physics

Binding Sites ; Crystallography, X-Ray ; Doxepin/chemistry/*metabolism ; Histamine Antagonists/chemistry/*metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Isomerism ; Ligands ; Models, Molecular ; Phosphates/chemistry/metabolism ; Protein Binding ; Protein Conformation ; Receptors, Adrenergic, beta-2/chemistry ; Receptors, Dopamine D3/chemistry ; Receptors, Histamine H1/*chemistry/*metabolism ; Substrate Specificity

2015-08-27

Nature Publishing Group (NPG)

0028-0836

1476-4687

Biology

Chemistry and Pharmacology

Medicine

Natural Sciences in General

Physics

2015-07-23

Nature Publishing Group (NPG)

0028-0836

1476-4687

Biology

Chemistry and Pharmacology

Medicine

Natural Sciences in General

Physics

Adult ; Amino Acid Sequence ; Amyloid/chemistry/drug effects/metabolism/ultrastructure ; Animals ; Base Sequence ; Cataract/congenital/*drug therapy/genetics/*metabolism/pathology ; Cell Line ; Child ; Crystallins/chemistry/genetics/metabolism/ultrastructure ; Dogs ; Female ; Humans ; Lanosterol/administration & dosage/*pharmacology/*therapeutic use ; Lens, Crystalline/drug effects/metabolism/pathology ; Male ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/genetics/metabolism/ultrastructure ; Pedigree ; Protein Aggregates/*drug effects ; Protein Aggregation, Pathological/*drug therapy/pathology

0022-2836

energy minimization ; homology modelling ; protein modelling ; protein tertiary structure ; side-chain conformation

Elsevier Journal Backfiles on ScienceDirect 1907 - 2002

Biology

Electronic Resource

0022-2836

Monte Carlo ; NMR structure determination ; conformational search ; global energy minimization ; protein folding

Elsevier Journal Backfiles on ScienceDirect 1907 - 2002

Biology

Electronic Resource

0097-8485

Elsevier Journal Backfiles on ScienceDirect 1907 - 2002

Chemistry and Pharmacology

Electronic Resource

1476-4687

Nature Archives 1869 - 2009

Biology

Chemistry and Pharmacology

Medicine

Natural Sciences in General

Physics

[Auszug] SIR-Nelson et al.1 reported the single-crystal structure of DNA dodecamer containing an oligo(dA)-oligo(dT) tract. This tract is a model of (dA)n-(dT)n that apparently differs from ordinary B-type DNA by some unusual properties, for example: (1) conformational stability; (2) ...

Electronic Resource

1072-8368

Nature Archives 1869 - 2009

Biology

Medicine

[Auszug] Crystallization of the 1:1 molecular complex between the β-lactamase TEM-1 and the β-lactamase inhibitory protein BLIP has provided an opportunity to put a stringent test on current protein-docking algorithms. Prior to the successful determination of the structure of the complex, nine ...

Electronic Resource

0006-3525

Chemistry ; Polymer and Materials Science

Wiley InterScience Backfile Collection 1832-2000

Chemistry and Pharmacology

Monte Carlo simulations [(N, V, T)-ensemble] were performed for the hydration shell of poly(dA-dT)·poly(dA-dT) in canonical B form and for the hydration shell of poly(dA) ·poly(dT) in canonical B conformation and in a conformation with narrow minor groove, highly inclined bases, but with a nearly zero-inclined base pair plane (B′ conformation). We introduced helical periodic boundary conditions with a rather small unit cell and a limited number of water molecules to reduce the dimensionality of the configuration space. The coordinates of local maxima of water density and the properties of one- and two-membered water bridges between polar groups of the DNA were obtained.The AT-alternating duplex hydration mirrors the dyad symmetry of polar group distribution. At the dApdT step, a water bridge between the two carbonyl oxygens O2 of thymines is formed as in the central base-pair step of Dickerson's dodecamer. In the major groove, 5-membered water chains along the tetranucleotide pattern d (TATA) · d (TATA) are observed.The hydration geometry of poly (dA) · poly(dT) in canonical B conformation is distinguished by autonomous primary hydration of the base-pair edges in both grooves. When this polymer adopts a conformation with highly inclined bases and narrow minor groove, the water density distribution in the minor groove is in excellent agreement with Dickerson's spine model. One local maximum per base pair of the first layer is located near the dyad axis between adjacent base pairs, and one local maximum per base pair in the second shell lies near the dyad axis of the base pair itself. The water bridge between the two strands formed within the first layer was observed with high probability. But the water molecules of the second layer do not have a statistically favored orientation necessary for bridging first layer waters. In the major groove, the hydration geometry of the (A · T) base-pair edge resembles the main features of the AT-pair hydration derived from other sequences for the canonical B form. The preference of the B′ conformation for oligo(dA) · oligo(dT) tracts may express the tendency to common hydration of base-pair edges of successive base pairs in the grooves of B-type DNA.The mean potential energy of hydration of canonical B-DNA was estimated to be -60 to -80 kJ/mole nucleotides in dependence on the (G · C) contents. Because of the small system size, this estimation is preliminary.

6 Ill.

Electronic Resource

0006-3525

Chemistry ; Polymer and Materials Science

Wiley InterScience Backfile Collection 1832-2000

Chemistry and Pharmacology

Conformational analysis of triple helics of a type of collagen was performed with typical collagen tripeptide sequences based on Gly-Pro-Ala, Gly-Ala-Hyp, and Gly-Ala-Ala. During energy minimization, the possibility of continual deformation of the pyrrolidine cycle was taken into account in order to achieve better accuracy in the resulting structure. The (Gly-Pro-Ala)n structure is almost isomorphic to the (Gly-Pro-Hyp)n structure obtained in the previous work [Tumanyan, V. G. & Esipova, N.G. (1982) Biopolymers 21, 475-497]. For a collagen-type structure, the optimal conformation of (Gly-Ala-Hyp)n tends to have a decreased unit twist (t = 15°), although the energy advantage with respect to the conformation with t = 45° is not so significant. A similar situation is observed for (Gly-Ala-Ala)n. In this case, the energy decrease during unwinding to t = 15° from t = 45° is quite small. The conformations of (Gly-Ala-Hyp)n and (Gly-Ala-Ala)n with t = 15° exhibit a similarity with a triple complex of polyproline II helices - a noncoiled coil such as (Gly-Pro-Hyp)n and (Gly-Pro-Ala)n. A similar structure may be postulated for subcomponent cq1 of the first component of a human complement containing substantial Gly-X-Pro and Gly-X-Y tripeptide derivatives in the primary structure (X, Y = any amino acid). The results suggest that the observed helical symmetry of collagen (t = 36°) is a consequence of superposition of diffraction patterns (for sufficiently long segments) from various helices (t varies from ∼15° for Gly-X-Hyp and Gly-X-Y to ∼56° for Gly-Pro-Ala). For short alternating segments, some unification of different helical structures is possible.

1 Ill.

Electronic Resource