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Conversation 10: Proceedings

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Structure, Motion, Interaction and Expression of Biological Macromolecules Volumes One and Two, Hard Cover 1998

The Proceedings of the Tenth Conversation held at The University-SUNY, Albany NY, June 17-21, 1997

Editors: Sarma & Sarma

ISBN: 0-940030-76-4 Volume 1;
ISBN: 0-940030-77-2 Volume 2;
ISBN: 0-940030-75-6 2 Volume Set

Just like the Conversation program, they constitute a tour de force in the discipline.

Structure, Motion, Interaction and Expression of Biological Macromolecules Volume 2

Theoretical foundations and a global overview of the known protein structures; induced conformational changes upon protein-protein association; regulatory apparatus of pp60c-Src protein; protein dynamics and NMR relaxation; structure, dynamics and function of metalloproteins.

tRNA recognition by aspartyl-tRNA synthase; RNA pseudoknots and 3D domain swaping; RNA psedoknots and RNA topoisomerase; theretical modeling of RNA 3-D structures; retroviral RNA-tetraloop substructure of the HIV-1 packaging signal; interactions of the HIV-1 rev protein with RRE RNA; structure of 5' stem-loop from human U4 snRNA; 750 MHz NMR and computer experiments on an anti-HIV-1 hammerhead ribozyme complex; ligation of hairpin ribozymes; exploration of G?U pairs in RNA by 15N NMR.

Triplet repeat genome and human diseases: trinucleotide repeat instability and slipped strand DNA; genetic control of microsatellite DNA instability; molecular dynamics of triplet repeats and mismatch pairs; molecular basis of triplet expansion; length polymorphism and gene regulation.

p53 tumor suppressor protein: DNA bending and steric constraints on conformation by p53; interactions between the p53 DNA binding domain and a DNA response element.

Volume 2, in its 296 pages, contains 23 chapters with 941 references to literature, 20 tables and 193 figures; 44 of the figures are four-color processed renditions.

Editors: Sarma & Sarma

Contents Volume 2

The Kappa-Tau Framework for Describing and Analyzing Protein Folds: Theoretical Foundations and a Global Overview of the Known Protein Structures
Dikeos Mario Soumpasis and Martin Christian Strahm

Molecular Surface Variability and Induced Conformational Changes Upon Protein-Protein Association
Raquel Norel, Shou L. Lin, Dong Xu, Haim J. Wolfson and Ruth Nussinov

The conformational change of Tyr-248 from the unbound to the bound state in protein-protein association from Nussinov et al.

Mechanisms of Regulation in the Regulatory Apparatus of pp60c-Src
Jeffery L. Reinking, Lisa N. Gentile, Marco Tessari, Geerten Vuister and Linda K. Nicholson

Studying Protein Dynamics with NMR Relaxation
David Fushman and David Cowburn

How Does the Oxidation State of a Metalloprotein Affect its Structure, Dynamics and Function?
Thomas C. Pochapsky, Tracy Arakaki, Nitin Jain, Sophia Kazanis, Teresa A. Lyons, Huaping Mo, Alexandra Patera, Gayathri Ratnaswamy and Xiaomei Ye

Enzyme-substrate Interactions in the Aspartyl-tRNA Synthetase System
John G. Arnez and Dino Moras

The Structure of an RNA Pseudoknot Shows 3D Domain Swapping
Susan E. Lietzke, Cindy L. Barnes, Vincent F. Malone, Joshua T. Jones and Craig E. Kundrot

The Construction of an RNA Knot and its Role in Demonstrating that E. coli DNA Topoisomerase III is an RNA Topoisomerase
Hui Wang, Russell J. Di Gate and Nadrian C. Seeman

A Reduced-Coordinate Approach to Modeling RNA 3-D Structures
Chang-Shung Tung

Packaging and Dimer Linkage in Retroviral RNA: NMR of a GGAG-tetraloop Substructure of the HIV-1 Packaging Signal
Lucia Pappalardo, Cui Liu, István Pelczer and Philip N. Borer

Design and Analysis of Organic Cations that Inhibit Interactions of the HIV-1 Rev Protein with RRE RNA
Ke Li, Ge Xiao, Ted Rigl, Arvind Kumar, David W. Boykin and W. David Wilson

Structure of the 5' Stem-Loop From Human U4 snRNA: Evidence for Destabilization of a Compact Conformation by 5-FU
William H. Gmeiner, Parag V. Sahasrabudhe and Junqu Sun

Freezing-induced Self-ligation of the Hairpin Ribozyme: Cationic Effects
Sergei A. Kazakov, Svetlana V. Balatskaya and Brian H. Johnston

750 MHz NMR and Computer Experiments on an Anti-HIV-1 Hammerhead Ribozyme Complex with a 17-mer DNA Substrate Analog of HIV-1 gag RNA
Rajendra P. Ojha, Madan M. Dhingra, Mukti H. Sarma, Yash P. Myer, Robert F. Setlik, Masayuki Shibata, A. Latiff Kazim, Rick L. Ornstein, Robert Rein, Christopher J. Turner and Ramaswamy H. Sarma

Probing G·U Pairing in RNA Using 15N NMR
Xiaohu Zhang, Barbara L. Gaffney and Roger A. Jones

Studies of the Dynamics of Adenine Amino Protons in DNA by 15N-Labeling and Heteronuclear NMR Spectroscopy
Ryszard Michalczyk and Irina M. Russu

Slipped Strand DNA (S-DNA and SI-DNA), Trinucleotide Repeat Instability and Mismatch Repair: A Short Review
Christopher E. Pearson and Richard R. Sinden

Genetic Control of Microsatellite Instability in Saccharomyces Cerevisiae
E. A. Sia, R. J. Kokoska, M. Dominska, P. Greenwell and T. D. Petes

Molecular Dynamics Simulations of DNA Molecules Containing d(GCC)n..d(GCC)n Fragments and C-C Mismatch Pairs
Rebecca M. Romero, Huai Yong Cheng, Michael Mitas and Ian S. Haworth

Toward the Understanding of the Molecular Basis of Triplet Expansion. Studies of the Single Stranded CCG and CGG DNA Trinucleotide Repeats by NMR
Xuening Huang and Xiaolian Gao

Structure-Function Relationship of the Insulin-Linked Polymorphic Region: Implications in Length Polymorphism and Gene Regulation
Paolo Catasti, Xian Chen, E. Morton Bradbury and Goutam Gupta

Interactions Between the P53 DNA Binding Domain and the P21/Waf1/Cip1 DNA Response Element
A. K. Nagaich, P. Balagurumoorthy, W. M. Miller, E. Appella, V. B. Zhurkin and R. E. Harrington

DNA Bending Induced by Tetrameric Binding of the p53 Tumor Suppressor Protein: Steric Constraints on Conformation
Stewart R. Durell, Robert L. Jernigan, Ettore Appella, Akhilesh K. Nagaich, Rodney E. Harrington and Victor B. Zhurkin

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