Molecular Graphics, Computer Modeling, and Sequence Analysis

Trus, B L.

Abstract

The sequence of some regular proteins, when correlated with other structural information, such as data from x-ray diffraction, fiber diffraction, electron microscopy, and spectroscopic analysis, can be used to evaluate models of protein or polymer structure. Four current studies involve the sequence analysis of keratin and other intermediate filaments (with NIAMS, NCI); sequence analysis of streptococcal proteins (with Rockefeller University); and computer models of biopolymers (with PSL, DCRT), and analysis of protein sequences from viruses and bacteria (with NIAMS, FIC). As new sequences of regular (helical) proteins become available, it will be relatively easy to model these sequences and describe their structures both graphically and quantitatively.

Funding Agency

• Agency: National Institute of Health (NIH)
• Institute: Center for Information Technology (CIT)
• Type: Intramural Research (Z01)
• Project #: 1Z01CT000090-08
• Application #: 3916959
• Support Year: 8
• Fiscal Year: 1988

Institution

• Name: Computer Research and Technology
• Country: United States

Publications

Zuo, Xiaobing; Wang, Jingbu; Foster, Trenton R et al. (2008) Global molecular structure and interfaces: refining an RNA:RNA complex structure using solution X-ray scattering data. J Am Chem Soc 130:3292-3

Schwieters, Charles D; Clore, G Marius (2008) A pseudopotential for improving the packing of ellipsoidal protein structures determined from NMR data. J Phys Chem B 112:6070-3

Kuszewski, John J; Thottungal, Robin Augustine; Clore, G Marius et al. (2008) Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm. J Biomol NMR 41:221-39

Buck, Christopher B; Cheng, Naiqian; Thompson, Cynthia D et al. (2008) Arrangement of L2 within the papillomavirus capsid. J Virol 82:5190-7

Tang, Chun; Schwieters, Charles D; Clore, G Marius (2007) Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR. Nature 449:1078-82

Schwieters, Charles D; Clore, G Marius (2007) A physical picture of atomic motions within the Dickerson DNA dodecamer in solution derived from joint ensemble refinement against NMR and large-angle X-ray scattering data. Biochemistry 46:1152-66

Luque, Daniel; Saugar, Irene; Rodriguez, Jose F et al. (2007) Infectious bursal disease virus capsid assembly and maturation by structural rearrangements of a transient molecular switch. J Virol 81:6869-78

Calabrese, Massimiliano; Atzori, Matteo; Bernardi, Valentina et al. (2007) Cortical atrophy is relevant in multiple sclerosis at clinical onset. J Neurol 254:1212-20

Bazin, Pierre-Louis; Cuzzocreo, Jennifer L; Yassa, Michael A et al. (2007) Volumetric neuroimage analysis extensions for the MIPAV software package. J Neurosci Methods 165:111-21

Trus, Benes L; Newcomb, William W; Cheng, Naiqian et al. (2007) Allosteric signaling and a nuclear exit strategy: binding of UL25/UL17 heterodimers to DNA-Filled HSV-1 capsids. Mol Cell 26:479-89