Protein structures in solution by nuclear magnetic resonance and distance geometry. The polypeptide fold of the basic pancreatic trypsin inhibitor determined using two different algorithms, DISGEO and DISMAN |
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| Authors: | G Wagner W Braun T F Havel T Schaumann N Go K Wüthrich |
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| Affiliation: | 1. Institut für Molekularbiologie und Biophysik Eidgenössische Technische Hochschule-Hönggerberg, CH-8093 Zürich, Switzerland;2. Department of Physics Kyushu University 33 Fukuoka 812, Japan;1. Department of Chemistry, Rhodes University, Grahamstown 6140, South Africa;2. Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa;3. Biomedical Biotechnology Research Unit (BioBRU), Rhodes University, Grahamstown 6140, South Africa;4. Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown 6140, South Africa;1. Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Avenue, Farmington, CT 06030-3305, USA;2. Rowland Institute at Harvard, 100 Edwin H. Land Boulevard, Cambridge, MA 02142, USA;1. A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, bld. 2, 119071, Moscow, Russian Federation;2. Institute of Mathematical Problems of Biology, RAS, Institutskaya str. 4, Pushchino, 142290, Russian Federation;3. M.K. Ammosov North-Eastern Federal University, Belinskiy str., 58, Suite 312, Yakutsk, 677980, Republic of Sakha (Yakutia), Russian Federation;4. Dep. “Protein Factory”, NBICS Center, National Research Centre “Kurchatov Institute”, Akad. Kurchatova sqr., 1, Moscow, 123182, Russian Federation;1. Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany;2. Institute of Biochemistry, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany;3. Vertex Pharmaceuticals Inc., Cambridge, MA 02139, USA |
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| Abstract: | A set of conformational restraints derived from nuclear magnetic resonance (n.m.r.) measurements on solutions of the basic pancreatic trypsin inhibitor (BPTI) was used as input for distance geometry calculations with the programs DISGEO and DISMAN. Five structures obtained with each of these algorithms were systematically compared among themselves and with the crystal structure of BPTI. It is clear that the protein architecture observed in single crystals of BPTI is largely preserved in aqueous solution, with local structural differences mainly confined to the protein surface. The results confirm that protein conformations determined in solution by combined use of n.m.r. and distance geometry are a consequence of the experimental data and do not depend significantly on the algorithm used for the structure determination. The data obtained further provide an illustration that long intramolecular distances in proteins, which are comparable with the radius of gyration, are defined with high precision by relatively imprecise nuclear Overhauser enhancement measurements of a large number of much shorter distances. |
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