Backbone dynamics of the A-domain of HMG1 as studied by 15N NMR spectroscopy. 1995

R W Broadhurst, and C H Hardman, and J O Thomas, and E D Laue
Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, UK.

The HMG-box sequence motif (approximately 80 residues) occurs in a number of abundant eukaryotic chromosomal proteins such as HMG1, which binds DNA without sequence specificity, but with "structure specificity", as well as in several sequence-specific transcription factors. HMG1 has two such boxes, A and B, which show approximately 30% sequence identity, and an acidic C-terminal tail. The boxes are responsible for the ability of the protein to bend DNA and bind to bent or distorted DNA. The structure of the HMG box has been determined by NMR spectroscopy for the B-domain of HMG1 [Weir et al. (1993) EMBO J. 12, 1311-1319; Read et al. (1993) Nucleic Acids Res. 21, 3427-3436) and for Drosophila HMG-D (Jones et al. (1994) Structure 2, 609-627]. It has an unusual twisted L-shape, suggesting that the protein might tumble anisotropically in solution. In this paper we report studies of the A-domain from HMG1 using 15N NMR spectroscopy which show that the backbone dynamics of the protein can be described by two different rotational correlation times of 9.0 +/- 0.5 and 10.8 +/- 0.5 ns. We show that the relaxation data can be analyzed by assuming that the protein is a rigid, axially symmetric ellipsoid undergoing anisotropic rotational diffusion; the global rotational diffusion constants, D parallel and D perpendicular, were estimated as 2.47 x 10(7) and 1.49 x 10(7) s-1, respectively. By estimating the angle between the amide bond vectors and the major axis of the rotational diffusion tensor from the family of structures determined by NMR spectroscopy [see accompanying paper, Hardman et al. (1995) Biochemistry 34, 16596-16607], we were able to show that the ellipsoid spectral density equation can reproduce the major features of the 15N T1 and T2 profiles of the three helices in the HMG1 A-domain. The backbone dynamics of the A-domain were then compared with those of the B-domain and the HMG box from HMG-D. This comparison strongly supported the differences observed in the orientation of helix I in the three structures, where the B-domain appears to be more similar to HMG-D than it is to the A-domain. These differences may turn out to be related to subtle differences in the DNA-binding properties of the A- and B-domains of HMG1.

UI MeSH Term Description Entries
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D009587 Nitrogen Isotopes Stable nitrogen atoms that have the same atomic number as the element nitrogen but differ in atomic weight. N-15 is a stable nitrogen isotope. Nitrogen Isotope,Isotope, Nitrogen,Isotopes, Nitrogen
D009682 Magnetic Resonance Spectroscopy Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING). In Vivo NMR Spectroscopy,MR Spectroscopy,Magnetic Resonance,NMR Spectroscopy,NMR Spectroscopy, In Vivo,Nuclear Magnetic Resonance,Spectroscopy, Magnetic Resonance,Spectroscopy, NMR,Spectroscopy, Nuclear Magnetic Resonance,Magnetic Resonance Spectroscopies,Magnetic Resonance, Nuclear,NMR Spectroscopies,Resonance Spectroscopy, Magnetic,Resonance, Magnetic,Resonance, Nuclear Magnetic,Spectroscopies, NMR,Spectroscopy, MR
D011487 Protein Conformation The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). Conformation, Protein,Conformations, Protein,Protein Conformations
D004247 DNA A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). DNA, Double-Stranded,Deoxyribonucleic Acid,ds-DNA,DNA, Double Stranded,Double-Stranded DNA,ds DNA
D004330 Drosophila A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology. Fruit Fly, Drosophila,Drosophila Fruit Flies,Drosophila Fruit Fly,Drosophilas,Flies, Drosophila Fruit,Fly, Drosophila Fruit,Fruit Flies, Drosophila
D006609 High Mobility Group Proteins A family of low-molecular weight, non-histone proteins found in chromatin. HMG Proteins,Calf Thymus Chromatin Protein HMG,High Mobility Group Chromosomal Proteins
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D001665 Binding Sites The parts of a macromolecule that directly participate in its specific combination with another molecule. Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining
D013816 Thermodynamics A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed) Thermodynamic

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