53 research outputs found
Solution NMR views of dynamical ordering of biomacromolecules.
No full textTo understand the mechanisms related to the 'dynamical ordering' of macromolecules and biological systems, it is crucial to monitor, in detail, molecular interactions and their dynamics across multiple timescales. Solution nuclear magnetic resonance (NMR) spectroscopy is an ideal tool that can investigate biophysical events at the atomic level, in near-physiological buffer solutions, or even inside cells. Scope of Review In the past several decades, progress in solution NMR has significantly contributed to the elucidation of three-dimensional structures, the understanding of conformational motions, and the underlying thermodynamic and kinetic properties of biomacromolecules. This review discusses recent methodological development of NMR, their applications and some of the remaining challenges. Major Conclusions Although a major drawback of NMR is its difficulty in studying the dynamical ordering of larger biomolecular systems, current technologies have achieved considerable success in the structural analysis of substantially large proteins and biomolecular complexes over 1 MDa and have characterised a wide range of timescales across which biomolecular motion exists. While NMR is well suited to obtain local structure information in detail, it contributes valuable and unique information within hybrid approaches that combine complementary methodologies, including solution scattering and microscopic techniques. General Significance For living systems, the dynamic assembly and disassembly of macromolecular complexes is of utmost importance for cellular homeostasis and, if dysregulated, implied in human disease. It is thus instructive for the advancement of the study of the dynamical ordering to discuss the potential possibilities of solution NMR spectroscopy and its applications. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato
Protein NMR Structure Refinement Based on Bayesian Inference for Dynamical Ordering of Biomacromolecules
No full textProtein structure determination in living cells
No full textTo date, in-cell NMR has elucidated various aspects of protein behaviour by associating structures in physiological conditions. Meanwhile, current studies of this method mostly have deduced protein states in cells exclusively based on ‘indirect’ structural information from peak patterns and chemical shift changes but not ‘direct’ data explicitly including interatomic distances and angles. To fully understand the functions and physical properties of proteins inside cells, it is indispensable to obtain explicit structural data or determine three-dimensional (3D) structures of proteins in cells. Whilst the short lifetime of cells in a sample tube, low sample concentrations, and massive background signals make it difficult to observe NMR signals from proteins inside cells, several methodological advances help to overcome the problems. Paramagnetic effects have an outstanding potential for in-cell structural analysis. The combination of a limited amount of experimental in-cell data with software for ab initio protein structure prediction opens an avenue to visualise 3D protein structures inside cells. Conventional nuclear Overhauser effect spectroscopy (NOESY)-based structure determination is advantageous to elucidate the conformations of side-chain atoms of proteins as well as global structures. In this article, we review current progress for the structure analysis of proteins in living systems and discuss the feasibility of its future works
Chapter 5. Protein Structure Determination in Living Cells from NOE-derived Distance Restraints
No full text1SDP-04 Dynamics of intrinsically disordered proteins in living cells(1SDP Protein Dynamics and Function in Cells elucidated by in-cell NMR and High Performance Computing,Symposium,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))
No full text3P080 A refinement method for NMR protein structure determination based on Bayesian inference(01E. Protein: Measurement & Analysis,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))
No full textActive Directional Wave Absorption Theory
No full textPanel segment type wave-makers are being used to realize multi-directional irregular waves in laboratory wave basins. In order to reproduce the real sea condition, the wave-maker should generate the incident waves, at the same time absorb reflected waves from model structures. The present study was conducted to give a multi-directional wave absorption theory as the first step of developing multi-directional absorbing wave making system. First a multidirectional wave absorption theory was presented for waves in a rectangular basin with reflective side walls. The theory relates the reflected wave profile to the motion of the wave board. Second practical approximation methods were given to realize the real time operation. Last the performance of the methods were analysed theoretically for a typical wave experiment condition. The result of the analysis showed that these methods have sufficient capability of absorbing reflected multi-directional irregular waves
NMR solution structure of a chymotrypsin inhibitor from the Taiwan cobra Naja naja atra
No full textThe Taiwan cobra (Naja naja atra) chymotrypsin inhibitor (NACI) consists of 57 amino acids and is related to other Kunitz-type inhibitors such as bovine pancreatic trypsin inhibitor (BPTI) and Bungarus fasciatus fraction IX (BF9), another chymotrypsin inhibitor. Here we present the solution structure of NACI. We determined the NMR structure of NACI with a root-mean-square deviation of 0.37 Å for the backbone atoms and 0.73 Å for the heavy atoms on the basis of 1,075 upper distance limits derived from NOE peaks measured in its NOESY spectra. To investigate the structural characteristics of NACI, we compared the three-dimensional structure of NACI with BPTI and BF9. The structure of the NACI protein comprises one 310-helix, one α-helix and one double-stranded antiparallel β-sheet, which is comparable with the secondary structures in BPTI and BF9. The RMSD value between the mean structures is 1.09 Å between NACI and BPTI and 1.27 Å between NACI and BF9. In addition to similar secondary and tertiary structure, NACI might possess similar types of protein conformational fluctuations as reported in BPTI, such as Cys14–Cys38 disulfide bond isomerization, based on line broadening of resonances from residues which are mainly confined to a region around the Cys14–Cys38 disulfide bond
Cyclic Bending Deformation and Fracture of Al and Al-1.0mass%Mg Alloy
No full textAbstractThe characteristics of cyclic bending deformation and fatigue fracture are studied on polycrystalline aluminum and Al-1.0mass%Mg alloy from the metallurgical point of view. It is found that the fatigue life mainly depends on grain size and the kind of materials. Cracks are preferentially formed at grain boundaries inclined 40 – 60°to the tension-compression direction, suggesting that shear stress affects the crack formation. EBSD measurements reveal the inhomogeneity of deformation. Intense development of sub-grain is seen in the grain interior close to a crack. It indicates that the work hardening close to grain boundaries triggers the crack formation
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