Structure calculation of biological macromolecules from NMR data

1998 ◽  
Vol 31 (2) ◽  
pp. 145-237 ◽  
Author(s):  
PETER GÜNTERT
Keyword(s):  
Single Crystals ◽  
Structural Information ◽  
Three Dimensional ◽  
Protein Structure Determination ◽  
Biological Properties ◽  
Dimensional Structure ◽  
Biological Macromolecules ◽  
X Ray Diffraction ◽  
Three Dimensional Structure ◽  
Comparable Accuracy

The relationship between amino acid sequence, three-dimensional structure and biological function of proteins is one of the most intensely pursued areas of molecular biology and biochemistry. In this context, the three-dimensional structure has a pivotal role, its knowledge being essential to understand the physical, chemical and biological properties of a protein (Branden & Tooze, 1991; Creighton, 1993). Until 1984 structural information at atomic resolution could only be determined by X-ray diffraction techniques with protein single crystals (Drenth, 1994). The introduction of nuclear magnetic resonance (NMR) spectroscopy (Abragam, 1961) as a technique for protein structure determination (Wüthrich, 1986) has made it possible to obtain structures with comparable accuracy also in a solution environment that is much closer to the natural situation in a living being than the single crystals required for protein crystallography.

Three Dimensional structure and organization of diploid chromosomes by optical section microscopy

1987 ◽  
Vol 45 ◽  
pp. 633-635
Author(s):  
David A. Agard ◽  
Yasushi Hiraoka ◽  
John W. Sedat
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Developmental State ◽  
Mitotic Cell ◽  
Biological Properties ◽  
Dimensional Structure ◽  
Specific Gene ◽  
Three Dimensional Structure ◽  
Complementary Techniques ◽  
Dynamic Structures

In an effort to understand the complex relationship between structure and biological function within the nucleus, we have embarked on a program to examine the three-dimensional structure and organization of Drosophila melanogaster embryonic chromosomes. Our overall goal is to determine how DNA and proteins are organized into complex and highly dynamic structures (chromosomes) and how these chromosomes are arranged in three dimensional space within the cell nucleus. Futher, we hope to be able to correlate structual data with such fundamental biological properties as stage in the mitotic cell cycle, developmental state and transcription at specific gene loci.Towards this end, we have been developing methodologies for the three-dimensional analysis of non-crystalline biological specimens using optical and electron microscopy. We feel that the combination of these two complementary techniques allows an unprecedented look at the structural organization of cellular components ranging in size from 100A to 100 microns.

scholarly journals Structural characterization of quaternary selenites of tungsten(VI), A 2W3SeO12 (A = NH4, Cs, Rb, K or Tl)

2021 ◽  
Vol 77 (4) ◽  
pp. 406-411
Author(s):  
Vineela Balisetty ◽  
Kanamaluru Vidyasagar
Keyword(s):  
Three Dimensional ◽  
Spectroscopic Studies ◽  
Solid State Reactions ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
Compound K ◽  
Three Dimensional Structure ◽  
Thermal And Spectroscopic Studies ◽  
Anionic Framework

The quaternary A 2W3SeO12 (A = NH4, Cs, Rb, K or Tl) selenites have been prepared in the form of single crystals by hydrothermal and novel solid-state reactions. They were characterized by X-ray diffraction, thermal and spectroscopic studies. All of them have a hexagonal tungsten oxide (HTO) related [W3SeO12]2− anionic framework with pyramidally coordinated Se4+ ions. The known A 2W3SeO12 (A = NH4, Cs or Rb) compounds are isostructural with the Cs2W3TeO12 compound and have a non-centrosymmetric layered structure containing intra-layer Se—O bonds. The new compound K2W3SeO12(α) is isostructural with the K2W3TeO12 compound and has a centrosymmetric three-dimensional structure containing interlayer Se—O bonds. It is inferred that the new Tl2W3SeO12 compound has the same three-dimensional structure as K2W3SeO12(α).

Zona Pellucida Proteins, Fibrils, and Matrix

2020 ◽  
Vol 89 (1) ◽  
pp. 695-715
Author(s):  
Eveline S. Litscher ◽  
Paul M. Wassarman
Keyword(s):  
Extracellular Matrix ◽  
Zona Pellucida ◽  
Three Dimensional ◽  
Structural Features ◽  
Biological Properties ◽  
Preimplantation Development ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Early Embryos ◽  
N Terminus

The zona pellucida (ZP) is an extracellular matrix that surrounds all mammalian oocytes, eggs, and early embryos and plays vital roles during oogenesis, fertilization, and preimplantation development. The ZP is composed of three or four glycosylated proteins, ZP1–4, that are synthesized, processed, secreted, and assembled into long, cross-linked fibrils by growing oocytes. ZP proteins have an immunoglobulin-like three-dimensional structure and a ZP domain that consists of two subdomains, ZP-N and ZP-C, with ZP-N of ZP2 and ZP3 required for fibril assembly. A ZP2–ZP3 dimer is located periodically along ZP fibrils that are cross-linked by ZP1, a protein with a proline-rich N terminus. Fibrils in the inner and outer regions of the ZP are oriented perpendicular and parallel to the oolemma, respectively, giving the ZP a multilayered appearance. Upon fertilization of eggs, modification of ZP2 and ZP3 results in changes in the ZP's physical and biological properties that have important consequences. Certain structural features of ZP proteins suggest that they may be amyloid-like proteins.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of a single variable domain of the immunoglobulin superfamily in amphioxus,Amphi-IgSF-V

2014 ◽  
Vol 70 (8) ◽  
pp. 1072-1075 ◽  
Author(s):  
Bo Jiang ◽  
Yanjie Liu ◽  
Rong Chen ◽  
Zhenbao Wang ◽  
Mansoor Tariq ◽  
...  
Keyword(s):  
Immune System ◽  
Structural Information ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Immunoglobulin Superfamily ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
System A ◽  
Human Immunoglobulins

Amphioxus is regarded as an essential animal model for the study of immune evolution. Discovery of new molecules with the immunoglobulin superfamily (IgSF) variable (V) domain in amphioxus would help in studying the evolution of IgSF V molecules in the immune system. A protein was found which just contains only one IgSF V domain in amphioxus, termedAmphi-IgSF-V; it has over 30% sequence identity to the V domains of human immunoglobulins and mammalian T-cell receptors. In order to clarify the three-dimensional structure of this new molecule in amphioxus,Amphi-IgSF-V was expressed, purified and crystallized, and diffraction data were collected to a resolution of 1.95 Å. The crystal belonged to space groupP3221, with unit-cell parametersa=b= 53.9,c= 135.5 Å. The Matthews coefficient and solvent content were calculated to be 2.58 Å3 Da−1and 52.38%, respectively. The results will provide structural information to study the evolution of IgSF V molecules in the immune system.

scholarly journals Three-dimensional structure of CdX (X=Se,Te) nanocrystals by total x-ray diffraction

2007 ◽  
Vol 102 (4) ◽  
pp. 044304 ◽  
Author(s):  
S. K. Pradhan ◽  
Z. T. Deng ◽  
F. Tang ◽  
C. Wang ◽  
Y. Ren ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Three Dimensional Structure

COMPUTER SIMULATION OF BIOLOGICAL MACROMOLECULES IN GENERALIZED ENSEMBLES

1999 ◽  
Vol 10 (08) ◽  
pp. 1521-1530 ◽  
Author(s):  
ULRICH H. E. HANSMANN
Keyword(s):  
Computer Simulation ◽  
Protein Folding ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Biological Macromolecules ◽  
Three Dimensional Structure ◽  
Ensemble Techniques ◽  
Folding Simulations ◽  
Protein Models ◽  
Structure Of Proteins

For many years the emphasis in protein-folding simulations has been laid as to how to predict the three-dimensional structure of proteins. Only recently has there be a shift in interest towards the thermodynamics of folding. We show that generalized-ensemble techniques are well suited to study both questions for realistic protein models.

scholarly journals X-Ray Diffraction of Magnetically Oriented Microcrystals of Protein

2014 ◽  
Vol 70 (a1) ◽  
pp. C349-C349
Author(s):  
Shu Tsukui ◽  
Fumiko Kimura ◽  
Kimihiko Mizutani ◽  
Bunzo Mikami ◽  
Tsunehisa Kimura
Keyword(s):  
Single Crystal ◽  
Three Dimensional ◽  
Water Soluble ◽  
Dimensional Structure ◽  
Diffraction Measurement ◽  
X Ray Diffraction ◽  
Consolidation Process ◽  
X Ray ◽  
Three Dimensional Structure

Elucidation of the three-dimensional structure of biomolecules is of great importance because the three-dimensional structure is closely related to biological functions. X-ray single-crystal analysis is powerful method to analyze the structure, but it is sometimes difficult to grow a crystal sufficiently large for conventional or even synchrotron single-crystal X-ray measurement. We recently reported on a magnetically oriented microcrystal array (MOMA) [1] that is a composite in which microcrystals are aligned three-dimensionally in polymer matrix. Microcrystals are suspended in an ultraviolet-curable monomer and rotated non-uniformly in a static magnetic field to achieve three dimensional crystal alignment. Then, the monomer is photopolymerized to maintain the achieved alignment. We have successfully demonstrated that X-ray single crystal structure determinations through MOMA are possible for low molecular weight compounds [2] as well as protein. [3] However, the method with MOMA has two drawbacks: (i) the sample microcrystals cannot be recovered from a MOMA, which is especially serious problem in case of proteins, and (ii) the alignment is deteriorated during the consolidation process, causing low resolution. In this study, we attempt to solve these problems. First, we use a water-soluble sol as microcrystalline media and consolidate the alignment by gelation, which makes the recovery of microcrystals possible. Second, a magnetically oriented microcrystal suspension (MOMS) is used for in-situ X-ray diffraction measurement, which makes the sample recovery possible and enhances the resolution. We use lysozyme as a model protein for both cases. The in-situ method with in-house X-ray diffractometer gave diffraction spots about 3.0 Å resolutions. We plan to perform the same experiment at SPring-8.

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