scholarly journals The dimensions and shapes of the furanose rings in nucleic acids

1972 ◽  
Vol 130 (2) ◽  
pp. 453-465 ◽  
Author(s):  
S. Arnott ◽  
D. W. L. Hukins
Keyword(s):  
Nucleic Acids ◽  
Model Building ◽  
Molecular Model ◽  
Relative Orientation ◽  
Ring Conformation ◽  
Mean Values ◽  
Pyrimidine Base ◽  
X Ray ◽  
X Ray Crystallography ◽  
Ring Puckering

A survey was made of the geometry of furanose rings in β-nucleotides and β-nucleosides (as monomers related to nucleic acids) for which structures have been determined by X-ray crystallography. Mean values, and estimated standard deviations from them, were calculated for bond-lengths, bond-angles and conformation-angles. For parameters with values dependent on ring-puckering, separate calculations were made for each ring type. (The rings are puckered in one of three conformations: C-2- or C-3-endo or C-3-exo; C-2-exo has not been observed.) The results were used to compute standard furanose rings with C-2-endo, C-3-endo and C-3-exo conformations for use in nucleic acid molecular model-building. The survey also showed that the only other conformation-angle in nucleotides dependent on the furanose ring conformation corresponds to the relative orientation of the purine (or pyrimidine) base and the ring.

X-Ray Diffraction and Molecular Model Building Studies of The Interaction of Actinomycin with Nucleic Acids

Nature ◽  
1963 ◽  
Vol 198 (4880) ◽  
pp. 538-540 ◽  
Author(s):  
L. D. HAMILTON ◽  
W. FULLER ◽  
E. REICH
Keyword(s):  
Nucleic Acids ◽  
Model Building ◽  
Molecular Model ◽  
X Ray Diffraction ◽  
X Ray

Using cryo-electron microscopy maps for X-ray structure determination of homologues

2020 ◽  
Vol 76 (1) ◽  
pp. 63-72
Author(s):  
Lingxiao Zeng ◽  
Wei Ding ◽  
Quan Hao
Keyword(s):  
Electron Microscopy ◽  
Hybrid Method ◽  
Model Building ◽  
Test Cases ◽  
X Ray ◽  
X Ray Crystallography ◽  
Sequence Identity ◽  
Whole Process ◽  
Cryo Electron Microscopy

The combination of cryo-electron microscopy (cryo-EM) and X-ray crystallography reflects an important trend in structural biology. In a previously published study, a hybrid method for the determination of X-ray structures using initial phases provided by the corresponding parts of cryo-EM maps was presented. However, if the target structure of X-ray crystallography is not identical but homologous to the corresponding molecular model of the cryo-EM map, then the decrease in the accuracy of the starting phases makes the whole process more difficult. Here, a modified hybrid method is presented to handle such cases. The whole process includes three steps: cryo-EM map replacement, phase extension by NCS averaging and dual-space iterative model building. When the resolution gap between the cryo-EM and X-ray crystallographic data is large and the sequence identity is low, an intermediate stage of model building is necessary. Six test cases have been studied with sequence identity between the corresponding molecules in the cryo-EM and X-ray structures ranging from 34 to 52% and with sequence similarity ranging from 86 to 91%. This hybrid method consistently produced models with reasonable R work and R free values which agree well with the previously determined X-ray structures for all test cases, thus indicating the general applicability of the method for X-ray structure determination of homologues using cryo-EM maps as a starting point.

scholarly journals Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7

2008 ◽  
Vol 3 (7) ◽  
pp. 1171-1179 ◽  
Author(s):  
Gerrit Langer ◽  
Serge X Cohen ◽  
Victor S Lamzin ◽  
Anastassis Perrakis
Keyword(s):  
Model Building ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals Structural basis for the binding of SNAREs to the multisubunit tethering complex Dsl1

2020 ◽  
Author(s):  
Sophie M. Travis ◽  
Kevin DAmico ◽  
I-Mei Yu ◽  
Safraz Hamid ◽  
Gabriel Ramirez-Arellano ◽  
...  
Keyword(s):  
Membrane Trafficking ◽  
Relative Orientation ◽  
Snare Complex ◽  
Structural Basis ◽  
Binding Modes ◽  
Range Interaction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Long Range Interaction ◽  
Target Membrane

AbstractMultisubunit tethering complexes (MTCs) are large (250 to >750 kDa), conserved macromolecular machines that are essential for SNARE-mediated membrane fusion in all eukaryotes. MTCs are thought to function as organizers of membrane trafficking, mediating the initial, long-range interaction between a vesicle and its target membrane and promoting the formation of membrane-bridging SNARE complexes. Previously, we reported the structure of the Dsl1 complex, the simplest known MTC, which is essential for COPI-mediated transport from the Golgi to the endoplasmic reticulum (ER). This structure suggested how the Dsl1 complex might function to tether a vesicle to its target membrane by binding at one end to the COPI coat and at the other end to ER SNAREs. Here, we use x-ray crystallography to investigate these Dsl1-SNARE interactions in greater detail. The Dsl1 complex comprises three subunits that together form a two-legged structure with a central hinge. Our results show that distal regions of each leg bind N-terminal Habc domains of the ER SNAREs Sec20 (a Qb-SNARE) and Use1 (a Qc-SNARE). The observed binding modes appear to anchor the Dsl1 complex to the ER target membrane while simultaneously ensuring that both SNAREs are in open conformations with their SNARE motifs available for assembly. The proximity of the two SNARE motifs, and therefore their ability to enter the same SNARE complex, depends on the relative orientation of the two Dsl1 legs.

scholarly journals Solving a new R2lox protein structure by microcrystal electron diffraction

2019 ◽  
Vol 5 (8) ◽  
pp. eaax4621 ◽  
Author(s):  
Hongyi Xu ◽  
Hugo Lebrette ◽  
Max T. B. Clabbers ◽  
Jingjing Zhao ◽  
Julia J. Griese ◽  
...  
Keyword(s):  
Protein Structure ◽  
Electron Diffraction ◽  
Model Building ◽  
Protein Structures ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Potential Map ◽  
Metal Cofactor ◽  
And Function

Microcrystal electron diffraction (MicroED) has recently shown potential for structural biology. It enables the study of biomolecules from micrometer-sized 3D crystals that are too small to be studied by conventional x-ray crystallography. However, to date, MicroED has only been applied to redetermine protein structures that had already been solved previously by x-ray diffraction. Here, we present the first new protein structure—an R2lox enzyme—solved using MicroED. The structure was phased by molecular replacement using a search model of 35% sequence identity. The resulting electrostatic scattering potential map at 3.0-Å resolution was of sufficient quality to allow accurate model building and refinement. The dinuclear metal cofactor could be located in the map and was modeled as a heterodinuclear Mn/Fe center based on previous studies. Our results demonstrate that MicroED has the potential to become a widely applicable tool for revealing novel insights into protein structure and function.

1. The roots of biochemistry

2021 ◽  
pp. 1-23
Author(s):  
Mark Lorch
Keyword(s):  
Nucleic Acids ◽  
20Th Century ◽  
19Th Century ◽  
Structural Biology ◽  
Ribonucleic Acid ◽  
Alcoholic Beverages ◽  
X Ray ◽  
X Ray Crystallography ◽  
History Of ◽  
The 19Th Century

This chapter traces the history of biochemistry, which is linked to the understanding of arguably the oldest uses of biotechnology—fermentation and the production of alcoholic beverages and cheese. In the 19th century, at the same time as the fermentation debates and enzymology flourished, the nature of proteins was under scrutiny. The chapter then considers the contribution that X-ray crystallography has made to structural biology. By the mid-20th century, the structures of the two massive molecular players, protein and nucleic acids (DNA along with ribonucleic acid), and their myriad roles were in place. It was becoming apparent that these were the fundamental molecular machines that marshal the chemistry within cells.

N-Glycoside Complexes of Nickel(II); Probing Carbohydrate - Transition Metal Interactions

2009 ◽  
Vol 62 (3) ◽  
pp. 265 ◽  
Author(s):  
Dale Jones ◽  
Marcelis van Holst ◽  
Shigenobu Yano ◽  
Tomoaki Tanase ◽  
Janice Aldrich-Wright
Keyword(s):  
Chelate Ring ◽  
Chair Conformation ◽  
Nickel Atom ◽  
Cd Spectra ◽  
Metal Centre ◽  
Ring Conformation ◽  
X Ray ◽  
X Ray Crystallography ◽  
Metal Interactions ◽  
Helical Configuration

Nickel(ii) complexes prepared from d- and l-arabinose (d-ara and l-ara) and 1,2-diaminoethane (en), [Ni(en-d-ara)2](ClO4)2·2H2O 1 and [Ni(en-l-ara)2](ClO4)2·2H2O 2 (where en-d-ara is 1-((2-aminoethyl)amino)-1-deoxy-d-arabinose) were synthesized and characterized by absorption spectroscopy, circular dichroism (CD), and X-ray crystallography. The CD spectra of 1 and 2 in the d–d transition region indicate a C2 chiral configuration around the metal centre. X-ray crystallography of 1 revealed that two 1-((2-aminoethyl)amino)-1-deoxy-d-arabinose ligands coordinate to the nickel atom in nearly C2 symmetry, through the C(2) hydroxy group of the arabinose moiety and two nitrogen atoms of the diamine in a meridional mode. This results in a Λ-C2-helical configuration around the metal centre. The arabinose ring adopts the rare α-1C4 chair conformation and the carbohydrate–chelate ring conformation is δ.

scholarly journals A practical method for efficient and optimal production of selenomethionine-labeled recombinant protein complexes in the insect cells

2018 ◽  
Author(s):  
Sabine Wenzel ◽  
Tsuyoshi Imasaki ◽  
Yuichiro Takagi
Keyword(s):  
Recombinant Protein ◽  
Recombinant Proteins ◽  
Model Building ◽  
Insect Cells ◽  
Protein Complexes ◽  
Practical Method ◽  
Optimal Production ◽  
X Ray ◽  
E Coli ◽  
X Ray Crystallography

AbstractThe use of Selenomethionine (SeMet) incorporated protein crystals for single or multiwavelength anomalous diffraction (SAD or MAD) to facilitate phasing has become almost synonymous with modern X-ray crystallography. The anomalous signals from SeMets can be used for phasing as well as sequence markers for subsequent model building. The production of large quantities of SeMet incorporated recombinant proteins is relatively straightforward when expressed in E. coli. In contrast, production of SeMet substituted recombinant proteins expressed in the insect cells is not as robust due to the toxicity of SeMet in eukaryotic systems. Previous protocols for SeMet-incorporation in the insect cells are laborious, and more suited for secreted proteins. In addition, these protocols have generally not addressed the SeMet toxicity issue, and typically result in low recovery of the labeled proteins. Here we report that SeMet toxicity can be circumvented by fully infecting insect cells with baculovirus. Quantitatively controlling infection levels using our Titer Estimation of Quality Control (TEQC) method allows for incorporation of substantial amounts of SeMet, resulting in an efficient and optimal production of labeled recombinant protein complexes. With the method described here, we were able to consistently reach incorporation levels of about 75% and protein yield of 60-90% compared to native protein expression.

scholarly journals Solving the first novel protein structure by 3D micro-crystal electron diffraction

2019 ◽  
Author(s):  
H. Xu ◽  
H. Lebrette ◽  
M.T.B. Clabbers ◽  
J. Zhao ◽  
J.J. Griese ◽  
...  
Keyword(s):  
Protein Structure ◽  
Electron Diffraction ◽  
Model Building ◽  
Protein Structures ◽  
X Ray ◽  
X Ray Crystallography ◽  
Unknown Protein ◽  
Potential Map ◽  
Crystal Electron ◽  
And Function

AbstractMicro-crystal electron diffraction (MicroED) has recently shown potential for structural biology. It enables studying biomolecules from micron-sized 3D crystals that are too small to be studied by conventional X-ray crystallography. However, to the best of our knowledge, MicroED has only been applied to re-determine protein structures that had already been solved previously by X-ray diffraction. Here we present the first unknown protein structure – an R2lox enzyme – solved using MicroED. The structure was phased by molecular replacement using a search model of 35% sequence identity. The resulting electrostatic scattering potential map at 3.0 Å resolution was of sufficient quality to allow accurate model building and refinement. Our results demonstrate that MicroED has the potential to become a widely applicable tool for revealing novel insights into protein structure and function, opening up new opportunities for structural biologists.

scholarly journals Phosphodiester models for cleavage of nucleic acids

2018 ◽  
Vol 14 ◽  
pp. 803-837 ◽  
Author(s):  
Satu Mikkola ◽  
Tuomas Lönnberg ◽  
Harri Lönnberg
Keyword(s):  
Nucleic Acids ◽  
Metal Ion ◽  
Molecular Model ◽  
Catalytic Efficiency ◽  
Biological Information ◽  
Rate Dependency ◽  
Mechanistic Studies ◽  
Metal Ion Binding ◽  
Ribonucleic Acids ◽  
X Ray Crystallography

Nucleic acids that store and transfer biological information are polymeric diesters of phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases, is one of the underlying biological processes. The remarkable catalytic efficiency of nucleases, together with the ability of ribonucleic acids to serve sometimes as nucleases, has made the cleavage of phosphodiesters a subject of intensive mechanistic studies. In addition to studies of nucleases by pH-rate dependency, X-ray crystallography, amino acid/nucleotide substitution and computational approaches, experimental and theoretical studies with small molecular model compounds still play a role. With small molecules, the importance of various elementary processes, such as proton transfer and metal ion binding, for stabilization of transition states may be elucidated and systematic variation of the basicity of the entering or departing nucleophile enables determination of the position of the transition state on the reaction coordinate. Such data is important on analyzing enzyme mechanisms based on synergistic participation of several catalytic entities. Many nucleases are metalloenzymes and small molecular models offer an excellent tool to construct models for their catalytic centers. The present review tends to be an up to date summary of what has been achieved by mechanistic studies with small molecular phosphodiesters.

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