Conformational Changes In GROEL Induced by a Protein Substrate

2000 ◽  
Vol 6 (S2) ◽  
pp. 258-259
Author(s):  
S. Falke ◽  
M. Fisher ◽  
E. Gogol
Keyword(s):  
Conformational Changes ◽  
Three Dimensional ◽  
Central Cavity ◽  
En Bloc ◽  
Protein Substrate ◽  
E Coli ◽  
X Ray Crystallography ◽  
Denatured Protein ◽  
Intermediate Domain ◽  
Substrate Binding Sites

The GroEL/GroES chaperonin system of E. coli facilitates nucleotide dependent folding of select proteins. The structure of GroEL has been described by three-dimensional electron microscopy and at higher resolution by X-ray crystallography. The GroEL oligomer is a cylindrical tetradecamer composed of two heptameric rings of 57 kDa protein subunits, stacked back to back. Each subunit is comprised of two large domains, equatorial and apical, connected by a smaller intermediate domain. The intermediate “hinge” domain links the apical and equatorial domain and provides flexibility for en bloc rearrangement associated with nucleotide and GroES binding. Equatorial domains are responsible for interactions between the two heptamers and contain the ATPase activity of GroEL. Each ring of GroEL has a central cavity that is the binding site for denatured protein substrate. GroES and denatured substrate binding sites are located on the apical domains facing the central cavity.

scholarly journals Water–protein interactions from high–resolution protein crystallography

2004 ◽  
Vol 359 (1448) ◽  
pp. 1191-1206 ◽  
Author(s):  
Masayoshi Nakasako
Keyword(s):  
Hydrogen Bond ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Three Dimensional ◽  
Water Molecules ◽  
Aqueous Environment ◽  
Hydration Water ◽  
X Ray Crystallography ◽  
Physico Chemical ◽  
Domain Motions

To understand the role of water in life at molecular and atomic levels, structures and interactions at the protein–water interface have been investigated by cryogenic X–ray crystallography. The method enabled a much clearer visualization of definite hydration sites on the protein surface than at ambient temperature. Using the structural models of proteins, including several hydration water molecules, the characteristics in hydration structures were systematically analysed for the amount, the interaction geometries between water molecules and proteins, and the local and global distribution of water molecules on the surface of proteins. The tetrahedral hydrogen–bond geometry of water molecules in bulk solvent was retained at the interface and enabled the extension of a three–dimensional chain connection of a hydrogen–bond network among hydration water molecules and polar protein atoms over the entire surface of proteins. Networks of hydrogen bonds were quite flexible to accommodate and/or to regulate the conformational changes of proteins such as domain motions. The present experimental results may have profound implications in the understanding of the physico–chemical principles governing the dynamics of proteins in an aqueous environment and a discussion of why water is essential to life at a molecular level.

Proteolytic Control of Bacteriophage HK97 Capsid Maturation.

1998 ◽  
Vol 4 (S2) ◽  
pp. 984-985
Author(s):  
Robert L. Duda ◽  
James F. Conway ◽  
Naiqian Cheng ◽  
Alasdair C. Steven ◽  
Roger W. Hendrix
Keyword(s):  
Conformational Changes ◽  
Three Dimensional ◽  
Temperate Bacteriophage ◽  
Covalent Bonds ◽  
E Coli ◽  
Cryo Electron Microscopy ◽  
Dimensional Reconstruction ◽  
Capsid Maturation ◽  
Icosahedral Capsid ◽  
Icosahedral Particle

HK97 is a tailed temperate bacteriophage of E. coli that builds an icosahedral capsid using steps that include regulated assembly, proteolysis, radical conformational changes and the formation of novel covalent bonds (Fig. 1). This pathway is being exploited as a model system to explore how the formation of multiprotein complexes can be regulated by each of these mechanisms. We have identified and purified at least four intermediates (Prohead I, Prohead II, Head I and Head II) and examined them by cryo-electron microscopy and three dimensional reconstruction procedures (Fig. 2). Comparison of particle reconstructions at resolution of about 25 - 30 A have lead to major insights into the causes and purposes of the regulated changes that we have also characterized biochemically and genetically.Prohead I consists of 420 copies of the 42 kDa gp5 capsid protein arranged as 72 blister-shaped morphological capsomers in a thick walled hollow T=7 icosahedral particle with a diameter of -470 Å.

scholarly journals Mass Spectrometry and Structural Biology Techniques in the Studies on the Coronavirus-Receptor Interaction

Molecules ◽  
2020 ◽  
Vol 25 (18) ◽  
pp. 4133
Author(s):  
Danuta Witkowska
Keyword(s):  
Mass Spectrometry ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Three Dimensional ◽  
Cell Receptor ◽  
Receptor Protein ◽  
Receptor Interaction ◽  
S Protein ◽  
X Ray Crystallography ◽  
Huge Impact

Mass spectrometry and some other biophysical methods, have made substantial contributions to the studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and human proteins interactions. The most interesting feature of SARS-CoV-2 seems to be the structure of its spike (S) protein and its interaction with the human cell receptor. Mass spectrometry of spike S protein revealed how the glycoforms are distributed across the S protein surface. X-ray crystallography and cryo-electron microscopy made huge impact on the studies on the S protein and ACE2 receptor protein interaction, by elucidating the three-dimensional structures of these proteins and their conformational changes. The findings of the most recent studies in the scope of SARS-CoV-2-Human protein-protein interactions are described here.

scholarly journals Three-dimensional structures ofPlasmodium falciparumspermidine synthase with bound inhibitors suggest new strategies for drug design

2015 ◽  
Vol 71 (3) ◽  
pp. 484-493 ◽  
Author(s):  
Janina Sprenger ◽  
Bo Svensson ◽  
Jenny Hålander ◽  
Jannette Carey ◽  
Lo Persson ◽  
...  
Keyword(s):  
Binding Sites ◽  
Drug Targets ◽  
Enzymatic Reaction ◽  
Three Dimensional ◽  
Binding Mode ◽  
Polyamine Biosynthesis ◽  
X Ray ◽  
X Ray Crystallography ◽  
Substrate Binding Sites ◽  
New Strategies

The enzymes of the polyamine-biosynthesis pathway have been proposed to be promising drug targets in the treatment of malaria. Spermidine synthase (SpdS; putrescine aminopropyltransferase) catalyzes the transfer of the aminopropyl moiety from decarboxylatedS-adenosylmethionine to putrescine, leading to the formation of spermidine and 5′-methylthioadenosine (MTA). In this work, X-ray crystallography was used to examine ligand complexes of SpdS from the malaria parasitePlasmodium falciparum(PfSpdS). Five crystal structures were determined ofPfSpdS in complex with MTA and the substrate putrescine, with MTA and spermidine, which was obtained as a result of the enzymatic reaction taking place within the crystals, with dcAdoMet and the inhibitor 4-methylaniline, with MTA and 4-aminomethylaniline, and with a compound predicted in earlierin silicoscreening to bind to the active site of the enzyme, benzimidazol-(2-yl)pentan-1-amine (BIPA). In contrast to the other inhibitors tested, the complex with BIPA was obtained without any ligand bound to the dcAdoMet-binding site of the enzyme. The complexes with the aniline compounds and BIPA revealed a new mode of ligand binding toPfSpdS. The observed binding mode of the ligands, and the interplay between the two substrate-binding sites and the flexible gatekeeper loop, can be used in the design of new approaches in the search for new inhibitors of SpdS.

scholarly journals Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication

2020 ◽  
Author(s):  
Benjamin M. Akiyama ◽  
Monica E. Graham ◽  
Zoe O′Donoghue ◽  
J. David Beckham ◽  
Jeffrey S. Kieft
Keyword(s):  
Single Molecule ◽  
Conformational Changes ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Reading Frame ◽  
X Ray Crystallography ◽  
Single Molecule Fret ◽  
High Sequence Conservation ◽  
Rna Genome ◽  
Viral Lifecycle

ABSTRACTMosquito-borne flaviviruses (MBFVs) including dengue, West Nile, yellow fever, and Zika viruses have an RNA genome encoding one open reading frame flanked by 5′ and 3′ untranslated regions (UTRs). The 3′ UTRs of MBFVs contain regions of high sequence conservation in structured RNA elements known as dumbbells (DBs) that regulate translation and replication of the viral RNA genome, functions proposed to depend on the formation of an RNA pseudoknot. To understand how DB structure provides this function, we used x-ray crystallography and structural modeling to reveal the details of its three-dimensional fold. The structure confirmed the predicted pseudoknot and molecular modeling revealed how conserved sequences form a four-way junction that appears to stabilize the pseudoknot. Single-molecule FRET suggests that the DB pseudoknot is a stable element that can regulate the switch between translation and replication during the viral lifecycle by modulating long-range RNA conformational changes.

scholarly journals Structure of DnmZ, a nitrososynthase in the Streptomyces peucetius anthracycline biosynthetic pathway

2015 ◽  
Vol 71 (10) ◽  
pp. 1205-1214 ◽  
Author(s):  
Lauren Sartor ◽  
Charmaine Ibarra ◽  
Ahmad Al-Mestarihi ◽  
Brian O. Bachmann ◽  
Jessica L. Vey
Keyword(s):  
Substrate Specificity ◽  
Natural Product ◽  
Crystal Structures ◽  
Conformational Changes ◽  
Biosynthetic Pathway ◽  
Three Dimensional ◽  
Structural Features ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography

The anthracyclines are a class of highly effective natural product chemotherapeutics and are used to treat a range of cancers, including leukemia. The toxicity of the anthracyclines has stimulated efforts to further diversify the scaffold of the natural product, which has led to renewed interest in the biosynthetic pathway responsible for the formation and modification of this family of molecules. DnmZ is an N-hydroxylating flavin monooxygenase (a nitrososynthase) that catalyzes the oxidation of the exocyclic amine of the sugar nucleotide dTDP-L-epi-vancosamine to its nitroso form. Its specific role in the anthracycline biosynthetic pathway involves the synthesis of the seven-carbon acetal moiety attached to C4 of L-daunosamine observed in the anthracycline baumycin. Here, X-ray crystallography was used to elucidate the three-dimensional structure of DnmZ. Two crystal structures of DnmZ were yielded: that of the enzyme alone, solved to 3.00 Å resolution, and that of the enzyme in complex with thymidine diphosphate, the nucleotide carrier portion of the substrate, solved to 2.74 Å resolution. These models add insights into the structural features involved in substrate specificity and conformational changes involved in thymidine diphosphate binding by the nitrososynthases.

scholarly journals Congruent Docking of Dimeric Kinesin and ncd into Three-dimensional Electron Cryomicroscopy Maps of Microtubule–Motor ADP Complexes

1999 ◽  
Vol 10 (6) ◽  
pp. 2063-2074 ◽  
Author(s):  
Keiko Hirose ◽  
Jan Löwe ◽  
Maria Alonso ◽  
Robert A. Cross ◽  
Linda A. Amos
Keyword(s):  
Conformational Changes ◽  
Bound States ◽  
Three Dimensional ◽  
Coiled Coil ◽  
Direct Interaction ◽  
Electron Cryomicroscopy ◽  
X Ray ◽  
X Ray Crystallography ◽  
Microtubule Motor ◽  
Atomic Coordinates

We present a new map showing dimeric kinesin bound to microtubules in the presence of ADP that was obtained by electron cryomicroscopy and image reconstruction. The directly bound monomer (first head) shows a different conformation from one in the more tightly bound empty state. This change in the first head is amplified as a movement of the second (tethered) head, which tilts upward. The atomic coordinates of kinesin·ADP dock into our map so that the tethered head associates with the bound head as in the kinesin dimer structure seen by x-ray crystallography. The new docking orientation avoids problems associated with previous predictions; it puts residues implicated by proteolysis-protection and mutagenesis studies near the microtubule but does not lead to steric interference between the coiled-coil tail and the microtubule surface. The observed conformational changes in the tightly bound states would probably bring some important residues closer to tubulin. As expected from the homology with kinesin, the atomic coordinates of nonclaret disjunctional protein (ncd)·ADP dock in the same orientation into the attached head in a map of microtubules decorated with dimeric ncd·ADP. Our results support the idea that the observed direct interaction between the two heads is important at some stages of the mechanism by which kinesin moves processively along microtubules.

Macromolecular Crystallographic Computing

2010 ◽  
pp. 1-36
Author(s):  
Kostas Bethanis ◽  
Petros Giastas ◽  
Trias Thireou ◽  
Vassilis Atlamazoglou
Keyword(s):  
Escherichia Coli ◽  
Conformational Changes ◽  
Three Dimensional ◽  
Structural Proteomics ◽  
X Ray ◽  
X Ray Crystallography ◽  
Future Developments ◽  
Protein X

Structural genomics or structural proteomics can be defined as the quest to obtain the three-dimensional structures of all proteins. Single-crystal X-ray crystallography provides the most direct, accurate and in most of the cases the only way of forming images of macromolecules. Using crystallography, threedimensional images have been made of thousands of macromolecules, especially proteins and nucleic acids. These give detailed information about their activity, their mechanism for recognizing and binding substrates and effectors, and the conformational changes which they may undergo. This chapter presents the basic crystallographic procedure steps and a thorough survey of the computational software used most frequently by protein X-ray crystallographers. The determination of the structure of 2[4Fe-4S] ferredoxin from Escherichia coli. is examined as a case study of implementation of these steps and programs. Finally, some of the perspectives of the field of computational X-ray crystallography are noted showing the future developments in the ceaseless evolution of new methods and proliferation of new programs.

Ribosome Structural Organization

1974 ◽  
Vol 32 ◽  
pp. 332-333
Author(s):  
James A. Lake
Keyword(s):  
Ribosomal Proteins ◽  
Structural Organization ◽  
Three Dimensional ◽  
Small Subunit ◽  
Structural Studies ◽  
X Ray Diffraction ◽  
Specific Antibodies ◽  
X Ray ◽  
E Coli ◽  
Complete Sequences

The understanding of ribosome structure has advanced considerably in the last several years. Biochemists have characterized the constituent proteins and rRNA's of ribosomes. Complete sequences have been determined for some ribosomal proteins and specific antibodies have been prepared against all E. coli small subunit proteins. In addition, a number of naturally occuring systems of three dimensional ribosome crystals which are suitable for structural studies have been observed in eukaryotes. Although the crystals are, in general, too small for X-ray diffraction, their size is ideal for electron microscopy.

3-D reconstruction of molecular shape from microcrystal thin sections

1983 ◽  
Vol 41 ◽  
pp. 748-749
Author(s):  
S. Cusack ◽  
J.-C. Jésior
Keyword(s):  
Three Dimensional ◽  
Molecular Shape ◽  
Biological Molecules ◽  
Fourier Space ◽  
Single Particles ◽  
Thin Sections ◽  
Standard Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).

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