<i>MASSHA</i>– a graphics system for rigid-body modelling of macromolecular complexes against solution scattering data

Konarev, Petr V.; Petoukhov, Maxim V.; Svergun, Dmitri I.

doi:10.1107/s0021889801006100

Cited by 147 publications

(116 citation statements)

References 35 publications

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“…Relative positions of the domains were found with an automated procedure that iteratively rotates their envelope functions to minimize the discrepancy with the ab initio low resolution structure. The models were displayed using the program MASSHA (36). R g , maximum intraparticle distances (D max ), envelope functions, and scattering curves were calculated from these atomic coordinates by the CRYSOL program taking into account the influence of the hydration shell (37).…”

Section: Methodsmentioning

confidence: 99%

Free Human Mitochondrial GrpE Is a Symmetric Dimer in Solution

Borges

Fischer

Craievich

et al. 2003

Journal of Biological Chemistry

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The co-chaperone GrpE is essential for the activities of the Hsp70 system, which assists protein folding. GrpE is present in several organisms, and characterization of homologous GrpEs is important for developing structure-function relationships. Cloning, producing, and conformational studies of the recombinant human mitochondrial GrpE are reported here. Circular dichroism measurements demonstrate that the purified protein is folded. Thermal unfolding of human GrpE measured both by circular dichroism and differential scanning calorimetry differs from that of prokaryotic GrpE. Analytical ultracentrifugation data indicate that human GrpE is a dimer, and the sedimentation coefficient agrees with an elongated shape model. Small angle x-ray scattering analysis shows that the protein possesses an elongated shape in solution and demonstrates that its envelope, determined by an ab initio method, is similar to the high resolution envelope of Escherichia coli GrpE bound to DnaK obtained from single crystal x-ray diffraction. However, in these conditions, the E. coli GrpE dimer is asymmetric because the monomer that binds DnaK adopts an open conformation. It is of considerable importance for structural GrpE research to answer the question of whether the GrpE dimer is only asymmetric while bound to DnaK or also as a free dimer in solution. The low resolution structure of human GrpE presented here suggests that GrpE is a symmetric dimer when not bound to DnaK. This information is important for understanding the conformational changes GrpE undergoes on binding to DnaK.

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Section: Methodsmentioning

confidence: 99%

Free Human Mitochondrial GrpE Is a Symmetric Dimer in Solution

Borges

Fischer

Craievich

et al. 2003

Journal of Biological Chemistry

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“…Twelve independent ab initio reconstructions were performed and then averaged using DAMAVER [39], which also provides a value of normalized spatial discrepancy (NSD) representing a measure of similarity among different models (for ideally superimposed similar objects, NSD tends to 0; it exceeds 1 if the objects differ systematically from one another). Rigid body modeling was performed using MASSHA [42]. The tool allows one to display and manipulate atomic structures and low resolution models minimizing the discrepancy value χ (formula (1)) against the experimental data.…”

Section: Small Angle X-ray Scatteringmentioning

confidence: 99%

The Salmonella enterica ZinT structure, zinc affinity and interaction with the high-affinity uptake protein ZnuA provide insight into the management of periplasmic zinc

Ilari

Alaleona

Tria

et al. 2014

Biochimica et Biophysica Acta (BBA) - General Subjects

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This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues.Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. Background: In Gram-negative bacteria the ZnuABC transporter ensures adequate zinc import in Zn(II)-poor environments, like those encountered by pathogens within the infected host. Recently, the metal-binding protein ZinT was suggested to operate as an accessory component of ZnuABC in periplasmic zinc recruitment. Since ZinT is known to form a ZinT-ZnuA complex in the presence of Zn(II) it was proposed to transfer Zn(II) to ZnuA. The present work was undertaken to test this claim. Methods: ZinT and its structural relationship with ZnuA have been characterized by multiple biophysical techniques (X-ray crystallography, SAXS, analytical ultracentrifugation, fluorescence spectroscopy). Results: The metal-free and metal-bound crystal structures of Salmonella enterica ZinT show one Zn(II) binding site and limited structural changes upon metal removal. Spectroscopic titrations with Zn(II) yield a K D value of 22 ± 2 nM for ZinT, while those with ZnuA point to one high affinity (K D b 20 nM) and one low affinity Zn(II) binding site (K D in the micromolar range). Sedimentation velocity experiments established that Zn(II)-bound ZinT interacts with ZnuA, whereas apo-ZinT does not. The model of the ZinT-ZnuA complex derived from small angle X-ray scattering experiments points to a disposition that favors metal transfer as the metal binding cavities of the two proteins face each other. Conclusions: ZinT acts as a Zn(II)-buffering protein that delivers Zn(II) to ZnuA. General significance: Knowledge of the ZinT-ZnuA relationship is crucial for understanding bacterial Zn(II) uptake.

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“…The programs CRYSOL for X-rays (Svergun et al, 1995) and CRYSON for neutrons (Svergun et al, 1998) allow the user to calculate the scattering profiles from atomic models of macromolecular structures. A rigid body modelling suite including programs MASSHA and SASREF is also available to characterize macromolecular complexes in terms of the structure of subunits (Konarev et al, 2001;Petoukhov & Svergun, 2005). Most of the programs belonging to ATSAS run on multiple hardware platforms (Windows PC, Linux, Mac OSX, different UNIX flavours).…”

Section: Introductionmentioning

confidence: 99%

ATSAS 2.1 – towards automated and web-supported small-angle scattering data analysis

et al. 2007

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Small‐angle scattering (SAS) is frequently employed for screening large numbers of samples and for studying these samples under different conditions, including space‐ and time‐resolved analysis. These measurements produce immense amounts of data, especially on modern high‐flux and high‐brilliance sources (e.g. third‐generation synchrotrons). In biological SAS, like high‐throughput macromolecular crystallography, large‐scale analysis of proteins and macromolecular complexes is also emerging. Automation of data analysis becomes an indispensable prerequisite for adequate evaluation of high‐throughput SAS experiments. Here a prototype of an automated data‐analysis system for isotropic solution scattering based on the further development of the programs belonging to the package ATSAS 2.1 is reported. This system allows the major analysis tasks starting from the raw data processing and, for monodisperse systems, finishing with a three‐dimensional model, to be performed automatically. Convenient web interfaces for the online use of individual ATSAS programs are also provided.

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MASSHA– a graphics system for rigid-body modelling of macromolecular complexes against solution scattering data

Cited by 147 publications

References 35 publications

Free Human Mitochondrial GrpE Is a Symmetric Dimer in Solution

Free Human Mitochondrial GrpE Is a Symmetric Dimer in Solution

The Salmonella enterica ZinT structure, zinc affinity and interaction with the high-affinity uptake protein ZnuA provide insight into the management of periplasmic zinc

ATSAS 2.1 – towards automated and web-supported small-angle scattering data analysis

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