Morphological aspects of oligomeric protein structures

Ponstingl, Hannes; Kabir, Thomas; Gorse, Denise; Thornton, Janet M.

doi:10.1016/j.pbiomolbio.2004.07.010

Cited by 74 publications

(79 citation statements)

References 66 publications

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“…The means and medians of the percentage of total surface area increase as a function of the oligomeric state of the homo-oligomers (Table II), though the distributions for some of the oligomers have too few structures for statistical significance. The mean percent monomer ASA involved in the oligomerization surface for n ¼ 2, 3, 4, and 6 agrees with similar data measured for a smaller set of homo-oligomers by Postingl et al 22 This is to be expected, as in general a monomer must bind a greater number of other monomers in a homooligomer as the oligomeric state increases. The percentage of surface area involved in oligomerization for AF2331 is above the mean for every oligomeric state save for 11-mers.…”

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confidence: 90%

The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of α + β fold

et al. 2009

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The structure of AF2331, a 11-kDa orphan protein of unknown function from Archaeoglobus fulgidus, was solved by Se-Met MAD to 2.4 Å resolution. The structure consists of an a 1 b fold formed by an unusual homodimer, where the two core b-sheets are interdigitated, containing strands alternating from both subunits. The decrease in solvent-accessible surface area upon dimerization is unusually large (3960 Å 2 ) for a protein of its size. The percentage of the total surface area buried in the interface (41.1%) is one of the largest observed in a nonredundant set of homodimers in the PDB and is above the mean for nearly all other types of homo-oligomers. AF2331 has no sequence homologs, and no structure similar to AF2331 could be found in the PDB using the CE, TM-align, DALI, or SSM packages. The protein has been identified in Pfam 23.0 as the archetype of a new superfamily and is topologically dissimilar to all other proteins with the ''3-Layer (BBA) Sandwich'' fold in CATH. Therefore, we propose that AF2331 forms a novel a 1 b fold. AF2331 contains multiple negatively charged surface clusters and is located on the same operon as the basic protein AF2330. We hypothesize that AF2331 and AF2330 may form a charge-stabilized complex in vivo, though the role of the negatively charged surface clusters is not clear.

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confidence: 90%

The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of α + β fold

et al. 2009

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“…The pVirB8 AT dimer interface buries 1,720 Å 2 of accessible surface area, corresponding to 10% of the total monomer accessible surface area. This interface is larger than the other crystal contacts in our structure and larger than the average crystal contact in the Protein Data Bank (PDB), although it is slightly smaller than the average dimer interface (21). In addition, we observe highly conserved residues participating in dimer formation.…”

Section: Discussioncontrasting

confidence: 50%

“…21 and references therein). Despite wide variation in the values of these properties, the size of the interface and, to a lesser extent, the degree of hydrophobicity or the presence of conserved residues, can aid differentiation of biological interfaces from crystal contacts (21). The pVirB8 AT dimer interface buries 1,720 Å 2 of accessible surface area, corresponding to 10% of the total monomer accessible surface area.…”

Section: Discussionmentioning

confidence: 99%

Agrobacterium tumefaciens VirB8 structure reveals potential protein–protein interaction sites

Bailey

Ward²,

Middleton³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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Bacterial type IV secretion systems (T4SS) translocate DNA and͞or proteins to recipient cells, thus providing a mechanism for conjugative transfer of genetic material and bacterial pathogenesis. Here we describe the first structure of a core component from the archetypal Agrobacterium tumefaciens T4SS: the 2.2-Å resolution crystal structure of the VirB8 periplasmic domain (pVirB8 AT ). VirB8 forms a dimer in the crystal, and we identify residues likely important for stabilization of the dimer interface. Structural comparison of pVirB8 AT with Brucella suis VirB8 confirms that the monomers have a similar fold. In addition, the pVirB8 AT dimer superimposes very closely on the B. suis VirB8 dimer, supporting the proposal that dimer formation in the crystal reflects selfinteractions that are biologically significant. The evolutionary conservation level for each residue was obtained from a data set of 84 VirB8 homologs and projected onto the protein structure to indicate conserved surface patches that likely contact other T4SS proteins.bacterial protein export ͉ conjugation ͉ type IV secretion T ype IV secretion systems (T4SS) function as conjugation systems, DNA uptake͞release systems, and effector protein translocator systems (1) and are required for virulence of several human pathogens including Bartonella henselae, Bordetella pertussis, Brucella suis, Helicobacter pylori, and Legionella pneumophila, as well as the plant pathogen Agrobacterium tumefaciens (2). The A. tumefaciens T4SS is composed of 12 proteins, VirB1-11 and VirD4. The known properties of these components are well reviewed (1), and each contributes to one or more functional subgroups. The A. tumefaciens system genetically transforms plant cells with a specific DNA element, called the T-DNA. VirB4, VirB11, and VirD4 are NTPases located at the inner membrane that may provide energy for DNA transfer or assembly of the secretion system. VirB6-VirB10 likely form a ''core'' complex that spans the inner and outer membranes. VirB2, VirB5, and VirB7 assemble the pilus. VirB1 is a lytic transglycosidase thought to promote T4SS assembly by lysis of the peptidoglycan layer. Crystal structures of several T4SS components have been published, including homologs of hexameric NTPases VirB11 and VirD4 (3, 4), VirB5 (5), VirB8, and VirB10 (6). A hexameric structure for A. tumefaciens VirB4 has been recently proposed (7).A. tumefaciens VirB8 is a bitopic membrane protein with a short N-terminal cytoplasmically exposed domain, a transmembrane helix, and a large C-terminal periplasmic domain. A T-DNA immunoprecipitation assay has identified contacts between the DNA substrate and six of the T4SS components, including VirB8 (8). It was recently proposed that VirB8 is the scaffold for polar assembly of the A. tumefaciens T4SS (9). Yeast two-hybrid interaction studies suggest that the periplasmic portion of VirB8 contacts VirB1, VirB4, VirB9, VirB10, and VirB11 (10, 11). Biochemical studies confirm that VirB8 interacts with VirB9, VirB10, and itself in vitro (11), and that ...

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“…One general approach to study the interaction between two proteins is to obtain a crystal structure of the protein-protein complex and then investigate the atomic properties of the protein-protein interface. Many studies have analyzed the characteristics of protein-protein interfaces in an effort to search for the factors that contribute to the affinity and specificity of protein-protein interactions [1][2][3][4][5]. These analyses show that the two surfaces of a protein-protein interface usually show high degrees of geometric and chemical complementarities.…”

Section: Introductionmentioning

confidence: 99%

Characterization of Protein–Protein Interfaces

et al. 2007

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We analyze the characteristics of protein-protein interfaces using the largest datasets available from the Protein Data Bank (PDB). We start with a comparison of interfaces with protein cores and noninterface surfaces. The results show that interfaces differ from protein cores and non-interface surfaces in residue composition, sequence entropy, and secondary structure. Since interfaces, protein cores, and non-interface surfaces have different solvent accessibilities, it is important to investigate whether the observed differences are due to the differences in solvent accessibility or differences in functionality. We separate out the effect of solvent accessibility by comparing interfaces with a set of residues having the same solvent accessibility as the interfaces. This strategy reveals residue distribution propensities that are not observable by comparing interfaces with protein cores and noninterface surfaces. Our conclusions are that there are larger numbers of hydrophobic residues, particularly aromatic residues, in interfaces, and the interactions apparently favored in interfaces include the opposite charge pairs and hydrophobic pairs. Surprisingly, Pro-Trp pairs are over represented in interfaces, presumably because of favorable geometries. The analysis is repeated using three datasets having different constraints on sequence similarity and structure quality. Consistent results are obtained across these datasets. We have also investigated separately the characteristics of heteromeric interfaces and homomeric interfaces.

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Morphological aspects of oligomeric protein structures

Cited by 74 publications

References 66 publications

The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of α + β fold

The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of α + β fold

Agrobacterium tumefaciens VirB8 structure reveals potential protein–protein interaction sites

Characterization of Protein–Protein Interfaces

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