In Meso Crystal Structure and Docking Simulations Suggest an Alternative Proteoglycan Binding Site in the Opca Outer Membrane Adhesin.

Published on Apr 1, 2008in Proteins2.501
· DOI :10.1002/prot.21841
Vadim Cherezov61
Estimated H-index: 61
(OSU: Ohio State University),
Wei Liu35
Estimated H-index: 35
(OSU: Ohio State University)
+ 4 AuthorsMartin Caffrey56
Estimated H-index: 56
OpcA is an integral outer membrane adhesin protein from Neisseria meningitidis, the causative agent of meningococcal meningitis and septicemia. It binds to sialic acid (SA)-containing polysaccharides on the surface of epithelial cells. The crystal structure of OpcA showed that the protein adopts a 10-stranded β-barrel structure, with five extensive loop regions on the extracellular side of the membrane. These form a crevice structure, lined with basic residues, which was hypothesized to act as the binding site for polysaccharide ligands. In the current study, a distinctly different OpcA structure has been obtained using crystals grown from a lipidic mesophase. Comparison of the two structures shows that the largest loop (L2), which closes over the end of the β-barrel in the original crystal form, adopts a much more extended structure by reaching outward and away from the protein. The difference in conformation may be attributable to the absence of zinc ions from the crystallization conditions for the in meso crystal form: in the original structure, two zinc ions were bound to the external loops. Molecular dynamics (MD) simulations performed on the two OpcA models in a lipid bilayer environment demonstrated pronounced loop mobility. These observations support the view that the loop regions of OpcA are capable of a high degree of conformational flexibility. The original binding site for polysaccharide is not present in the in meso crystal form, and is disrupted during MD simulations. Docking analysis suggests a putative alternative location for the SA ligand in the new crystal form of OpcA. Proteins 2008. © 2007 Wiley-Liss, Inc.
  • References (44)
  • Citations (35)
📖 Papers frequently viewed together
80 Citations
2,516 Citations
711 Citations
78% of Scinapse members use related papers. After signing in, all features are FREE.
#1Peter J. Bond (University of Oxford)H-Index: 35
#2Jeremy P. Derrick (University of Manchester)H-Index: 28
Last. Mark S.P. Sansom (University of Oxford)H-Index: 68
view all 3 authors...
Mobility of extracellular loops may play an important role in the function of outer membrane proteins from Gram-negative bacteria. Molecular dynamics simulations of OpcA from Neisseria meningitidis, embedded in a lipid bilayer, have been used to explore the relationship between the crystal structure and dynamic function of this protein. The results suggest that the crystal environment may constrain the membrane protein structure in a nonphysiological state. The presence of lipids and physiologic...
30 CitationsSource
#1Vadim Cherezov (OSU: Ohio State University)H-Index: 61
#2Eiki Yamashita (Purdue University)H-Index: 35
Last. Martin Caffrey (OSU: Ohio State University)H-Index: 56
view all 6 authors...
80 CitationsSource
#1Satoshi MurakamiH-Index: 26
#2Ryosuke Nakashima (Osaka University)H-Index: 11
Last. Akihito Yamaguchi (Osaka University)H-Index: 50
view all 5 authors...
AcrB is a principal multidrug efflux transporter in Escherichia coli that cooperates with an outer-membrane channel, TolC, and a membrane-fusion protein, AcrA. Here we describe crystal structures of AcrB with and without substrates. The AcrB–drug complex consists of three protomers, each of which has a different conformation corresponding to one of the three functional states of the transport cycle. Bound substrate was found in the periplasmic domain of one of the three protomers. The voluminous...
489 CitationsSource
#1Friederike Lehmann (Griffith University)H-Index: 3
#2Evelin Tiralongo (Griffith University)H-Index: 19
Last. Joe Tiralongo (Griffith University)H-Index: 18
view all 3 authors...
Sialic acids consist of a family of acidic ninecarbon sugars that are typically located at the terminal positions of a variety of glycoconjugates. Naturally occurring sialic acids show an immense diversity of structure, and this reflects their involvement in a variety of biologically important processes. One such process involves the direct participation of sialic acids in recognition events through specific interactions with lectins, a family of proteins that recognise and bind sugars. This rev...
172 CitationsSource
#1Vadim Cherezov (UL: University of Limerick)H-Index: 61
#2J. Clogston (OSU: Ohio State University)H-Index: 5
Last. Martin Caffrey (UL: University of Limerick)H-Index: 56
view all 4 authors...
189 CitationsSource
#1Mikhail A. Lomize (UM: University of Michigan)H-Index: 5
#2Andrei L. Lomize (UM: University of Michigan)H-Index: 23
Last. Henry I. Mosberg (UM: University of Michigan)H-Index: 50
view all 4 authors...
Summary: The Orientations of Proteins in Membranes (OPM) database provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank whose spatial arrangements in the lipid bilayer have been calculated theoretically and compared with experimental data. The database allows analysis, sorting and searching of membrane proteins based on their structural classification, species, destination membrane, numbers of transmembrane segments and subunits, numbers of secondar...
738 CitationsSource
#1Hongming ChenH-Index: 17
#2Paul D. LyneH-Index: 2
Last. Jin LiH-Index: 3
view all 5 authors...
Four of the most well-known, commercially available docking programs, FlexX, GOLD, GLIDE, and ICM, have been examined for their ligand-docking and virtual-screening capabilities. The relative performance of the programs in reproducing the native ligand conformation from starting SMILES strings for 164 high-resolution protein−ligand complexes is presented and compared. Applying only the native scoring functions, the latest versions of these four docking programs were also used to conduct virtual ...
145 CitationsSource
#1James C. Phillips (UIUC: University of Illinois at Urbana–Champaign)H-Index: 1
#2Rosemary Braun (UIUC: University of Illinois at Urbana–Champaign)H-Index: 13
Last. Klaus Schulten (UIUC: University of Illinois at Urbana–Champaign)H-Index: 123
view all 10 authors...
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomo- lecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD ...
9,590 CitationsSource
#1Jeremy Moore (University of Manchester)H-Index: 2
#2Simon Bailey (University of Manchester)H-Index: 10
Last. Jeremy P. Derrick (University of Manchester)H-Index: 28
view all 7 authors...
Abstract The adhesion of the pathogen Neisseria meningitidis to host cell surface proteoglycan, mediated by the integral outer membrane proteins OpcA and Opa, plays an important part in the processes of colonization and invasion by the bacterium. The precise specificities of the OpcA and Opa proteins are, however, unknown. Here we use a fluorescence-based binding assay to show that both proteins bind to mono- and disaccharides with high affinity. Binding of saccharides caused a quench in the int...
42 CitationsSource
#1Jianghong AnH-Index: 8
#2Maxim TotrovH-Index: 38
Last. Ruben AbagyanH-Index: 77
view all 3 authors...
We developed a new computational algorithm for the accurate identification of ligand binding envelopes rather than surface binding sites. We performed a large scale classification of the identified envelopes according to their shape and physicochemical properties. The predicting algorithm, called PocketFinder, uses a transformation of the Lennard-Jones potential calculated from a three-dimensional protein structure and does not require any knowledge about a potential ligand molecule. We validate...
278 CitationsSource
Cited By35
Abstract The lipid cubic phase (LCP) has been used extensively as a medium for crystallizing membrane proteins. It is an attractive environment in which to perform such studies because it incorporates a lipid bilayer. It is therefore considered a useful and a faithful biomembrane mimetic. Here we bring together evidence that supports this view. Biophysical characterizations are described demonstrating that the cubic phase is a porous medium into and out of which water-soluble molecules can diffu...
1 CitationsSource
#1Edinson Puentes-Cala (MPG: Max Planck Society)H-Index: 1
#2Jens Harder (MPG: Max Planck Society)H-Index: 32
The betaproteobacterium Castellaniella defragrans 65Phen grows on monoterpenes at concentrations toxic to many bacteria. Tolerance mechanisms include modifications of the membrane fatty acid composition and the mineralization of monoterpenes. In this study, we characterized an efflux transporter associated to the monoterpene metabolism. The inner-membrane transporter AmeD (apolar monoterpene efflux) affiliated to the HAE3 (hydrophobe/amphiphile efflux) family within the Resistance-Nodulation-Div...
#1Jialu Zha (CAS: Chinese Academy of Sciences)
#2Dianfan Li (CAS: Chinese Academy of Sciences)H-Index: 20
Membrane proteins constitute an integral part of biomembrane and play key roles in fundamental biological and physiological processes such as metabolism, signaling, and ion homeostasis. About half of all drug targets are membrane proteins. Elucidation of three-dimensional structures of membrane proteins by X-ray crystallography can provide mechanistic insights for their cellular activity and reveal atomic resolution of architectural details for rational design of novel therapeutics. However, the...
Cryo-electron microscopy (cryo-EM) has produced density maps of various resolutions. Although α-helices can be detected from density maps at 5–8 A resolutions, β-strands are challenging to detect at such density maps due to close-spacing of β-strands. The variety of shapes of β-sheets adds the complexity of β-strands detection from density maps. We propose a new approach to model traces of β-strands for β-barrel density regions that are extracted from cryo-EM density maps. In the test containing...
8 CitationsSource
Oct 2, 2016 in BIOINFORMATICS (International Conference on Bioinformatics)
#1Dong Si (UW: University of Washington)H-Index: 8
Cryo-electron microscopy (Cryo-EM) has become central to the study of large-scale molecular interactions and has produced three-dimensional (3D) density maps at various resolutions. Secondary structure element (SSE) identification from volumetric protein density maps is critical for de novo backbone structure derivation in cryo-EM. Multiple methods have been developed to detect helix and β-sheet from density maps at medium resolutions (~5-10A). β-barrel as a special β-sheet structure has been fo...
3 CitationsSource
The dipole interaction model is a classical electromagnetic theory for calculating circular dichroism (CD) resulting from the π-π* transitions of amides. The theoretical model, pioneered by J. Applequist, is assembled into a package, DInaMo, written in Fortran allowing for treatment of proteins. DInaMo reads Protein Data Bank formatted files of structures generated by molecular mechanics or reconstructed secondary structures. Crystal structures cannot be used directly with DInaMo; they either ne...
2 CitationsSource
Most human diseases, not involving infection, progress due to protein misfolding. Cystic fibrosis, cancers, neurodegenerative diseases, amyloidoses, cataracts and sickle cell anaemia are prime examples1. Protein folding is the assumption by a linear polypeptide of a 3D form that can engage in functional interactions. Getting it right is a delicate balancing act with mere kTs in favour of the correctly folded form2. In contrast to their soluble counterparts, membrane proteins must navigate a part...
11 CitationsSource
The lipid cubic phase or in meso method is a robust approach for crystallizing membrane proteins for structure determination. The uptake of the method is such that it is experiencing what can only be described as explosive growth. This timely, comprehensive and up-to-date review introduces the reader to the practice of in meso crystallogenesis, to the associated challenges and to their solutions. A model of how crystallization comes about mechanistically is presented for a more rational approach...
98 CitationsSource
Aug 1, 2014 in EMBC (International Conference of the IEEE Engineering in Medicine and Biology Society)
#1Dong Si (ODU: Old Dominion University)H-Index: 8
#2Jing He (ODU: Old Dominion University)H-Index: 14
Electron cryo-microscopy (Cryo-EM) technique produces 3-dimensional (3D) density images of proteins. When resolution of the images is not high enough to resolve the molecular details, it is challenging for image processing methods to enhance the molecular features. β-barrel is a particular structure feature that is formed by multiple β-strands in a barrel shape. There is no existing method to derive β-strands from the 3D image of a β-barrel at medium resolutions. We propose a new method, StrandR...
9 CitationsSource
Background Osteopontin (Eta, secreted sialoprotein 1, opn) is secreted from different cell types including cancer cells. Three splice variant forms namely osteopontin-a, osteopontin-b and osteopontin-c have been identified. The main astonishing feature is that osteopontin-c is found to be elevated in almost all types of cancer cells. This was the vital point to consider it for sequence analysis and structure predictions which provide ample chances for prognostic, therapeutic and preventive cance...
10 CitationsSource