A novel method for packing quality assessment of transmembrane α-helical domains in proteins (original) (raw)
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A novel method for packing quality assessment of transmembrane alpha-helical domains in proteins
Biochemistry. Biokhimii͡a, 2007
Here we present a novel method for assessment of packing quality for transmembrane (TM) domains of alpha-helical membrane proteins (MPs), based on analysis of available high-resolution experimental structures of MPs. The presented concept of protein-membrane environment classes permits quantitative description of packing characteristics in terms of membrane accessibility and polarity of the nearest protein groups. We demonstrate that the method allows identification of native-like conformations among the large set of theoretical MP models. The developed "membrane scoring function" will be of use for optimization of TM domain packing in theoretical models of MPs, first of all G-protein coupled receptors.
Journal of Chemical Information and Modeling, 2007
Integral membrane proteins (MPs) are pharmaceutical targets of exceptional importance. Modern methods of three-dimensional protein structure determination often fail to supply the fast growing field of structurebased drug design with the requested MPs' structures. That is why computational modeling techniques gain a special importance for these objects. Among the principal difficulties limiting application of these methods is the low quality of the MPs' models built in silico. In this series of two papers we present a computational approach to the assessment of the packing "quality" of transmembrane (TM) R-helical domains in proteins. The method is based on the concept of protein environment classes, whereby each amino acid residue is described in terms of its environment polarity and accessibility to the membrane. In the first paper we analyze a nonredundant set of 26 TM R-helical domains and compute the residues' propensities to five predefined classes of membrane-protein environments. Here we evaluate the proposed approach only by various test sets, cross-validation protocols and ability of the method to delimit the crystal structure of visual rhodopsin, and a number of its erroneous theoretical models. More advanced validation of the method is given in the second article of this series. We assume that the developed "membrane score" method will be helpful in optimizing computer models of TM domains of MPs, especially G-protein coupled receptors.
A Method to Assess Correct/Misfolded Structures of Transmembrane Domains of Membrane Proteins
Motivation: Integral membrane proteins (MP) are pharmaceutical targets of exceptional importance since more than 50 % of currently marketed drugs target these objects. Due to technical difficulties, modern experimental methods often fail to determine 3D structure of MPs. Computational methods for modeling MPs structure and assessment of these models' quality may be very helpful in this case. Results: We propose a novel method for quantitative estimation of the transmembrane (TM) domains models' quality. The approach is based on the concept of environmental profile. A non-redundant set of 26 high-resolution X-ray structures of α-helical TM domains is used to define five classes of residues' environment, considering polarity of nearest protein surrounding and accessibility for a given residue. Residues' preferences for each environment class are calculated. The main results are: (1) The proteins length correlates with the proposed scoring function values, defining a way to differentiate "well-folded" structures from misfolded ones; (2) The method efficiently delineates crystallographic structure of visual rhodopsin both in a set of twelve its computer models, containing certain errors and ensemble of artificially generated misfolded structures of rhodopsin; (3) Photosynthetic MPs demonstrate different score-length dependency, suggesting distinct packing characteristics for these proteins.
Modelling the structures of G protein-coupled receptors aided by three-dimensional validation
BMC Bioinformatics, 2008
Background G protein-coupled receptors (GPCRs) are abundant, activate complex signalling and represent the targets for up to ~60% of pharmaceuticals but there is a paucity of structural data. Bovine rhodopsin is the first GPCR for which high-resolution structures have been completed but significant variations in structure are likely to exist among the GPCRs. Because of this, considerable effort has been expended on developing in silico tools for refining structures of individual GPCRs. We have developed REPIMPS, a modification of the inverse-folding software Profiles-3D, to assess and predict the rotational orientation and vertical position of helices within the helix bundle of individual GPCRs. We highlight the value of the method by applying it to the Baldwin GPCR template but the method can, in principle, be applied to any low- or high-resolution membrane protein template or structure. Results 3D models were built for transmembrane helical segments of 493 GPCRs based on the Baldwin template, and the models were then scored using REPIMPS and Profiles-3D. The compatibility scores increased significantly using REPIMPS because it takes into account the physicochemical properties of the (lipid) environment surrounding the helix bundle. The arrangement of helices in the helix bundle of the 493 models was then altered systematically by rotating the individual helices. For most GPCRs in the set, changes in the rotational position of one or more helices resulted in significant improvement in the compatibility scores. In particular, for most GPCRs, a rotation of helix VII by 240–300° resulted in improved scores. Bovine rhodopsin modelled using this method showed 3.31 Å RMSD to its crystal structure for 198 Cα atom pairs, suggesting the utility of the method even when starting with idealised structures such as the Baldwin template. Conclusion We have developed an in silico tool which can be used to test the validity of, and refine, models of GPCRs with respect to helix rotation and vertical position based on the physicochemical properties of amino acids and the surrounding environment. The method can be applied to any multi-pass membrane protein and potentially can be used in combination with other high-throughput methodologies to generate and refine models of membrane proteins.
Frontiers in Physics
Biological cell is the fundamental building block of every living system. The plasma membrane, a phospholipid bilayer consisting of two asymmetric leaflets, defines its existence by separating the interior from the exterior. This low dielectric barrier selectively prevents the passage of hydrophilic and charged compounds including small ions. Integral transmembrane proteins span the entire bilayer and take part in small-molecule transport and complex signaling pathways while functioning as receptors and/or ion channels. These proteins carry important biological functions and hence are attractive drug targets. Present review considers the members of two important protein superfamilies that provided the major pharmaceutical drug-targets, viz., Cys-loop pentameric ligand gated ion channels (pLGICs) and class A G-protein-coupled receptors (GPCRs). The crystal structures of integral membrane proteins (IMPs) are difficult to obtain. Their unavailability has limited the structural investigation and associated structure-based drug designing (SBDD). However, recent advancement in crystallographic techniques yielded some important crystal structures. The advancement of computational science guided IMPs study even in the absence of crystal structures through the homology/comparative modeling approaches. These proteins possess multiple ligand binding sites including both orthosteric and allosteric sites. Addressing the multidimensional problem of understanding the structure and dynamics of such big proteins, multisite-protein-ligand complexes is now possible with molecular dynamics simulation approach, enabled with highly enhanced computational power. Overall the discussion highlights the understanding of structure-function relationship that guides SBDD of these interesting and important transmembrane proteins.
Determining membrane protein structures: still a challenge!
Trends in Biochemical Sciences, 2007
Determination of structures and dynamics events of transmembrane proteins is important for the understanding of their function. Analysis of such events requires high-resolution 3D structures of the different conformations coupled with molecular dynamics analyses describing the conformational pathways. However, the solution of 3D structures of transmembrane proteins at atomic level remains a particular challenge for structural biochemists-the need for purified and functional transmembrane proteins causes a 'bottleneck'. There are various ways to obtain 3D structures: X-ray diffraction, electron microscopy, NMR and modelling; these methods are not used exclusively of each other, and the chosen combination depends on several criteria. Progress in this field will improve knowledge of ligand-induced activation and inhibition of membrane proteins in addition to aiding the design of membrane-protein-targeted drugs. Purification and characterization Because TMPs comprise a hydrophobic core inserted into the lipid bilayer and hydrophilic domains on either side of Review
Automated method for modeling seven-helix transmembrane receptors from experimental data
Biophysical Journal, 1995
A rule-based automated method is presented for modeling the structures of the seven transmembrane helices of G-protein-coupled receptors. The structures are generated by using a simulated annealing Monte Carlo procedure that positions and orients rigid helices to satisfy structural restraints. The restraints are derived from analysis of experimental information from biophysical studies on native and mutant proteins, from analysis of the sequences of related proteins, and from theoretical considerations of protein structure. Calculations are presented for two systems. The method was validated through calculations using appropriate experimental information for bacteriorhodopsin, which produced a model structure with a root mean square (rms) deviation of 1.87 A from the structure determined by electron microscopy. Calculations are also presented using experimental and theoretical information available for bovine rhodopsin to assign the helices to a projection density map and to produce a model of bovine rhodopsin that can be used as a template for modeling other G-proteincoupled receptors.
NMR Investigation of Structures of G-protein Coupled Receptor Folding Intermediates
Journal of Biological Chemistry, 2016
Folding of G-protein coupled receptors (GPCRs) according to the two-stage model (Popot et al., Biochemistry 29(1990), 4031) is postulated to proceed in 2 steps: Partitioning of the polypeptide into the membrane followed by diffusion until native contacts are formed. Herein we investigate conformational preferences of fragments of the yeast Ste2p receptor using NMR. Constructs comprising the first, the first two and the first three transmembrane (TM) segments, as well as a construct comprising TM1-TM2 covalently linked to TM7 were examined. We observed that the isolated TM1 does not form a stable helix nor does it integrate well into the micelle. TM1 is significantly stabilized upon interaction with TM2, forming a helical hairpin reported previously (Neumoin et al., Biophys. J. 96(2009), 3187), and in this case the protein integrates into the hydrophobic interior of the micelle. TM123 displays a strong tendency to oligomerize, but hydrogen exchange data reveal that the center of TM3 is solvent exposed. In all GPCRs so-far structurally characterized TM7 forms many contacts with TM1 and TM2. In our study TM127 integrates well into the hydrophobic environment, but TM7 does not stably pack against the remaining helices. Topology mapping in microsomal membranes also indicates that TM1 does not integrate in a membrane-spanning fashion, but that TM12, TM123 and TM127 adopt predominantly native-like topologies. The data from our study would be consistent with the retention of individual helices of incompletely synthesized GPCRs in the vicinity of the translocon until the complete receptor is released into the membrane interior.
ChemInform, 2007
We describe a set of tests designed to check the ability of the new "membrane score" method (see the first paper of this series) to assess the packing quality of transmembrane (TM) R-helical domains in proteins. The following issues were addressed: (1) Whether there is a relation between the score (S mem) of a model and its closeness to the "nativelike" conformation? (2) Is it possible to recognize a correct model among misfolded and erroneous ones? (3) To what extent the score of a homology-built model is sensitive to errors in sequence alignment? To answer the first question, two test cases were considered: (i) Several models of bovine aquaporin-1 (target protein) were built on the structural templates provided by its homologs with known X-ray structure. (ii) Side chains in the spatial models of visual rhodopsin and cytochrome c oxidase were rebuilt based on the backbone scaffolds taken from their crystal structures, and the resulting models were iteratively fitted into the full-atom X-ray conformations. It was shown that the higher the S mem value of a model is, the lower its root-mean-square deviation is from the "correct" (crystal) structure of a target. Furthermore, the "membrane score" method successfully identifies the rhodopsin crystal structure in an ensemble of "rotamer-type" decoys, thus providing the way to optimize mutual orientations of R-helices in models of TM domains. Finally, being applied to a set of homology models of rhodopsin built on its crystal structure with systematically shifted alignment, the approach demonstrates a prominent ability to detect alignment errors. We therefore assume that the "membrane score" method will be helpful in optimization of in silico models of TM domains in proteins, especially those in GPCRs.