Membrane protein structure: prediction versus reality (original) (raw)
Building and analyzing protein interactome networks by cross-species comparisons
BMC Systems Biology, 2010
Background: A genomic catalogue of protein-protein interactions is a rich source of information, particularly for exploring the relationships between proteins. Numerous systems-wide and small-scale experiments have been conducted to identify interactions; however, our knowledge of all interactions for any one species is incomplete, and alternative means to expand these network maps is needed. We therefore took a comparative biology approach to predict protein-protein interactions across five species (human, mouse, fly, worm, and yeast) and developed InterologFinder for research biologists to easily navigate this data. We also developed a confidence score for interactions based on available experimental evidence and conservation across species. Results: The connectivity of the resultant networks was determined to have scale-free distribution, small-world properties, and increased local modularity, indicating that the added interactions do not disrupt our current understanding of protein network structures. We show examples of how these improved interactomes can be used to analyze a genome-scale dataset (RNAi screen) and to assign new function to proteins. Predicted interactions within this dataset were tested by co-immunoprecipitation, resulting in a high rate of validation, suggesting the high quality of networks produced. Conclusions: Protein-protein interactions were predicted in five species, based on orthology. An InteroScore, a score accounting for homology, number of orthologues with evidence of interactions, and number of unique observations of interactions, is given to each known and predicted interaction. Our website http://www. interologfinder.org provides research biologists intuitive access to this data.
eLS, 2001
Abbreviations 3D-PSSM three-dimensional position specific scoring matrix CASP critical assessment of structure prediction HMM hidden Markov model PSI-BLAST position-specific iterative basic local search and alignment tool rmsd root mean square deviation SCOP structural classification of proteins
NClassG+: A classifier for non-classically secreted Gram-positive bacterial proteins
BMC Bioinformatics, 2011
Background: Most predictive methods currently available for the identification of protein secretion mechanisms have focused on classically secreted proteins. In fact, only two methods have been reported for predicting nonclassically secreted proteins of Gram-positive bacteria. This study describes the implementation of a sequencebased classifier, denoted as NClassG+, for identifying non-classically secreted Gram-positive bacterial proteins.
BMC Bioinformatics, 2009
Background: Knowledge of structural class is used by numerous methods for identification of structural/functional characteristics of proteins and could be used for the detection of remote homologues, particularly for chains that share twilight-zone similarity. In contrast to existing sequence-based structural class predictors, which target four major classes and which are designed for high identity sequences, we predict seven classes from sequences that share twilight-zone identity with the training sequences.
Cellular and Molecular Life Sciences, 2010
Membrane protein function is determined by the relative organization of the protein domains with respect to the membrane. We have experimentally verified the topology of a protein with diverse orientations arising from a single primary sequence (the cellular prion protein, PrP C ), a novel somatostatin truncated receptor, and the Golgi-associated protein GPBP 91 . Tagging with fluorescent proteins (FP) allows location of their expression at the plasma membrane or at endomembranes, but does not inform about their orientation. Exploiting the pH dependency of some FPs, we developed a pH exchange assay in which extracellularly exposed FPs are quenched by application of low pH buffer. We constructed standards to demonstrate and calibrate the assay, and the method was adapted for acidic organelle membrane proteins. This method can serve as a proof of concept, experimentally confirming and/or discriminating in living cells among theoretical topology predictions, providing the proportion of inside/outside orientation for proteins with multiple forms.
TOPTMH: TOPOLOGY PREDICTOR FOR TRANSMEMBRANE α-HELICES
Journal of Bioinformatics and Computational Biology, 2010
Alpha-helical transmembrane proteins mediate many key biological processes and represent 20-30% of all genes in many organisms. Due to the difficulties in experimentally determining their high-resolution 3D structure, computational methods that predict their topology (transmembrane helical segments and their orientation) are essential in advancing the understanding of membrane proteins' structures and functions.
Sub-cellular biochemistry, 2008
Lipids play important roles in cellular dysfunction leading to disease. Although a major role for phospholipids is in defining the membrane permeability barrier, phospholipids play a central role in a diverse range of cellular processes and therefore are important factors in cellular dysfunction and disease. This review is focused on the role of phospholipids in normal assembly and organization of the membrane proteins, multimeric protein complexes, and higher order supercomplexes. Since lipids have no catalytic activity, it is difficult to determine their function at the molecular level. Lipid function has generally been defined by affects on protein function or cellular processes. Molecular details derived from genetic, biochemical, and structural approaches are presented for involvement of phosphatidylethanolamine and cardiolipin in protein organization. Experimental evidence is presented that changes in phosphatidylethanolamine levels results in misfolding and topological misori...
Structural analysis of a Peptide fragment of transmembrane transporter protein bilitranslocase
PloS one, 2012
Using a combination of genomic and post-genomic approaches is rapidly altering the number of identified human influx carriers. A transmembrane protein bilitranslocase (TCDB 2.A.65) has long attracted attention because of its function as an organic anion carrier. It has also been identified as a potential membrane transporter for cellular uptake of several drugs and due to its implication in drug uptake, it is extremely important to advance the knowledge about its structure. However, at present, only the primary structure of bilitranslocase is known. In our work, transmembrane subunits of bilitranslocase were predicted by a previously developed chemometrics model and the stability of these polypeptide chains were studied by molecular dynamics (MD) simulation. Furthermore, sodium dodecyl sulfate (SDS) micelles were used as a model of cell membrane and herein we present a high-resolution 3D structure of an 18 amino acid residues long peptide corresponding to the third transmembrane par...
Journal of Biological Chemistry, 2010
Concanavalin A (ConA), which is not a glycoprotein, is synthesized as a glycoprotein precursor (pro-ConA) which is post-translationally processed. This processing results in the loss of a small glycopeptide with a high mannose oligosaccharide. Carrington et al. (Car-rington, D. M., Auffret, A., and Hanke, D. E. (1985) Nature 313, 64-66) determined the nucleotide sequence of a cDNA for pro-ConA, and in the derived amino acid sequence the only glycosylation site is in the middle of the molecule. Furthermore, the derived amino acid sequence of the putative precursor of ConA was found not to be colinear with that of ConA. Here we show that pro-ConA is located primarily in an endoplasmic reticulum-rich organelle fraction. Pro-ConA was purified from this fraction and subjected to amino acid sequencing. The first 12 amino acids at the N-terminal end of pro-ConA correspond to amino acids 119-130 of mature ConA, and to amino acids 30-41 of the putative pre-pro-ConA, the sequence of which was derived from the nucleotide sequence of a cDNA. Amino acid sequencing of a tryptic glycopeptide with the high mannose side chain showed that the first 17 amino acids of this peptide correspond to amino acids 154-170 of pre-pro-ConA. The last six amino acids in this series correspond to the first six amino acids of mature ConA. These data fully support the hypothesis of Carrington et d. that the biosynthesis of ConA involves a post-translational peptide cleavage, transposition, and ligation within the original polypeptide. Pro-ConA from the organelle fraction does not bind to Sephadex G-50, indicating that it has no lectin activity. The processing of pro-ConA apparently imparts biological activity to this lectin.
Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL)
Journal of Computational Chemistry, 2012
We present the Molecular Software Library (MSL), a Cþþ library for molecular modeling. MSL is a set of tools that supports a large variety of algorithms for the design, modeling, and analysis of macromolecules. Among the main features supported by the library are methods for applying geometric transformations and alignments, the implementation of a rich set of energy functions, side chain optimization, backbone manipulation, calculation of solvent accessible surface area, and other tools. MSL has a number of unique features, such as the ability of storing alternative atomic coordinates (for modeling) and multiple amino acid identities at the same backbone position (for design). It has a straightforward mechanism for extending its energy functions and can work with any type of molecules. Although the code base is large, MSL was created with ease of developing in mind. It allows the rapid implementation of simple tasks while fully supporting the creation of complex applications. Some of the potentialities of the software are demonstrated here with examples that show how to program complex and essential modeling tasks with few lines of code. MSL is an ongoing and evolving project, with new features and improvements being introduced regularly, but it is mature and suitable for production and has been used in numerous protein modeling and design projects. MSL is open-source software, freely downloadable at http://msl-libraries.org. We propose it as a common platform for the development of new molecular algorithms and to promote the distribution, sharing, and reutilization of computational methods.
In silico evaluation of the influence of the translocon on partitioning of membrane segments
BMC Bioinformatics, 2014
Background: The locations of the TM segments inside the membrane proteins are the consequence of a cascade of several events: the localizing of the nascent chain to the membrane, its insertion through the translocon, and the conformation adopted to reach its stable state inside the lipid bilayer. Even though the hydrophobic h-region of signal peptides and a typical TM segment are both composed of mostly hydrophobic side chains, the translocon has the ability to determine whether a given segment is to be inserted into the membrane. Our goal is to acquire robust biological insights into the influence of the translocon on membrane insertion of helices, obtained from the in silico discrimination between signal peptides and transmembrane segments of bitopic proteins. Therefore, by exploiting this subtle difference, we produce an optimized scale that evaluates the tendency of each amino acid to form sequences destined for membrane insertion by the translocon. Results: The learning phase of our approach is conducted on carefully chosen data and easily converges on an optimal solution called the PMIscale (Potential Membrane Insertion scale). Our study leads to two striking results. Firstly, with a very simple sliding-window prediction method, PMIscale enables an efficient discrimination between signal peptides and signal anchors. Secondly, PMIscale is also able to identify TM segments and to localize them within protein sequences. Conclusions: Despite its simplicity, the localization method based on PMIscale nearly attains the highest level of TM topography prediction accuracy as the current state-of-the-art prediction methods. These observations confirm the prominent role of the translocon in the localization of TM segments and suggest several biological hypotheses about the physical properties of the translocon.
Biology Direct, 2011
Background: Volutin granules appear to be universally distributed and are morphologically and chemically identical to acidocalcisomes, which are electron-dense granular organelles rich in calcium and phosphate, whose functions include storage of phosphorus and various metal ions, metabolism of polyphosphate, maintenance of intracellular pH, osmoregulation and calcium homeostasis. Prokaryotes are thought to differ from eukaryotes in that they lack membrane-bounded organelles. However, it has been demonstrated that as in acidocalcisomes, the calcium and polyphosphate-rich intracellular "volutin granules (polyphosphate bodies)" in two bacterial species, Agrobacterium tumefaciens, and Rhodospirillum rubrum, are membrane bound and that the vacuolar protontranslocating pyrophosphatases (V-H + PPases) are present in their surrounding membranes. Volutin granules and acidocalcisomes have been found in organisms as diverse as bacteria and humans.
Wzx flippase-mediated membrane translocation of sugar polymer precursors in bacteria
Environmental Microbiology, 2013
Bacterial cell surface polysaccharides confer resistance to external stress and promote survival in biotic and abiotic environments. Glycan assembly often occurs at the periplasmic leaflet of the inner membrane (IM) from undecaprenyl pyrophosphate (UndPP)-linked polysaccharide units via the Wzx/ Wzy-dependent pathway. Wzx is an integral IM protein found in Gram-negative and Gram-positive bacteria that mediates IM translocation of UndPP-linked sugar repeats from the cytoplasmic to the periplasmic leaflet; interaction of Wzx with other assembly proteins is indirectly supported by genetic evidence. Topological mapping has indicated 12 a-helical transmembrane segments (TMS), with the number of charged TMS residues fluctuating based on the mapping method used. A novel Wzx tertiary structure model has been built, allowing for substrate-binding or energy-coupling roles to be proposed for functionally important charged and aromatic TMS residues. It has also led to a proposed antiport-like mechanism of Wzx function. Exquisite substrate specificity of Wzx proteins was recently revealed in distinguishing between UndPP-linked substrates with identical main-chain sugar repeats, but differing in the chemical composition of a terminal sugar side-branch cap. The objective of this review is to synthesize the most up-to-date knowledge concerning Wzx flippases and to provide perspective for future investigations in this burgeoning field.
Frontiers in microbiology, 2016
Pseudomonas aeruginosa is a Gram-negative bacterium that produces highly varied lipopolysaccharide (LPS) structures. The O antigen (O-Ag) in the LPS is synthesized through the Wzx/Wzy-dependent pathway where lipid-linked O-Ag repeats are polymerized by Wzy. Horizontal-gene transfer has been associated with O-Ag diversity. The O-Ag present on the surface of serotypes O5 and O16, differ in the intra-molecular bonds, α and β, respectively; the latter arose from the action of three genes in a serotype converting unit acquired from bacteriophage D3, including a β-polymerase (Wzyβ). To further our understanding of O-polymerases, the inner membrane (IM) topology of Wzyβ was determined using a dual phoA-lacZα reporter system wherein random 3' gene truncations were localized to specific loci with respect to the IM by normalized reporter activities as determined through the ratio of alkaline phosphatase activity to β-galactosidase activity. The topology of Wzyβ developed through this appr...
Predicting protein-protein binding sites in membrane proteins
BMC Bioinformatics, 2009
Background: Many integral membrane proteins, like their non-membrane counterparts, form either transient or permanent multi-subunit complexes in order to carry out their biochemical function. Computational methods that provide structural details of these interactions are needed since, despite their importance, relatively few structures of membrane protein complexes are available. Results: We present a method for predicting which residues are in protein-protein binding sites within the transmembrane regions of membrane proteins. The method uses a Random Forest classifier trained on residue type distributions and evolutionary conservation for individual surface residues, followed by spatial averaging of the residue scores. The prediction accuracy achieved for membrane proteins is comparable to that for non-membrane proteins. Also, like previous results for non-membrane proteins, the accuracy is significantly higher for residues distant from the binding site boundary. Furthermore, a predictor trained on non-membrane proteins was found to yield poor accuracy on membrane proteins, as expected from the different distribution of surface residue types between the two classes of proteins. Thus, although the same procedure can be used to predict binding sites in membrane and non-membrane proteins, separate predictors trained on each class of proteins are required. Finally, the contribution of each residue property to the overall prediction accuracy is analyzed and prediction examples are discussed. Conclusion: Given a membrane protein structure and a multiple alignment of related sequences, the presented method gives a prioritized list of which surface residues participate in intramembrane protein-protein interactions. The method has potential applications in guiding the experimental verification of membrane protein interactions, structure-based drug discovery, and also in constraining the search space for computational methods, such as protein docking or threading, that predict membrane protein complex structures.
BMC biology, 2017
Transmembrane helices (TMHs) frequently occur amongst protein architectures as means for proteins to attach to or embed into biological membranes. Physical constraints such as the membrane's hydrophobicity and electrostatic potential apply uniform requirements to TMHs and their flanking regions; consequently, they are mirrored in their sequence patterns (in addition to TMHs being a span of generally hydrophobic residues) on top of variations enforced by the specific protein's biological functions. With statistics derived from a large body of protein sequences, we demonstrate that, in addition to the positive charge preference at the cytoplasmic inside (positive-inside rule), negatively charged residues preferentially occur or are even enriched at the non-cytoplasmic flank or, at least, they are suppressed at the cytoplasmic flank (negative-not-inside/negative-outside (NNI/NO) rule). As negative residues are generally rare within or near TMHs, the statistical significance is ...
Coronavirus envelope protein: current knowledge
Virology Journal, 2019
Background: Coronaviruses (CoVs) primarily cause enzootic infections in birds and mammals but, in the last few decades, have shown to be capable of infecting humans as well. The outbreak of severe acute respiratory syndrome (SARS) in 2003 and, more recently, Middle-East respiratory syndrome (MERS) has demonstrated the lethality of CoVs when they cross the species barrier and infect humans. A renewed interest in coronaviral research has led to the discovery of several novel human CoVs and since then much progress has been made in understanding the CoV life cycle. The CoV envelope (E) protein is a small, integral membrane protein involved in several aspects of the virus' life cycle, such as assembly, budding, envelope formation, and pathogenesis. Recent studies have expanded on its structural motifs and topology, its functions as an ion-channelling viroporin, and its interactions with both other CoV proteins and host cell proteins. Main body: This review aims to establish the current knowledge on CoV E by highlighting the recent progress that has been made and comparing it to previous knowledge. It also compares E to other viral proteins of a similar nature to speculate the relevance of these new findings. Good progress has been made but much still remains unknown and this review has identified some gaps in the current knowledge and made suggestions for consideration in future research. Conclusions: The most progress has been made on SARS-CoV E, highlighting specific structural requirements for its functions in the CoV life cycle as well as mechanisms behind its pathogenesis. Data shows that E is involved in critical aspects of the viral life cycle and that CoVs lacking E make promising vaccine candidates. The high mortality rate of certain CoVs, along with their ease of transmission, underpins the need for more research into CoV molecular biology which can aid in the production of effective anti-coronaviral agents for both human CoVs and enzootic CoVs.
Methods in molecular biology (Clifton, N.J.), 2010
A protocol is described using lipid mutants and thiol-specific chemical reagents to study lipid-dependent and host-specific membrane protein topogenesis by the substituted-cysteine accessibility method as applied to transmembrane domains (SCAM). SCAM is adapted to follow changes in membrane protein topology as a function of changes in membrane lipid composition. The strategy described can be adapted to any membrane system.
Mathematical Characterization of Protein Transmembrane Regions
The Scientific World Journal, 2013
Graphical bioinformatics has paved a unique way of mathematical characterization of proteins and proteomic maps. The graphics representations and the corresponding mathematical descriptors have proved to be useful and have provided unique solutions to problems related to identification, comparisons, and analyses of protein sequences and proteomics maps. Based on sequence information alone, these descriptors are independent from physiochemical properties of amino acids and evolutionary information. In this work, we have presented invariants from amino acid adjacency matrix and decagonal isometries matrix as potential descriptors of protein sequences. Encoding protein sequences into amino acid adjacency matrix is already well established. We have shown its application in classification of transmembrane and nontransmembrane regions of membrane protein sequences. We have introduced the dodecagonal isometries matrix, which is a novel method of encoding protein sequences based on decagona...
Topological mapping methods for α-helical bacterial membrane proteins - an update and a guide
2013
Integral membrane proteins with a-helical transmembrane segments (TMS) are known to play important and diverse roles in prokaryotic cell physiology. The net hydrophobicity of TMS directly corresponds to the observed difficulties in expressing and purifying these proteins, let alone producing sufficient yields for structural studies using two-/three-dimensional (2D/3D) crystallographic or nuclear magnetic resonance methods. To gain insight into the function of these integral membrane proteins, topological mapping has become an important tool to identify exposed and membrane-embedded protein domains. This approach has led to the discovery of protein tracts of functional importance and to the proposition of novel mechanistic hypotheses. In this review, we synthesize the various methods available for topological mapping of a-helical integral membrane proteins to provide investigators with a comprehensive reference for choosing techniques suited to their particular topological queries and available resources.
BMC Bioinformatics, 2010
Background A large proportion of an organism's genome encodes for membrane proteins. Membrane proteins are important for many cellular processes, and several diseases can be linked to mutations in them. With the tremendous growth of sequence data, there is an increasing need to reliably identify membrane proteins from sequence, to functionally annotate them, and to correctly predict their topology. Results We introduce a technique called structural fragment clustering, which learns sequential motifs from 3D structural fragments. From over 500,000 fragments, we obtain 213 statistically significant, non-redundant, and novel motifs that are highly specific to α-helical transmembrane proteins. From these 213 motifs, 58 of them were assigned to function and checked in the scientific literature for a biological assessment. Seventy percent of the motifs are found in co-factor, ligand, and ion binding sites, 30% at protein interaction interfaces, and 12% bind specific lipids such as gly...
Prediction of membrane-protein topology from first principles
Proceedings of the National Academy of Sciences, 2008
The current best membrane-protein topology-prediction methods are typically based on sequence statistics and contain hundreds of parameters that are optimized on known topologies of membrane proteins. However, because the insertion of transmembrane helices into the membrane is the outcome of molecular interactions among protein, lipids and water, it should be possible to predict topology by methods based directly on physical data, as proposed >20 years ago by Kyte and Doolittle. Here, we present two simple topology-prediction methods using a recently published experimental scale of position-specific amino acid contributions to the free energy of membrane insertion that perform on a par with the current best statistics-based topology predictors. This result suggests that prediction of membrane-protein topology and structure directly from first principles is an attainable goal, given the recently improved understanding of peptide recognition by the translocon.
Planar substrate-binding site dictates the specificity of ECF-type nickel/cobalt transporters
Cell Research, 2013
The energy-coupling factor (ECF) transporters are multi-subunit protein complexes that mediate uptake of transition-metal ions and vitamins in about 50% of the prokaryotes, including bacteria and archaea. Biological and structural studies have been focused on ECF transporters for vitamins, but the molecular mechanism by which ECF systems transport metal ions from the environment remains unknown. Here we report the first crystal structure of a NikM, TtNikM2, the substrate-binding component (S component) of an ECF-type nickel transporter from Thermoanaerobacter tengcongensis. In contrast to the structures of the vitamin-specific S proteins with six transmembrane segments (TSs), TtNikM2 possesses an additional TS at its N-terminal region, resulting in an extracellular N-terminus. The highly conserved N-terminal loop inserts into the center of TtNikM2 and occludes a region corresponding to the substrate-binding sites of the vitamin-specific S components. Nickel binds to NikM via its coordination to four nitrogen atoms, which are derived from Met1, His2 and His67 residues. These nitrogen atoms form an approximately square-planar geometry, similar to that of the metal ion-binding sites in the amino-terminal Cu 2+-and Ni 2+-binding (ATCUN) motif. Replacements of residues in NikM contributing to nickel coordination compromised the Ni-transport activity. Furthermore, systematic quantum chemical investigation indicated that this geometry enables NikM to also selectively recognize Co 2+. Indeed, the structure of TtNikM2 containing a bound Co 2+ ion has almost no conformational change compared to the structure that contains a nickel ion. Together, our data reveal an evolutionarily conserved mechanism underlying the metal selectivity of EcfS proteins, and provide insights into the ion-translocation process mediated by ECF transporters.
Scientific Reports, 2019
Because of the lack of cell wall, Micoplasma species require a fine control of membrane fluidity and integrity. mg517 is an essential gene of Mycoplasma genitalium responsible for the biosynthesis of membrane glycoglycerolipids. It encodes for a unique glycosyltransferase (MG517) with processive activity, transferring activated glycosyl donors to either nude diacylglycerol or already glycosylated diacylglycerol. This dual activity, asserted to different enzymes in other species, is sensitive to and regulated by the presence of anionic lipid vesicles in vitro. We present here a computational model of the C-terminus domain of MG517 that complements a previous structural model of the N-terminus domain. By means of sequence analysis, molecular dynamics and metadynamics simulations, we have identified a short α-helix at the apical C-terminus of MG517 with clear amphipathic character. Binding to a membrane model is thermodynamically favored which suggests that this structural element guides the adhesion of MG517 to the cell membrane. We have experimentally verified that truncation of part of this helix causes a substantial reduction of glycoglycerolipids synthesis. the model proposes that MG517 recognizes and binds the diacylglycerol substrate embedded in the membrane by means of this α-helix at the C-terminus together with a previously identified binding pocket at the N-terminus. Membrane proteins can either be "peripheral" or "integral" depending on how they associate to the lipid bilayer 1. From one hand, peripheral membrane proteins bind only temporarily at one side of the membrane (monotopic interaction) or are bound to other proteins by weak noncovalent interactions at the membrane interface. The reversible attachment of peripheral membrane proteins has shown to regulate cell signaling and many other important cellular events 2. Such a protein-membrane association can be easily disrupted with the use of alkaline and high ionic strength buffers that leave the lipid bilayer intact 1. On the other hand, the binding to the membrane of integral membrane proteins is strong and permanent, usually adopting structural functions such as transporters, linkers, channels and proteins responsible for cell adhesion 3. Integral membrane proteins can only be extracted from the membrane by disrupting the lipidic bilayer, using either detergents or organic solvents 4,5. Depending on the way integral membrane proteins are embedded in the membrane, these are termed monotopic, bitopic or polytopic proteins 6. Monotopic integral membrane proteins associate permanently to only one face of membrane. Bitopic and polytopic integral membrane proteins exhibit one or more transmembrane segments that cross the membrane at different levels 7,8. The 1,2-diacylglycerol 3-glucosyltransferase from Acholeplasma laidlawii (AlMGS), a cell wall-less prokaryote, is a good representative of monotopic enzymes, from which the molecular details of peripheral protein-membrane binding can be drawn 8. The charge density and curvature properties of the A. laidlawii membrane is controlled by this monoglucosyldiacylglycerol synthase (AlMGS) and the diglucosyldiacylglycerol synthase (AlDGS), which are associated to the cyosolic side of the membrane. These two glycolipid synthases are glycosyltransferases (GT) that catalyze the transfer of glucosyl residues from uridine diphosphoglucose (UDPGlc) to a diacylglycerol (DAG) acceptor, sequentially synthesizing monoglucosyl diacylglycerol (GlcDAG) and diglucosyl diacylglycerol (GlcGlcDAG), respectively 9. The molar ratio between these two glucolipids at the membrane affects its curvature and is adjusted by the activity of these two enzymes, which is altered by different stimuli, including ionic strength and aliphatic chains composition. The use of detergents are required to extract AlMGS from the membrane, albeit
Life at the border: adaptation of proteins to anisotropic membrane environment
Protein science : a publication of the Protein Society, 2014
This review discusses main features of transmembrane (TM) proteins which distinguish them from water-soluble proteins and allow their adaptation to the anisotropic membrane environment. We overview the structural limitations on membrane protein architecture, spatial arrangement of proteins in membranes and their intrinsic hydrophobic thickness, co-translational and post-translational folding and insertion into lipid bilayers, topogenesis, high propensity to form oligomers, and large-scale conformational transitions during membrane insertion and transport function. Special attention is paid to the polarity of TM protein surfaces described by profiles of dipolarity/polarizability and hydrogen-bonding capacity parameters that match polarity of the lipid environment. Analysis of distributions of Trp resides on surfaces of TM proteins from different biological membranes indicates that interfacial membrane regions with preferential accumulation of Trp indole rings correspond to the outer ...
Prediction of membrane protein structures with complex topologies using limited constraints
Proceedings of the National Academy of Sciences, 2009
Reliable structure-prediction methods for membrane proteins are important because the experimental determination of high-resolution membrane protein structures remains very difficult, especially for eukaryotic proteins. However, membrane proteins are typically longer than 200 aa and represent a formidable challenge for structure prediction. We have developed a method for predicting the structures of large membrane proteins by constraining helix–helix packing arrangements at particular positions predicted from sequence or identified by experiments. We tested the method on 12 membrane proteins of diverse topologies and functions with lengths ranging between 190 and 300 residues. Enforcing a single constraint during the folding simulations enriched the population of near-native models for 9 proteins. In 4 of the cases in which the constraint was predicted from the sequence, 1 of the 5 lowest energy models was superimposable within 4 Å on the native structure. Near-native structures cou...
A survey of integral α-helical membrane proteins
Journal of Structural and Functional Genomics, 2009
Membrane proteins serve as cellular gatekeepers, regulators, and sensors. Prior studies have explored the functional breadth and evolution of proteins and families of particular interest, such as the diversity of transport-associated membrane protein families in prokaryotes and eukaryotes, the composition of integral membrane proteins, and family classification of all human G-protein coupled receptors. However, a comprehensive analysis of the content and evolutionary associations between membrane proteins and families in a diverse set of genomes is lacking. Here, a membrane protein annotation pipeline was developed to define the integral membrane genome and associations between 21,379 proteins from 34 genomes; most, but not all of these proteins belong to 598 defined families. The pipeline was used to provide target input for a structural genomics project that successfully cloned, expressed, and purified 61 of our first 96 selected targets in yeast. Furthermore, the methodology was applied (1) to explore the evolutionary history of the substrate-binding transmembrane domains of the human ABC transporter superfamily, (2) to identify the multidrug resistance-associated membrane proteins in whole genomes, and (3) to identify putative new membrane protein families.