Prediction of the general structure of OmpF and PhoE from the sequence and structure of porin from Rhodobacter capsulatus. Orientation of porin in the membrane

RECOGNITION OF TRANSMEMBRANE SEGMENTS IN PROTEINS: REVIEW AND CONSISTENCY-BASED BENCHMARKING OF INTERNET SERVERS

Membrane proteins perform a number of crucial functions as transporters, receptors, and components of enzyme complexes. Identification of membrane proteins and prediction of their topology is thus an important part of genome annotation. We present here an overview of transmembrane segments in protein sequences, summarize data from large-scale genome studies, and report results of benchmarking of several popular internet servers.

TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins

MOTIVATION

Transmembrane beta-barrel (TMB) proteins are embedded in the outer membranes of mitochondria, Gram-negative bacteria and chloroplasts. These proteins perform critical functions, including active ion-transport and passive nutrient intake. Therefore, there is a need for accurate prediction of secondary and tertiary structure of TMB proteins. Traditional homology modeling methods, however, fail on most TMB proteins since very few non-homologous TMB structures have been determined. Yet, because TMB structures conform to specific construction rules that restrict the conformational space drastically, it should be possible for methods that do not depend on target-template homology to be applied successfully.

RESULTS

We develop a suite (TMBpro) of specialized predictors for predicting secondary structure (TMBpro-SS), beta-contacts (TMBpro-CON) and tertiary structure (TMBpro-3D) of transmembrane beta-barrel proteins. We compare our results to the recent state-of-the-art predictors transFold and PRED-TMBB using their respective benchmark datasets, and leave-one-out cross-validation. Using the transFold dataset TMBpro predicts secondary structure with per-residue accuracy (Q(2)) of 77.8%, a correlation coefficient of 0.54, and TMBpro predicts beta-contacts with precision of 0.65 and recall of 0.67. Using the PRED-TMBB dataset, TMBpro predicts secondary structure with Q(2) of 88.3% and a correlation coefficient of 0.75. All of these performance results exceed previously published results by 4% or more. Working with the PRED-TMBB dataset, TMBpro predicts the tertiary structure of transmembrane segments with RMSD <6.0 A for 9 of 14 proteins. For 6 of 14 predictions, the RMSD is <5.0 A, with a GDT_TS score greater than 60.0.

AVAILABILITY

http://www.igb.uci.edu/servers/psss.html.

TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins

We have developed a web-server, TMBETA-NET for discriminating outer membrane proteins and predicting their membrane spanning β-strand segments. The amino acid compositions of globular and outer membrane proteins have been systematically analyzed and a statistical method has been proposed for discriminating outer membrane proteins. The prediction of membrane spanning segments is mainly based on feed forward neural network and refined with β-strand length. Our program takes the amino acid sequence as input and displays the type of the protein along with membrane-spanning β-strand segments as a stretch of highlighted amino acid residues. Further, the probability of residues to be in transmembrane β-strand has been provided with a coloring scheme. We observed that outer membrane proteins were discriminated with an accuracy of 89% and their membrane spanning β-strand segments at an accuracy of 73% just from amino acid sequence information. The prediction server is available at .

Neural network-based prediction of transmembrane β-strand segments in outer membrane proteins

Prediction of transmembrane beta-strands in outer membrane proteins (OMP) is one of the important problems in computational chemistry and biology. In this work, we propose a method based on neural networks for identifying the membrane-spanning beta-strands. We introduce the concept of "residue probability" for assigning residues in transmembrane beta-strand segments. The performance of our method is evaluated with single-residue accuracy, correlation, specificity, and sensitivity. Our predicted segments show a good agreement with experimental observations with an accuracy level of 73% solely from amino acid sequence information. Further, the predictive power of N- and C-terminal residues in each segments, number of segments in each protein, and the influence of cutoff probability for identifying membrane-spanning beta-strands will be discussed. We have developed a Web server for predicting the transmembrane beta-strands from the amino acid sequence, and the prediction results are available at http://psfs.cbrc.jp/tmbeta-net/.

A HMM-based method to predict the transmembrane regions of beta-barrel membrane proteins

A novel method is developed to model and predict the transmembrane regions of beta-barrel membrane proteins. It is based on a Hidden Markov model (HMM) with architecture obeying those proteins' construction principles. The HMM is trained and tested on a non-redundant set of 11 beta-barrel membrane proteins known to date at atomic resolution with a jack-knife procedure. As a result, the method correctly locates 97% of 172 transmembrane beta-strands. Out of the 11 proteins, the barrel size for ten proteins and the overall topology for seven proteins are correctly predicted. Additionally, it successfully assigns the entire topology for two new beta-barrel membrane proteins that have no significant sequence homology to the 11 proteins. Predicted topology for two candidates for beta-barrel structure of the outer mitochondrial membrane is also presented in the paper.

The structure of bacterial outer membrane proteins

Integral membrane proteins come in two types, alpha-helical and beta-barrel proteins. In both types, all hydrogen bonding donors and acceptors of the polypeptide backbone are completely compensated and buried while nonpolar side chains point to the membrane. The alpha-helical type is more abundant and occurs in cytoplasmic (or inner) membranes, whereas the beta-barrels are known from outer membranes of bacteria. The beta-barrel construction is described by the number of strands and the shear number, which is a measure for the inclination angle of the beta-strands against the barrel axis. The common right-handed beta-twist requires shear numbers slightly larger than the number of strands. Membrane protein beta-barrels contain between 8 and 22 beta-strands and have a simple topology that is probably enforced by the folding process. The smallest barrels form inverse micelles and work as enzymes or they bind to other macromolecules. The medium-range barrels form more or less specific pores for nutrient uptake, whereas the largest barrels occur in active Fe(2+) transporters. The beta-barrels are suitable objects for channel engineering, because the structures are simple and because many of these proteins can be produced into inclusion bodies and recovered therefrom in the exact native conformation.

Prediction of the membrane-spanning beta-strands of the major outer membrane protein of Chlamydia

There is preliminary experimental evidence indicating that the major outer-membrane protein (MOMP) of Chlamydia is a porin. We tested this hypothesis for the MOMP of the mouse pneumonitis serovar of Chlamydia trachomatis using two secondary structure prediction methods. First, an algorithm that calculates the mean hydrophobicity of one side of putative beta-strands predicted the positions of 16 transmembrane segments, a structure common to known porins. Second, outer loops typical of porins were assigned using an artificial neural network trained to predict the topology of bacterial outer-membrane proteins with a predominance of beta-strands. A topology model based on these results locates the four variable domains (VDs) of the MOMP on the outer loops and the five constant domains on beta-strands and the periplasmic turns. This model is consistent with genetic analysis and immunological and biochemical data that indicate the VDs are surface exposed. Furthermore, it shows significant homology with the consensus porin model of the program FORESST, which contrasts a proposed secondary structure against a data set of 349 proteins of known structure. Analysis of the MOMP of other chlamydial species corroborated our predicted model.

Characterization of omp200, a porin gene complex from Bacteroides fragilis: omp121 and omp71, gene sequence, deduced amino acid sequences and predictions of porin structure

The high MW porin protein complex (Omp200, composed of Omp121 and Omp71) from Bacteroides fragilis ATCC 25285 was purified and tryptic peptide sequences were used to design degenerate oligonucleotide primers which were then used as a first step in amplification, identification and sequencing of the omp121 gene (GenBank Accession Number AF357210). Sequence analysis revealed an open reading frame of 3378 bases. The deduced amino acid sequence (which contained the experimentally determined peptide sequences) has 1125 or 1116 amino acids (depending on which start codon is used); the mature protein consists of 1096 amino acids, has a predicted MW of 121.4 and a theoretical pI of 6.32. It is preceded by a 29 or 18 amino acid signal peptide which includes a typical hydrophobic region near the N-terminus (VLVLVL). Hydropathy plots of the deduced amino acid sequence of B. fragilis Omp121 display striking similarity with those of Escherichia coli OmpC (a 16-stranded porin) and FepA (a 22-stranded ligand-gated transport protein). Three-dimensional modeling of B. fragilis Omp121 (based on 1D and 3D sequence profiles, coupled with secondary structure and solvation potential information) indicated that the closest homologues in terms in fold conservation were the E. coli 16-stranded porins (e.g. OsmA) and 22-stranded ligand gated transport proteins (e.g. FepA). The omp71 gene sequence was identified using the tryptic peptides to search the published Bacteroides genome data base. We found that omp71 is located immediately downstream of omp121 and confirmed this with PCR analysis. Omp71 has no known homologues but does share some characteristics with the Porphyromonas RagB antigen.

Role of medium--and long-range interactions in discriminating globular and membrane proteins

The analysis of inter-residue interactions in protein structures provides considerable insight to understand their folding and stability. We have previously analyzed the role of medium- and long-range interactions in the folding of globular proteins. In this work, we study the distinct role of such interactions in the three-dimensional structures of membrane proteins. We observed a higher number of long-range contacts in the termini of transmembrane helical (TMH) segments, implying their role in the stabilization of helix-helix interactions. The transmembrane strand (TMS) proteins are having appreciably higher long-range contacts than that in all-beta class of globular proteins, indicating closer packing of the strands in TMS proteins. The residues in membrane spanning segments of TMH proteins have 1.3 times higher medium-range contacts than long-range contacts whereas that of TMS proteins have 14 times higher long-range contacts than medium-range contacts. Residue-wise analysis indicates that in TMH proteins, the residues Cys, Glu, Gly, Pro, Gln, Ser and Tyr have higher long-range contacts than medium-range contacts in contrast with all-alpha class of globular proteins. The charged residue pairs have higher medium-range contacts in all-alpha proteins, whereas hydrophobic residue pairs are dominant in TMH proteins. The information on the preference of residue pairs to form medium-range contacts has been successfully used to discriminate the TMH proteins from all-alpha proteins. The statistical significance of the results obtained from the present study has been verified using randomized structures of TMH and TMS protein templates.

Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network-based predictor

A method based on neural networks is trained and tested on a nonredundant set of beta-barrel membrane proteins known at atomic resolution with a jackknife procedure. The method predicts the topography of transmembrane beta strands with residue accuracy as high as 78% when evolutionary information is used as input to the network. Of the transmembrane beta-strands included in the training set, 93% are correctly assigned. The predictor includes an algorithm of model optimization, based on dynamic programming, that correctly models eight out of the 11 proteins present in the training/testing set. In addition, protein topology is assigned on the basis of the location of the longest loops in the models. We propose this as a general method to fill the gap of the prediction of beta-barrel membrane proteins.

Cloning of the mspA gene encoding a porin from Mycobacterium smegmatis

Porins form channels in the mycolic acid layer of mycobacteria and thereby control access of hydrophilic molecules to the cell. We purified a 100 kDa protein from Mycobacterium smegmatis and demonstrated its channel-forming activity by reconstitution in planar lipid bilayers. The mspA gene encodes a mature protein of 184 amino acids and an N-terminal signal sequence. MALDI mass spectrometry of the purified porin revealed a mass of 19 406 Da, in agreement with the predicted mass of mature MspA. Dissociation of the porin by boiling in 80% dimethyl sulphoxide yielded the MspA monomer, which did not form channels any more. Escherichia coli cells expressing the mspA gene produced the MspA monomer and a 100 kDa protein, which had the same channel-forming activity as whole-cell extracts of M. smegmatis with organic solvents. These proteins were specifically detected by a polyclonal antiserum that was raised to purified MspA of M. smegmatis. These results demonstrate that the mspA gene encodes a protein of M. smegmatis, which assembles to an extremely stable oligomer with high channel-forming activity. Database searches did not reveal significant similarities to any other known protein. Southern blots showed that the chromosomes of fast-growing mycobacterial species contain homologous sequences to mspA, whereas no hybridization could be detected with DNA from slow growing mycobacteria. These results suggest that MspA is the prototype of a new class of channel-forming proteins.

Prediction by a neural network of outer membrane beta-strand protein topology

An artificial neural network (NN) was trained to predict the topology of bacterial outer membrane (OM) beta-strand proteins. Specifically, the NN predicts the z-coordinate of Calpha atoms in a coordinate frame with the outer membrane in the xy-plane, such that low z-values indicate periplasmic turns, medium z-values indicate transmembrane beta-strands, and high z-values indicate extracellular loops. To obtain a training set, seven OM proteins (porins) with structures known to high resolution were aligned with their pores along the z-axis. The relationship between Calpha z-values and topology was thereby established. To predict the topology of other OM proteins, all seven porins were used for the training set. Z-values (topologies) were predicted for two porins with hitherto unknown structure and for OM proteins not belonging to the porin family, all with insignificant sequence homology to the training set. The results of topology prediction compare favorably with experimental topology data.

Hydrophobic distribution and spatial arrangement of amino acid residues in membrane proteins

The analysis of known three-dimensional structures of membrane proteins provides an opportunity to understand their structure and stability. In this article we analyse the hydrophobic variation of amino acid residues at various ranges in membrane and aqueous parts of membrane proteins. The numerical indices for several properties of amino acid residues in membrane proteins, such as surrounding hydrophobicity, gain in surrounding hydrophobicity, hydrophobic gain ratio, accessible surface area, preference of amino acid residues in the interior and surface parts, solvent accessible reduction ratio and buriedness, were set up. The relative preference of amino acid residues at various positions of membrane proteins were obtained in a very realistic approach.

Molecular characterization of a 40-kDa outer membrane protein, FomA, of Fusobacterium periodonticum and comparison with Fusobacterium nucleatum

The 40 kDa-outer membrane protein FomA of Fusobacterium periodonticum ATCC 33693 was found to exhibit heat modifiable properties, typical for a porin, and N-terminal sequencing indicated a close relationship to the porin FomA of Fusobacterium nucleatum. A polymerase chain reaction approach was therefore applied for sequencing the fomA gene of F. periodonticum, and nucleotide and deduced amino acid sequences were aligned and compared with the corresponding sequences of different strains of F. nucleatum. In all strains we found a common protein upstream of the fomA gene. The noncoding area upstream of the putative -35 region of the F. periodonticum fomA gene exhibited little sequence similarity with the F. nucleatum gene. The transcriptional unit of FomA, on the other hand, was very similar, with the similarities concentrated in domains that were interspersed with hypervariable regions. A topology model was made and compared with those made for F. nucleatum. This indicated that the great similarities reside in the membrane-spanning segments of the protein, while most cell surface exposed loops were hypervariable. The results strongly support the proposed model for FomA and also indicate that these taxa are related but on a lower level than the subspecies level. The codon usage of F. periodonticum is comparable to that of F. nucleatum, and the triplet AGA is the only codon used for arginine.

Electrophoretic analysis of the major outer membrane protein of Chlamydia psittaci reveals multimers which are recognized by protective monoclonal antibodies

Purified major outer membrane protein, detergent solubilized and reduced with dithiothreitol but not heated, gave an apparent molecular weight in sodium dodecyl sulfate (SDS)-polyacrylamide gels almost three times that observed for the heat-denatured SDS-treated peptide. This is similar to the behavior of porin trimers from gram-negative bacteria. Two protective monoclonal antibodies showed strong binding to the proposed trimer but not to denatured, monomeric major outer membrane protein.

Predictive evidence for a porin-type beta-barrel fold in CHIP28 and other members of the MIP family. A restricted-pore model common to water channels and facilitators

Water channels are the subject of much current attention, as they may be central for cell functions in a host of tissues. We have analyzed the possible field of facilitators and water channels of the MIP family based on structural predictions, on findings about the topology of CHIP28, and on the biophysical characteristics of water channels. We developed predictions for the following proteins: MIP26, NOD26, GLP, BIB, gamma-TIP, FA-CHIP, CHIP28k, WCH-CD1, and CHIP28. We utilized Kyte Doolittle hydrophobicity, Eisenberg's amphiphilicity, Chou-Fasman-Prevelige propensities, and our own Union algorithm. We found that hydrophobic amphiphilic segments likely to be transmembrane were consistently shorter than required for alpha-helical segments, but of the correct length for beta-strands. Turn propensity was high at frequent intervals, consistent with transmembrane beta-strands. We propose that these proteins fold as porin-like 16-stranded antiparallel beta-barrels. In water channels, from the size of molecules excluded, an extramembrane loop(s) would enter the pore and restrict it to a bottleneck with a width 4 A < or = w < or = 5 A. A similar but more mobile loop(s) would act as gate and binding site for the facilitators of the MIP family.

Sequence variability of the 40-kDa outer membrane proteins of Fusobacterium nucleatum strains and a model for the topology of the proteins

The complete nucleotide sequences of the fomA genes encoding the 40-kDa outer membrane proteins (OMPs) of strains ATCC 10953 and ATCC 25586 of Fusobacterium nucleatum were determined using the genomic DNA, or DNA fragments ligated into a vector plasmid, as template in a polymerase chain reaction. The deduced amino acid sequences of these two proteins were aligned with the amino acid sequence of the corresponding protein of F. nucleatum strain Fev1 and examined for conserved/variable polypeptide segments. A model for the topology of the 40-kDa OMPs is proposed on the basis of this alignment and application of the structural principles derived for OMPs of Escherichia coli. According to this model, sixteen polypeptide segments, which are highly conserved, traverse the outer membrane, thereby creating eight external loops, most of which are highly variable.

Influence of the lipid matrix on incorporation and function of LPS-free porin from Paracoccus denitrificans

We have studied the role of lipopolysaccharide (LPS) for the insertion of LPS-free porin from Paracoccus denitrificans into planar lipid bilayers and its function therein. For this, we reconstituted the porin into different asymmetric planar lipid bilayers with or without LPS and into symmetric phospholipid bilayers. LPS-free porin added to the various bilayer systems was found to induce a step-wise increase in membrane conductance with different incorporation rates, depending on the presence of LPS in the bilayer leaflet opposite to porin addition. The incorporation rate into asymmetric LPS/phospholipid membranes from the phospholipid side was more than 10-fold higher than that observed for pure phospholipid membranes. The porin formed general diffusion pores without any salt specificity. The mean single-channel conductance did not depend on the presence of LPS and was about 4.2 nS for a subphase containing 1 M KCl in all systems tested. At certain applied transmembrane voltages, which depended on membrane composition and were approximately greater than 100 mV for the LPS/phospholipid system, single-channel closing in three steps was observed. Differences in the voltage dependence of porin-channel closing could be correlated with the surface charge of the bilayer. From the voltage-dependent gating behaviour proof for an oriented incorporation of the porin molecules, depending on the side of porin addition, and evidence for their orientation could be derived. Measurements at temperatures above and below the beta<==>alpha phase transition temperature of LPS gave evidence for the influence of membrane rigidity on the gating behaviour.

Evidence that facilitative glucose transporters may fold as beta-barrels

A widely accepted model for the structure of the facilitative glucose transporters (GLUTs) predicts that they form 12 transmembrane alpha-helices and that the highly conserved sequence Ile-386-Ala-405 in GLUT1 is intracellular. We raised a polyclonal antibody against a synthetic peptide encompassing this conserved sequence and found that antibody treatment increased 2-deoxy-D-glucose (DOG) uptake in Xe-nopus oocytes expressing GLUT1, GLUT2, or GLUT4 only when applied to the extracellular side. This effect was dose dependent and was specifically blocked by competition with the peptide Ile-386-Ala-405; it was due to a decrease in the Km for the transport of DOG. To ascertain GLUT orientation, we raised anti-peptide antibodies against the last 21 and 25 C-terminal amino acids of GLUT1 and GLUT4, respectively, which were previously shown to be intracellular. These antibodies increased DOG uptake when injected into oocytes expressing GLUT1 and GLUT4, but not when added extracellularly. Prompted by the noted discrepancy, we found sequence similarity between GLUTs and porins, two of which are known from crystallography to form 16-stranded transmembrane antiparallel beta-barrels. Analysis of the hydrophobicity, amphiphilicity, and turn propensity of GLUT1 leads us to propose that GLUTs fold as porin-like transmembrane beta-barrels. This model is consistent with the results of the present antibody studies and also with previously published experimental evidence inconsistent with the 12-helix model.

Complete sequence of omp1, the structural gene encoding the 40-kDa outer membrane protein of Fusobacterium nucleatum strain Fev1

The sequence of the omp1 gene coding for the 40-kDa outer membrane protein (OMP) of the Gram- oral bacterium, Fusobacterium nucleatum strain Fev1, has been determined. Degenerate oligodeoxyribonucleotide primers were used to prime the amplification of a 120-mer sequence of the gene. This sequence was successively used for constructing new primers applied in asymmetrical, symmetrical, and inverse polymerase chain reaction using as template genomic DNA, self-ligated DNA fragments, or fragments ligated into either pGEM-7Zf+ or pACYC184. The codon usage of the gene was unusual in that A or T was used as the third base in the codon triplets in all cases, except for those amino acids (aa) which have only one or two possible codon choices. Only 35 of the 61 sense codons were used. The aa sequence of the protein was deduced; it consisted of 348 aa (M(r) 39,954), which is in good agreement with the 40-kDa size estimated from electrophoretic analyses. The mature protein was preceded by a 20-aa signal peptide.

Bacterial porins: structure and function

Within the class of integral membrane proteins, the bacterial porins display a remarkable resistance to denaturants and proteases. This stability is probably crucial for the formation of highly ordered, three-dimensional crystals. Structural analysis of these crystals has been possible in atomic detail. This analysis has revealed interesting features, such as the aromatic girdles, and has helped to explain several observations, including the porins' ability to discriminate between polar and non-polar solutes. Recent research has thus improved our understanding of the porins in a qualitative fashion.

Structure of porin refined at 1.8 A resolution

The crystal structure of porin from Rhodobacter capsulatus has been refined using the simulated annealing method. The final model consists of all 301 amino acid residues well obeying standard geometry, three calcium ions, 274 solvent molecules, three detergent molecules and one unknown ligand modeled as a detergent molecule. The final crystallographic R-factor is 18.6% based on 42,851 independent reflections in the resolution range 10 to 1.8 A. The model is described in detail.

Antigenic sites on porin of Haemophilus influenzae type b: mapping with synthetic peptides and evaluation of structure predictions

The major surface-located protein in the outer membrane of Haemophilus influenzae type b (Hib) is porin, molecular mass, 38 kDa, 341 amino acids. To define precisely the molecular reactivities of nine mouse monoclonal antibodies (MAbs) against Hib porin, overlapping hexapeptides corresponding to the entire sequence of porin were synthesized. The epitopes recognized by the MAbs were mapped by enzyme-linked immunosorbent assay to stretches of 6 to 11 amino acids. Antigenic sites between amino acids 112 and 126, 148 and 153, 162 and 172, and 318 and 325 were identified. The antigenic sites between amino acids 162 and 172 and between amino acids 318 and 325 were determined by flow cytometry to be on the bacterial cell surface. Four MAbs, POR.2, POR.3, POR.4, and POR.5, that react with amino acids 162 to 172 were able to discriminate among porins from the three major outer membrane protein subtypes of Hib, i.e., 1H, 2L, and 6U. A model for the topological organization of Hib porin was created by calculating the hydrophobicity, amphiphilicity, and turn propensity in its amino acid sequence. Determination of the molecular reactivities of the anti-Hib porin MAbs provided substantive evidence for the orientation of selected regions of porin in the outer membrane of Hib.

Molecular architecture and electrostatic properties of a bacterial porin

The integral membrane protein porin from Rhodobacter capsulatus consists of three tightly associated 16-stranded beta barrels that give rise to three distinct diffusion channels for small solutes through the outer membrane. The x-ray structure of this porin has revealed details of its shape, the residue distributions within the pore and at the membrane-facing surface, and the location of calcium sites. The electrostatic potential has been calculated and related to function. Moreover, potential calculations were found to predict the Ca2+ sites.