Preference functions for prediction of membrane-buried helices in integral membrane proteins

The Contribution of Hydrophobic Interactions to Conformational Changes of Inward/Outward Transmembrane Transport Proteins

Proteins transporting ions or other molecules across the membrane, whose proper concentration is required to maintain homeostasis, perform very sophisticated biological functions. The symport and antiport active transport can be performed only by the structures specially prepared for this purpose. In the present work, such structures in both In and Out conformations have been analyzed with respect to the hydrophobicity distribution using the FOD-M model. This allowed for identifying the role of individual protein chain fragments in the stabilization of the specific cell membrane environment as well as the contribution of hydrophobic interactions to the conformational changes between In/Out conformations.

The Spectrum of Design Solutions for Improving the Activity-Selectivity Product of Peptide Antibiotics against Multidrug-Resistant Bacteria and Prostate Cancer PC-3 Cells

The link between the antimicrobial and anticancer activity of peptides has long been studied, and the number of peptides identified with both activities has recently increased considerably. In this work, we hypothesized that designed peptides with a wide spectrum of selective antimicrobial activity will also have anticancer activity, and tested this hypothesis with newly designed peptides. The spectrum of peptides, used as partial or full design templates, ranged from cell-penetrating peptides and putative bacteriocin to those from the simplest animals (placozoans) and the Chordata phylum (anurans). We applied custom computational tools to predict amino acid substitutions, conferring the increased product of bacteriostatic activity and selectivity. Experiments confirmed that better overall performance was achieved with respect to that of initial templates. Nine of our synthesized helical peptides had excellent bactericidal activity against both standard and multidrug-resistant bacteria. These peptides were then compared to a known anticancer peptide polybia-MP1, for their ability to kill prostate cancer cells and dermal primary fibroblasts. The therapeutic index was higher for seven of our peptides, and anticancer activity stronger for all of them. In conclusion, the peptides that we designed for selective antimicrobial activity also have promising potential for anticancer applications.

Analyzing the effects of protecting osmolytes on solute–water interactions by solvatochromic comparison method: II. Globular proteins

Partitioning of 11 globular proteins was examined in aqueous dextran–PEG–sodium/potassium phosphate buffer (0.01 M K/NaPB, pH 7.4) two-phase systems (ATPSs) containing 0.5 M sorbitol.

Elevated protein carbonylation, and misfolding in sciatic nerve from db/db and Sod1(-/-) mice: plausible link between oxidative stress and demyelination

Diabetic peripheral polyneuropathy is associated with decrements in motor/sensory neuron myelination, nerve conduction and muscle function; however, the mechanisms of reduced myelination in diabetes are poorly understood. Chronic elevation of oxidative stress may be one of the potential determinants for demyelination as lipids and proteins are important structural constituents of myelin and highly susceptible to oxidation. The goal of the current study was to determine whether there is a link between protein oxidation/misfolding and demyelination. We chose two distinct models to test our hypothesis: 1) the leptin receptor deficient mouse (dbdb) model of diabetic polyneuropathy and 2) superoxide dismutase 1 knockout (Sod1(-/-) ) mouse model of in vivo oxidative stress. Both experimental models displayed a significant decrement in nerve conduction, increase in tail distal motor latency as well as reduced myelin thickness and fiber/axon diameter. Further biochemical studies demonstrated that oxidative stress is likely to be a potential key player in the demyelination process as both models exhibited significant elevation in protein carbonylation and alterations in protein conformation. Since peripheral myelin protein 22 (PMP22) is a key component of myelin sheath and has been found mutated and aggregated in several peripheral neuropathies, we predicted that an increase in carbonylation and aggregation of PMP22 may be associated with demyelination in dbdb mice. Indeed, PMP22 was found to be carbonylated and aggregated in sciatic nerves of dbdb mice. Sequence-driven hydropathy plot analysis and in vitro oxidation-induced aggregation of purified PMP22 protein supported the premise for oxidation-dependent aggregation of PMP22 in dbdb mice. Collectively, these data strongly suggest for the first time that oxidation-mediated protein misfolding and aggregation of key myelin proteins may be linked to demyelination and reduced nerve conduction in peripheral neuropathies.

Analysis of the peroxiredoxin family: using active-site structure and sequence information for global classification and residue analysis

Peroxiredoxins (Prxs) are a widespread and highly expressed family of cysteine-based peroxidases that react very rapidly with H₂O₂, organic peroxides, and peroxynitrite. Correct subfamily classification has been problematic because Prx subfamilies are frequently not correlated with phylogenetic distribution and diverge in their preferred reductant, oligomerization state, and tendency toward overoxidation. We have developed a method that uses the Deacon Active Site Profiler (DASP) tool to extract functional-site profiles from structurally characterized proteins to computationally define subfamilies and to identify new Prx subfamily members from GenBank(nr). For the 58 literature-defined Prx test proteins, 57 were correctly assigned, and none were assigned to the incorrect subfamily. The >3500 putative Prx sequences identified were then used to analyze residue conservation in the active site of each Prx subfamily. Our results indicate that the existence and location of the resolving cysteine vary in some subfamilies (e.g., Prx5) to a greater degree than previously appreciated and that interactions at the A interface (common to Prx5, Tpx, and higher order AhpC/Prx1 structures) are important for stabilization of the correct active-site geometry. Interestingly, this method also allows us to further divide the AhpC/Prx1 into four groups that are correlated with functional characteristics. The DASP method provides more accurate subfamily classification than PSI-BLAST for members of the Prx family and can now readily be applied to other large protein families.

Suitable transmembrane domain significantly increase the surface-expression level of Fc(epsilon)RIalpha in 293T cells

Evidence showed that the extracellular part of Fc(epsilon)RIalpha (FCR) with its own transmembrane domain (TMF) cannot be expressed as a transmembrane form in CHO cell line. However, FCR could be displayed on cell surface with the transmembrane domain (TM) of human IL2Ralpha (TMI). Theoretical analysis of TMF and TMI using TM prediction methods showed that TMI possessed strong orientation tendency to form "outside to inside" transmembrane mode from N-terminal to C-terminal, while TMF was prone to form "inside to outside" mode. Based on the analyzing results, the TM of Her2 (TMH) was studied and showed similar transmembrane mode as that of TMI, which implied that TMH might be a novel TM to obtain the surface display of FCR. Then, DNA sequences encoding TMH and TMF were fused to 3'-end of FCR gene, respectively. Fluorescent microscope observation indicated that FCR_TMH seemed to be located mainly on cell surface, while FCR_TMF appeared in endochylema. Flow cytometry analysis and Western blot also showed that the surface expression of FCR was enhanced significantly by TMH, while FCR_TMF could not be surface displayed in 293T cell. The experimental results were consistent with the theoretical predictions and demonstrated that the orientation tendency of TM may be very important in subcellular location of proteins.

Transmembrane structure predictions with hydropathy index/charge two-dimensional trajectories of stochastic dynamical systems

A novel algorithm is proposed for predicting transmembrane protein secondary structure from two-dimensional vector trajectories consisting of a hydropathy index and formal charge of a test amino acid sequence using stochastic dynamical system models. Two prediction problems are discussed. One is the prediction of transmembrane region counts; another is that of transmembrane regions, i.e. predicting whether or not each amino acid belongs to a transmembrane region. The prediction accuracies, using a collection of well-characterized transmembrane protein sequences and benchmarking sequences, suggest that the proposed algorithm performs reasonably well. An experiment was performed with a glutamate transporter homologue from Pyrococcus horikoshii. The predicted transmembrane regions of the five human glutamate transporter sequences and observations based on the computed likelihood are reported.

Occurrence of the aminoacyl-tRNA synthetases in high-molecular weight complexes correlates with the size of substrate amino acids

One of the distinctive and mysterious features of mammalian aminoacyl-tRNA synthetases (AARSs) is the existence of stable high-molecular weight complexes containing 10 out of 20 AARSs. The composition and structure of these complexes are conserved among multicellular animals. No specific function associated with these structures has been found, and there is no evident rationale for a particular separation of AARSs in "complex-bound" and "free" forms. We have demonstrated a strong association between the occurrence of AARSs in the complexes and the volume of their substrate amino acids. The significance of this association is discussed in terms of the structural organization of translation in the living cell.

A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction

A range of methods has been developed to predict transmembrane helices and their topologies. Although most of these algorithms give good predictions, no single method consistently outperforms the others. However, combining different algorithms is one approach that can potentially improve the accuracy of the prediction. We developed a new method that initially uses a hidden Markov model to predict alternative models for membrane spanning helices in proteins. The algorithm subsequently identifies the best among models by ranking them using a novel scoring function based on the folding energy of transmembrane helical fragments. This folding of helical fragments and the incorporation into membrane is modeled using CHARMm, extended with the Generalized Born surface area solvent model (GBSA/IM) with implicit membrane. The combined method reported here, TMHGB significantly increases the accuracy of the original hidden Markov model-based algorithm.

Plasma membrane topology of syncytial domains of herpes simplex virus type 1 glycoprotein K (gK): the UL20 protein enables cell surface localization of gK but not gK-mediated cell-to-cell fusion

Most spontaneously occurring mutations that cause extensive herpes simplex virus type 1 (HSV-1)-induced cell fusion are single amino acid changes within glycoprotein K (gK). Despite the strong genetic association of gK with virus-induced cell fusion, its direct involvement in cellular membrane fusion has been controversial, largely due to previously unsuccessful efforts to detect gK expression on virion and cellular surfaces. Recently, we showed that gK is expressed on HSV-1 virions and functioned in virus entry (T. P. Foster, G. V. Rybachuk, and K. G. Kousoulas, J. Virol. 75:12431-12438, 2001). To determine whether gK is expressed on cellular surfaces, as well as its membrane topology, we generated the recombinant viruses gKV5DI, gKV5DII, gKV5DIII, and gKV5DIVcontaining insertions of the V5 antigenic epitope within each of four domains of gK predicted to localize either in the cytoplasmic side or in the extracytoplasmic side of cellular membranes. Immunohistochemical and confocal microscopy analyses of infected cells showed that both wild-type and syncytial forms of gK were expressed on cell surfaces. Analysis of the topology of the V5-tagged gK revealed that gK domains I and IV were located extracellularly, whereas domains II and III were localized intracellularly. Transiently expressed gK failed to localize in cellular plasma membranes. In contrast, infection of gK-transfected cells with the gK-null virus DeltagK enabled expression of gK on cell surfaces, as well as gK-mediated membrane fusion. Transient-coexpression experiments revealed that the UL20 protein enabled cell surface expression of gK, but not gK-mediated cell-to-cell fusion, indicating that additional viral proteins are required for expression of the gK syncytial phenotype.

Transmembrane helix predictions revisited

Methods that predict membrane helices have become increasingly useful in the context of analyzing entire proteomes, as well as in everyday sequence analysis. Here, we analyzed 27 advanced and simple methods in detail. To resolve contradictions in previous works and to reevaluate transmembrane helix prediction algorithms, we introduced an analysis that distinguished between performance on redundancy-reduced high- and low-resolution data sets, established thresholds for significant differences in performance, and implemented both per-segment and per-residue analysis of membrane helix predictions. Although some of the advanced methods performed better than others, we showed in a thorough bootstrapping experiment based on various measures of accuracy that no method performed consistently best. In contrast, most simple hydrophobicity scale-based methods were significantly less accurate than any advanced method as they overpredicted membrane helices and confused membrane helices with hydrophobic regions outside of membranes. In contrast, the advanced methods usually distinguished correctly between membrane-helical and other proteins. Nonetheless, few methods reliably distinguished between signal peptides and membrane helices. We could not verify a significant difference in performance between eukaryotic and prokaryotic proteins. Surprisingly, we found that proteins with more than five helices were predicted at a significantly lower accuracy than proteins with five or fewer. The important implication is that structurally unsolved multispanning membrane proteins, which are often important drug targets, will remain problematic for transmembrane helix prediction algorithms. Overall, by establishing a standardized methodology for transmembrane helix prediction evaluation, we have resolved differences among previous works and presented novel trends that may impact the analysis of entire proteomes.

On filtering false positive transmembrane protein predictions

While helical transmembrane (TM) region prediction tools achieve high (>90%) success rates for real integral membrane proteins, they produce a considerable number of false positive hits in sequences of known nontransmembrane queries. We propose a modification of the dense alignment surface (DAS) method that achieves a substantial decrease in the false positive error rate. Essentially, a sequence that includes possible transmembrane regions is compared in a second step with TM segments in a sequence library of documented transmembrane proteins. If the performance of the query sequence against the library of documented TM segment-containing sequences in this test is lower than an empirical threshold, it is classified as a non-transmembrane protein. The probability of false positive prediction for trusted TM region hits is expressed in terms of E-values. The modified DAS method, the DAS-TMfilter algorithm, has an unchanged high sensitivity for TM segments ( approximately 95% detected in a learning set of 128 documented transmembrane proteins). At the same time, the selectivity measured over a non-redundant set of 526 soluble proteins with known 3D structure is approximately 99%, mainly because a large number of falsely predicted single membrane-pass proteins are eliminated by the DAS-TMfilter algorithm.

Basic charge clusters and predictions of membrane protein topology

The topology predictor SPLIT 4.0 (http://pref.etfos.hr) predicts the sequence location of transmembrane helices by performing an automatic selection of optimal amino acid attribute and corresponding preference functions. The best topological model is selected by choosing the highest absolute bias parameter that combines the bias in basic charge motifs and the bias in positive residues (the "positive inside rule") with the charge difference across the first transmembrane segment. Basic charge motifs, such as the BBB, BXXBB, and BBXXB motifs in alpha-helical integral membrane proteins, are significantly more frequent near cytoplasmic membrane surface than expected from the Arg/Lys (B) frequency. The predictor's accuracy is 99% for predicting 178 transmembrane helices in all membrane proteins or subunits of known 3D structure.

Mutations in LGI1 cause autosomal-dominant partial epilepsy with auditory features

The epilepsies are a common, clinically heterogeneous group of disorders defined by recurrent unprovoked seizures. Here we describe identification of the causative gene in autosomal-dominant partial epilepsy with auditory features (ADPEAF, MIM 600512), a rare form of idiopathic lateral temporal lobe epilepsy characterized by partial seizures with auditory disturbances. We constructed a complete, 4.2-Mb physical map across the genetically implicated disease-gene region, identified 28 putative genes (Fig. 1) and resequenced all or part of 21 genes before identifying presumptive mutations in one copy of the leucine-rich, glioma-inactivated 1 gene (LGI1) in each of five families with ADPEAF. Previous studies have indicated that loss of both copies of LGI1 promotes glial tumor progression. We show that the expression pattern of mouse Lgi1 is predominantly neuronal and is consistent with the anatomic regions involved in temporal lobe epilepsy. Discovery of LGI1 as a cause of ADPEAF suggests new avenues for research on pathogenic mechanisms of idiopathic epilepsies.

The multispanning membrane protein Ste24p catalyzes CAAX proteolysis and NH2-terminal processing of the yeast a-factor precursor

Saccharomyces cerevisiae Ste24p is a multispanning membrane protein implicated in the CAAX proteolysis step that occurs during biogenesis of the prenylated a-factor mating pheromone. Whether Ste24p acts directly as a CAAX protease or indirectly to activate a downstream protease has not yet been established. In this study, we demonstrate that purified, detergent-solubilized Ste24p directly mediates CAAX proteolysis in a zinc-dependent manner. We also show that Ste24p mediates a separate proteolytic step, the first NH(2)-terminal cleavage in a-factor maturation. These results establish that Ste24p functions both as a bona fide COOH-terminal CAAX protease and as an a-factor NH(2)-terminal protease. Importantly, this study is the first to directly demonstrate that a eukaryotic multispanning membrane protein can possess intrinsic proteolytic activity.

Predicting protein conformation by statistical methods

The unique folded structure makes a polypeptide a functional protein. The number of known sequences is about a hundred times larger than the number of known structures and the gap is increasing rapidly. The primary goal of all structure prediction methods is to obtain structure-related information on proteins, whose structures have not been determined experimentally. Besides this goal, the development of accurate prediction methods helps to reveal principles of protein folding. Here we present a brief survey of protein structure predictions based on statistical analyses of known sequence and structure data. We discuss the background of these methods and attempt to elucidate principles, which govern structure formation of soluble and membrane proteins.

Correction of the DNA sequence of the regB gene of Rhodobacter capsulatus with implications for the membrane topology of the sensor kinase regB

We corrected the previously published sequence for the regB gene, which encodes a histidine sensor kinase in Rhodobacter capsulatus. The deduced RegB amino acid sequence has an additional putative transmembrane domain at the N terminus. Analysis of RegB-PhoA and RegB-LacZ fusion proteins supports a topology model for RegB with six membrane-spanning domains.