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.     

First principles study of the structure, electronic state and stability of cations

Structural and electronic properties of semiconductor binary microclusters cations have been investigated using the B3LYP-DFT method in the ranges of n=1, 2 and m=1–7. Full structural optimization, adiabatic ionization potentials calculation and frequency analysis are performed with the basis of 6-311+G(d). The charged-induced structural changes in these cations have been discussed. The strong As–As bond is also favored over Al–As bonds in the cations in comparison with corresponding neutral cluster. With As_m forming the base, adding Al atom(s) in different positions would find the stable structures of cations quickly and correctly. , , and are predicted to be species with high stabilities and possible to be produced experimentally.     

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.     

Photoinduced multi-mode quantum dynamics of pyrrole at the – conical intersections

The photoinduced dynamics of pyrrole at the – S₀ and – S₀ conical intersections has been investigated by multi-mode time-dependent quantum wave-packet calculations. Diabatic potential-energy surfaces have been constructed for both conical intersection using accurate multi-reference ab initio electronic-structure calculations. In addition to the NH stretching coordinate, the three (four) symmetry-allowed coupling modes of A₂ (B₁) symmetry have been considered for the – S₀ (– S₀) conical intersections. Wave-packet dynamics calculations have been performed for three-dimensional models, taking account of the two dominant coupling modes of each conical intersection. The electronic population-transfer processes at the conical intersections, the branching ratio for the dissociation to the ground and excited states of the pyrrolyl radical, and their dependence on the initial preparation of the system have been investigated. It is shown that the excitation of the NH stretching mode strongly enhances the photodissociation rate, while the excitation of the strongest coupling mode has a pronounced effect on the branching ratio of the photodissociation process. Although the inclusion of the second (weaker) coupling mode has little effect on the electronic population dynamics, it leads to interesting changes of the nodal pattern of the wave packet at the conical intersections. The calculations provide insight into the effect of the multiple coupling modes on the process of direct photodissociation through a conical intersection.     

Current developments on beta-barrel membrane proteins: sequence and structure analysis, discrimination and prediction

beta-barrel membrane proteins perform a variety of functions, such as mediating non-specific, passive transport of ions and small molecules, selectively passing the molecules like maltose and sucrose and are involved in voltage dependent anion channels. Understanding the structural features of beta-barrel membrane proteins and detecting them in genomic sequences are challenging tasks in structural and functional genomics. In this review, with the survey of experimentally known amino acid sequences and structures, the characteristic features of amino acid residues in beta-barrel membrane proteins and novel parameters for understanding their folding and stability will be described. The development of statistical methods and machine learning techniques for discriminating beta-barrel membrane proteins from other folding types of globular and membrane proteins will be explained along with their relative importance. Further, different methods including hydrophobicity profiles, rule based approach, amino acid properties, neural networks, hidden Markov models etc. for predicting membrane spanning segments of beta-barrel membrane proteins will be discussed. In addition, the applications of discrimination techniques for detecting beta-barrel membrane proteins in genomic sequences will be outlined. In essence, this comprehensive review would provide an overall picture about beta-barrel membrane proteins starting from the construction of datasets to genome-wide applications.     

A short, simple and general approach for the synthesis of (3S,4S)-3-methoxy-4-methylamino pyrrolidine and (3S,4R)-3-methoxy-4-methylamino pyrrolidine

A general and efficient stereoselective approach for the synthesis of (3S,4S) and (3S,4R)-3-methoxy-4-methylamino pyrrolidines, a part of the structure of AG-7352, a naphthyridine antitumor agent and quinoline antibacterial compounds has been described.     

Determining the orientation of uniaxially rotating membrane proteins using unoriented samples: a 2H, 13C, AND 15N solid-state NMR investigation of the dynamics and orientation of a transmembrane helical bundle

Membrane protein orientation has traditionally been determined by NMR using mechanically or magnetically aligned samples. Here we show a new NMR approach that abolishes the need for preparing macroscopically aligned membranes. When the protein undergoes fast uniaxial rotation around the bilayer normal, the 0 degrees -frequency of the motionally averaged powder spectrum is identical to the frequency of the aligned protein whose alignment axis is along the magnetic field. Thus, one can use unoriented membranes to determine the orientation of the protein relative to the bilayer normal. We demonstrate this approach on the M2 transmembrane peptide (M2TMP) of influenza A virus, which is known to assemble into a proton-conducting tetrameric helical bundle. The fast uniaxial rotational diffusion of the M2TMP helical bundle around the membrane normal is characterized via 2H quadrupolar couplings, C-H and N-H dipolar couplings, 13C chemical shift anisotropies, and 1H T1rho relaxation times. We then show that 15N chemical shift anisotropy and N-H dipolar coupling measured on these powder samples can be analyzed to yield precise tilt angles and rotation angles of the helices. The data show that the tilt angle of the M2TMP helices depends on the membrane thickness to reduce the hydrophobic mismatch. Moreover, the orientation of a longer M2 peptide containing both the transmembrane domain and cytoplasmic residues is similar to the orientation of the transmembrane domain alone, suggesting that the transmembrane domain regulates the orientation of this protein and that structural information obtained from M2TMP may be extrapolated to the longer peptide. This powder-NMR approach for orientation determination is generally applicable and can be extended to larger membrane proteins.     

Statistical analysis and exposure status classification of transmembrane beta barrel residues

Several computational methods exist for the identification of transmembrane beta barrel proteins (TMBs) from sequence. Some of these methods also provide the transmembrane (TM) boundaries of the putative TMBs. The aim of this study is to (1) derive the propensities of the TM residues to be exposed to the lipid bilayer and (2) to predict the exposure status (i.e. exposed to the bilayer or hidden in protein structure) of TMB residues. Three novel propensity scales namely, BTMC, BTMI and HTMI were derived for the TMB residues at the hydrophobic core region of the outer membrane (OM), the lipid-water interface regions of the OM, and for the helical membrane proteins (HMPs) residues at the lipid-water interface regions of the inner membrane (IM), respectively. Separate propensity scales were derived for monomeric and functionally oligomeric TMBs. The derived propensities reflect differing physico-chemical properties of the respective membrane bilayer regions and were employed in a computational method for the prediction of the exposure status of TMB residues. Based on the these propensities, the conservation indices and the frequency profile of the residues, the transmembrane residues were classified into buried/exposed with an accuracy of 77.91% and 80.42% for the residues at the membrane core and the interface regions, respectively. The correlation of the derived scales with different physico-chemical properties obtained from the AAIndex database are also discussed. Knowledge about the residue propensities and burial status will be useful in annotating putative TMBs with unknown structure.     

膜蛋白跨膜区段的预测分析

将连续小波变换技术的时频局部化特点和氨基酸的疏水特性相结合,提出了一种用于预测膜蛋白跨膜区段数目和位置的新方法,以代码为1YST的膜蛋白为例,对小波尺度和疏水值的种类进行了选择,同时描述了该法对跨膜螺旋区数目和位置的预测分析过程.从膜蛋白数据库中随机抽取36个蛋白质(含跨膜螺旋区232)作为测试集,采用该方法对其跨膜螺旋区进行预测,其中222个跨膜螺旋区能被准确预测,准确率为96.1%.结果表明,该法具有较高的预测准确性.     

Mixed micelles of homologous perfluoropolyether anionic surfactants in water

The mixtures of sodium and ammonium salts of three homologous perfluoropolyether carboxylic acids having Cl-terminated perfluoroalkyl group (Cl-PFPE) and differing in the average molecular weight (MW) were examined. The surfactants, namely n2, n3 and n4, have two, three and four PFPE units, respectively. Each surfactant was studied alone and in mixture with the other surfactants with the same counterion. NMR chemical shifts were measured for each surfactant and for the mixtures in different concentrations. For a given mixture the micelle composition, X_i, can be determined from the observation of the chemical shifts of the micellar components. It was found that Cl-PFPE surfactant mixtures form in water mixed micelles which contain the surfactants in equilibrium with monomeric species. The analysis of NMR chemical shift variations allowed evaluating the partition of the various surfactants in the mixed aggregates as a function of the total concentration. Composition of mixed micelles resembles ideal mixing predictions particularly at high surfactant concentrations.     

Magnetic properties of the spinel-type

The spinel sulphide CuCr₂S₄ is a metallic ferromagnet with a Curie temperature , while CuHf₂S₄ has no magnetic anomaly. Magnetic properties of the quaternary spinel-type Cu(Cr_1-xHf_x)₂S₄ system have been studied. With increasing x the ferromagnetic properties are weakened gradually from a predominant ferromagnetic, a spin-glass, finally to a simple paramagnetic behavior. For the composition of x0.50, a re-entrant spin-glass phase could emerge, even though the Curie temperature is ill-defined as a ferromagnetic phase boundary. Specimens with x≥0.90 remain paramagnetic down to 4.2 K. A spin crossover phenomenon is found around 160 K in the specimens of x=0.50–0.70. A step-like anomaly is manifestly detected in the magnetization, which corresponds with the change of the spin state. This crossover indicates that the spin state converts from high temperature S=2 into low temperature states. In the ordered states in , the magnetic moment originates from only Cr³⁺ ions.     

The prediction of amphiphilic alpha-helices

A number of sequence-based analyses have been developed to identify protein segments, which are able to form membrane interactive amphiphilic alpha-helices. Earlier techniques attempted to detect the characteristic periodicity in hydrophobic amino acid residues shown by these structure and included the Molecular Hydrophobic Potential (MHP), which represents the hydrophobicity of amino acid residues as lines of isopotential around the alpha-helix and analyses based on Fourier transforms. These latter analyses compare the periodicity of hydrophobic residues in a putative alpha-helical sequence with that of a test mathematical function to provide a measure of amphiphilicity using either the Amphipathic Index or the Hydrophobic Moment. More recently, the introduction of computational procedures based on techniques such as hydropathy analysis, homology modelling, multiple sequence alignments and neural networks has led to the prediction of transmembrane alpha-helices with accuracies of the order of 95% and transmembrane protein topology with accuracies greater than 75%. Statistical approaches to transmembrane protein modeling such as hidden Markov models have increased these prediction levels to an even higher level. Here, we review a number of these predictive techniques and consider problems associated with their use in the prediction of structure / function relationships, using alpha-helices from G-coupled protein receptors, penicillin binding proteins, apolipoproteins, peptide hormones, lytic peptides and tilted peptides as examples.     

Solvent effects on the O NMR chemical shifts of 4-dimethylsulfoximide-1,1,1-trifluoro-3-alken-2-ones

A multi-linear-regression analysis using the Kamlet-Abbout-Taft (KAT) solvatochromic parameters in order to elucidate and quantify the solvent effects on the chemical shifts of three 4-dimethylsulfoximide-1,1,1-trifluoro-3-buten-2-ones is reported. The predominant conformational structures of compounds has been determined by energy minimization calculations using the Austin Model (AM1) semi-empirical method, which has been used to explain the NMR chemical shifts for CO and SO groups. The chemical shifts of carbonyl and sulfoximide oxygen’s of molecules showed similar dependencies (in ppm) on the solvent polarity-polarizability and the solvent hydrogen-bond-donor (HBD) acidities. The influence of solvent hydrogen-bond-acceptor (HBA) basicities was little significant.     

Atom transfer radical polymerization on the interior of the P22 capsid and incorporation of photocatalytic monomer crosslinks

We have successfully used atom transfer radical polymerization (ATRP) to form linear and crosslinked polyacrylamide and polyacrylate polymers, constrained within the virus like particle (VLP) derived from the bacteriophage P22. Polymerization of Tris(hydroxymethyl)methylacrylamide was initiated, in a spatially controlled manner, using macroinitiators derived from two different mutants of P22, S39C and K118C. Initiation from the S39C mutant results in spatially confined polymer growth on the interior of P22 while initiation from the K118C site results in a polymerized VLP in which some of the polymer is partially exposed on the outside of the capsid. Using the S39C macroinitiator we have demonstrated polymerization of aminoethyl methacrylate (AEMA) monomers, crosslinked by co-polymerization with the multifunctional monomer [Ru(5-methacrylamido-phenanthroline)₃]²⁺ resulting in an active photocatalytic P22 capsid particle.     

Synthesis of lariat organochalcogenoethers based on azacalix[3]arenes for the potentiometric detection of [UO2] ions

The syntheses of organochalcogen-supported azacalix[3]arenes are described in a one-pot manner in satisfactory yields. A remarkably selective potentiometric response was accomplished for uranyl ions over a variety of other metal ions, including alkali (Na⁺, K⁺), alkaline-earth (Mg²⁺, Ca²⁺, Ba²⁺), transition and heavy metal ions (Co²⁺, Ni²⁺, Cu²⁺, Ag⁺, Fe³⁺, Zn²⁺, Cd²⁺ and Pb²⁺) using an ion-selective electrode based on compound 3 incorporated into a polymeric (PVC) membrane.