Search for fucose binding domains in recently sequenced hypothetical proteins using molecular modeling techniques and structural analysis

The crystal structure of a fucose-binding lectin from the bacteria Pseudomonas aeruginosa in complex with α-L-fucose has been recently determined. It is a tetramer; each monomer displays a nine-stranded, antiparallel, β-sandwiched arrangement and contains two calcium ions that mediate the binding of fucose in a recognition mode unique among protein-carbohydrate interactions. In search of this type of unique interactions in other newly discovered protein sequences, we have used molecular modeling techniques to predict and analyze the 3-D structures of some proteins, which exhibited reasonable degree of homology with the amino acid sequence of the bacterial protein. A BLAST search with the sequence of Pseudomonas aeruginosa as query in the non-redundant sequence database identified four proteins from different species, three organisms from bacteria and one from archaea. We have modeled the structures of these proteins as well as those of the complexes with carbohydrates and studied the nature of physicochemical forces involved in the complex formation both in presence and absence of calcium. The calcium-binding loops have been found to be highly conserved both in terms of primary and tertiary structures in these proteins, although a less acidic character is observed in Photorhabdus lectin due to the absence of two aspartic acid residues on the calcium-binding loop which also resulted in lower binding affinity. All these structures exhibited highly negative electrostatic environment in the vicinity of the calcium-binding loops which was essential for neutralizing the positive charges of two closely situated Ca⁺² ions. The comparison of the binding affinities of some monosaccharides other than fucose, e.g. mannose and fructose, showed higher binding energies confirming the fucose specificity of these proteins.     

昆虫信息素结合蛋白的研究概况

在昆虫感受信息素的嗅觉反应中,信息素结合蛋白发挥了重要的作用。它作为脂溶性信息素的溶剂和载体,在亲水性淋巴液中起着运载信息素和使之失活的双重作用。由于它在昆虫识别信息素物质中起着重要的作用,近1 0年来,国内外对其进行了广泛、深入的研究。文章从信息素结合蛋白的生化特点、表达情况、代谢以及生理功能等方面的概况进行综述。     

Structure and function of cytoplasmic retinoid binding proteins

We examined the ligand protein interactions of two highly homologous cellular retinol binding proteins, CRBP and CRBP-II, and two highly homologous cellular retinoic acid binding proteins, CRABP-I and CRABP-II. While the crystal structures of all four have been determined, nuclear magnetic resonance studies provide a means for observing dynamic aspects of ligand protein interactions of these proteins in solution. The cellular functions of these proteins are less well understood. We have modeled retinoid flux between cytoplasmic retinoid proteins and model membranes and with nuclear receptors. Based on our in vitro studies, we propose that certain retinoids may indirectly influence retinoid signaling by displacing endogenous retinoids from the cytoplasmic proteins to the nuclear receptors.     

Novel classes of fatty acid and retinol binding protein from nematodes

Parasitic nematodes have recently been found to produce proteins which represent two new classes of fatty acid and retinoid binding protein. The first is the nematode polyprotein allergens/antigens (NPAs) which, as their name suggests, are synthesised as large polyproteins which are subsequently cleaved at regularly spaced sites to form multiple copies of a fatty acid binding protein of approximately 14.5 kDa. Binding studies using molecular environment-sensitive fluorescent ligands have shown that the binding site is highly unusual, producing blue-shifting in fluorescence to an unprecedented degree, suggesting a remarkably non-polar environment and isolation from solvent water. Computer-based structural predictions and biophysical observations have identified the NPAs as highly helical proteins which might form a four helix bundle, so constitute a new class of lipid binding protein from animals. The second class, like the NPAs, binds both fatty acids and retinol, but with a higher affinity for the latter. These are also highly helical but are structurally distinct from the NPAs. The biological function of these new classes of protein are discussed in the context of both the metabolic requirements of the parasites and the possible role of the proteins in control of the immune and inflammatory environment of the tissue sites parasitised.     

Nucleoplasmin: the archetypal molecular chaperone

Nucleoplasmin was the first protein to be described as a molecular chaperone. Studies of nucleoplasmin have resulted in advances in two areas of cell biology. Firstly, the pathway of nucleosome assembly in Xenopus oocytes and eggs has been elucidated and is the only assembly pathway known in detail. Nucleosome assembly represents the major chaperoning function of nucleoplasmin. Secondly, nucleoplasmin has been used to elucidate the transport of proteins into the nucleus, revealing a selective entry mechanism for nuclear proteins, passage through the nuclear pore complex, and a two-step mechanism of transport. The properties and functions of nucleoplasmin are reviewed, together with other proteins which are related either structurally or functionally to nucleoplasmin.     

Structure and mechanism of bacterial periplasmic transport systems

Bacterial periplasmic transport systems are complex, multicomponent permeases, present in Gram-negative bacteria. Many such permeases have been analyzed to various levels of detail. A generalized picture has emerged indicating that their overall structure consists of four proteins, one of which is a soluble periplasmic protein that binds the substrate and the other three are membrane bound. The liganded periplasmic protein interacts with the membrane components, which presumably form a complex, and which by a series of conformational changes allow the formation of an entry pathway for the substrate. The two extreme alternatives for such pathway involve either the formation of a nonspecific hydrophilic pore or the development of a ligand-binding site(s) on the membrane-bound complex. One of the membrane-bound components from each system constitutes a family of highly homologous proteins containing sequence domains characteristic of nucleotide-binding sites. Indeed, in several cases, they have been shown to bind ATP, which is thus postulated to be involved in the energy-coupling mechanism. Interestingly, eukaryotic proteins homologous to this family of proteins have been identified (mammalianmdr genes and Drosophilawhite locus), thus indicating that they perform a universal function, presumably related to energy coupling in membrane-related processes. The mechanism of energy coupling in periplasmic permeases is discussed.     

The RRM Protein NonA from Drosophila Forms a Complex with the RRM Proteins Hrb87F and S5 and the Zn Finger Protein PEP on hnRNA

The RRM protein NonA, an ubiquitous nuclear protein present in puffs on polytene chromosomes, has been immunopurified as a RNA–protein complex from Drosophila Kc cells. Three other proteins present in the complex have been identified: X4/PEP (protein on ecdysone puffs), a 100-kDa zinc finger RNA-binding protein; the 70-kDa S5 protein, an as yet uncharacterized RNA-binding protein; and P11/Hrb87F, a 38-kDa RRM protein homologous to hnRNP protein A1 from mammals. Monoclonal antibodies against any of the protein components coprecipitate all four proteins although at different ratios. NonA does not coprecipitate with the hrp40 hnRNP proteins and immunolocalizes in a pattern distinct of major hnRNP proteins. Like NonA, X4/PEP, S5, and P11/Hrb87F are present on active sites on polytene chromosomes. The precipitated NonA complex is enriched for certain protein encoding RNAs, notably, histone H3 and H4 RNA.     

囊泡转运蛋白SM蛋白家族的研究进展

真核细胞中含有多种不同功能的转运囊泡。虽然转运途径和携带物质各异,但细胞转运的基本分子机制却呈现出高度相似性和保守性。大多数转运途径都需要一种SNARE（Soluble NSF Attachment Protein Receptor）蛋白质复合体介导转运膜泡与靶膜的融合。同时,另一个蛋白家族,Secl／Muncl8蛋白（SM蛋白）也在囊泡运输中发挥重要作用。但是相比于对SNARE蛋白的认识的一致性,在不同的研究中SM蛋白的功能及其与SNARE复合体的相互作用方式却不尽相同。以下综述近年来有关SM蛋白结构和功能的研究进展,并归纳SM蛋白分子的作用机制、功能以及应用。     

Two trifluoperazine-binding sites on calmodulin predicted from comparative molecular modeling with troponin-C

Among the known regulatory proteins that are conformationally sensitive to the binding of calcium ions, calmodulin and troponin-C have the greatest primary sequence homology. This observation has led to the conclusion that the most accurate predicted molecular model of calmodulin would be based on the X-ray crystallographic coordinates of the highly refined structure of turkey skeletal troponin-C. This paper describes the structure of calmodulin built from such a premise. The resulting molecular model was subjected to conjugate gradient energy minimization to remove unacceptable intramolecular non-bonded contacts. In the analysis of the resulting structure, many features of calmodulin, including the detailed conformation of the Ca2+-binding loops, the amino- and carboxy-terminal hydrophobic patches of the Ca2+-bound form, and the several clusters of acidic residues can be reconciled with much of the previously published solution data. Calmodulin is missing the N-terminal helix characteristic of troponin-C. The deletion of three residues from the central helical linker (denoted D/E in troponin-C) shortens the molecule and changes the orientation of the two domains of calmodulin by 60 degrees relative to those in troponin-C. The molecular model has been used to derive two possible binding sites for the antipsychotic drug trifluoperazine, a potent competitive inhibitor of calmodulin activity.     

The pH-dependent unfolding mechanism of P2 myelin protein: an experimental and computational study

The P2 protein is a small, extrinsic protein of the myelin membrane in the peripheral nervous system that structurally belongs to the fatty acid binding proteins (FABPs) family, sharing with them a 10 strands beta-barrel structure. FABPs appear to be involved in cellular fatty acid transport, but very little is known about the role of P2 in the metabolism of peripheral myelin lipids. Study of protein conformation at different pHs is a useful tool for the characterization of the unfolding mechanisms and the intrinsic conformational properties of the protein, and may give insight into factors that guide protein folding pathways. In particular, low pH conditions have been shown to induce partially folded states in several proteins. In this paper, the acidic unfolding of purified P2 protein was studied with both spectroscopic techniques and molecular dynamics simulation. Both experimental and computational results indicate the presence of a partly folded state at low pH, which shows structural changes mainly involving the lid that is formed by the helix-turn-helix domain. The opening of the lid, together with a barrel relaxation, could regulate the ligand exchanges near the cell membrane, supporting the hypothesis that the P2 protein may transport fatty acids between Schwann cells and peripheral myelin.     

Loading efficacy and binding analysis of retinoids with milk proteins: a short review

In this review, the loading efficacies of retinoids with milk proteins are investigated. It has been shown that milk proteins β-lactoglobulin, α-, and β-caseins bind retinol and retinoic acid via hydrophobic, hydrophilic, and H-bonding contacts causing minor alterations of protein secondary structure. Hydrophobic contact is predominant in retinoid–protein conjugation and several amino acids are involved in complex formation, stabilized by H-bonding network. Loading efficacy of retinoid was about 30–50% with retinol forming more stable protein conjugates. Milk proteins can transport retinoid to target molecules.     

Setting up and running molecular dynamics simulations of membrane proteins

Molecular dynamics simulations have become a popular and powerful technique to study lipids and membrane proteins. We present some general questions and issues that should be considered prior to embarking on molecular dynamics simulation studies of membrane proteins and review common simulation methods. We suggest a practical approach to setting up and running simulations of membrane proteins, and introduce two new (related) methods to embed a protein in a lipid bilayer. Both methods rely on placing lipids and the protein(s) on a widely spaced grid and then 'shrinking' the grid until the bilayer with the protein has the desired density, with lipids neatly packed around the protein. When starting from a grid based on a single lipid structure, or several potentially different lipid structures (method 1), the bilayer will start well-packed but requires more equilibration. When starting from a pre-equilibrated bilayer, either pure or mixed, most of the structure of the bilayer stays intact, reducing equilibration time (method 2). The main advantages of these methods are that they minimize equilibration time and can be almost completely automated, nearly eliminating one time consuming step in MD simulations of membrane proteins.     

Sec1/Munc18蛋白的研究进展

大多数细胞包含许多种转运到不同目的地的囊泡.尽管存在许多特定的转运途径,根本的分子原则非常相似并在进化中保守.有充足的证据表明,膜融合除需要SNARE蛋白家族的参与外,也需要Sec1/Munc18(SM)蛋白;但是与SNARE蛋白功能的一致清楚相反,不同的实验系统得到的不同研究数据,使人们对于不同的SM蛋白的确切作用、作用位点和它们与SNARE蛋白的作用方式持不同观点.不同的SM蛋白与SNARE蛋白存在三种不同的作用模式.最近的研究确定,Munc18-1直接促进融合,并且它可能以所有三种模式与SNARE蛋白相互作用.本文综述了该领域的最新研究进展.     

Identification and functional characterization of the bile acid transport proteins in non-mammalian ileum and mammalian liver

It has been proposed that intracellular carrier proteins mediate active transport of the bile acids within hepatocytes and ileocytes, during the enterohepatic circulation. In mammalian species only ileal bile acid binding proteins have been so far identified, while liver cytosolic carriers have never been found. On the contrary, in non-mammalian vertebrates, only liver, and not ileal, bile acid binding proteins were reported. The aim of the present work is to find the missing cytosolic transport proteins. A bioinformatic search allowed us to identify a non-mammalian putative bile acid binding protein in the chicken ileum (cI-BABP), which we recombinantly expressed and purified. The protein exhibits the capability, tested by in vitro NMR experiments, of binding bile acids. Furthermore, strong NMR evidence reported that the human liver fatty acid binding protein (hL-FABP) can also bind bile acids. Taken together, these data strongly suggest that both cI-BABP and hL-FABP have a bile acid binding function in the two organisms, and support a previous hypothesis on the role of hL-FABP in regulating bile acid metabolism and determining bile acid pool size.     

The folate and thiamine transport proteins of lactobacillus casei

Two separate binding proteins, one specific for folate and the other for thiamine, have been isolated from membrane fragments of Lactobacillus casei. Purification to homogeneity was achieved by fractionation of the Triton-solubilized proteins with microgranular silica (Quso G-32) and Sephadex G-150. Amino acid analyses revealed that the folate (M_r = 25,000) and thiamine (M_r = 29,000) binders have unusually low polarity constants, 0.32 and 0.26, respectively. Evidence obtained with intact cells has established a direct role for these binding proteins in transport of the corresponding vitamins: (A) In each case, the processes of binding and transport showed similarities in substrate affinities and repression by excess vitamin in the growth medium. (B) Competition studies employing amethopterin, 5-formyl tetrahydrofolate, and 5-methyl tetrahydrofolate (for folate) and thiamine monophosphate and thiamine pyrophosphate (for thiamine) have shown that the ability of these compounds to inhibit the transport of the corresponding vitamins is paralleled by their ability to inhibit binding. (C) Amethopterin-resistant mutants which are defective in folate transport have a comparable defect in ability to bind folate. (D) Amethopterin-resistant cells which (compared with the parent cell line) contain folate transport systems with altered affinities for amethopterin also contain binding proteins whose affinities for amethopterin have changed by equivalent amounts. (E) Both the transport and binding of folate by one of the mutants were stimulated (approximately 3-fold) in parallel by the addition of mercaptoethanol.     

Simple models for the analysis of binding protein-dependent transport systems.

Mathematical modeling was used to evaluate experimental data for bacterial binding protein-dependent transport systems. Two simple models were considered in which ligand-free periplasmic binding protein interacts with the membrane-bound components of transport. In one, this interaction was viewed as a competition with the ligand-bound binding protein, whereas in the other, it was considered to be a consequence of the complexes formed during the transport process itself. Two sets of kinetic parameters were derived for each model that fit the available experimental results for the maltose system. By contrast, a model that omitted the interaction of ligand-free binding protein did not fit the experimental data. Some applications of the successful models for the interpretation of existing mutant data are illustrated, as well as the possibilities of using mutant data to test the original models and sets of kinetic parameters. Practical suggestions are given for further experimental design.     

Plasmodesmata: composition,structure and trafficking

Plasmodesmata are highly specialized gatable trans-wall channels that interconnect contiguous cells and function in direct cytoplasm-to-cytoplasm intercellular transport. Computer-enhanced digital imaging analysis of electron micrographs of plasmodesmata has provided new information on plasmodesmatal fine structure. It is now becoming clear that plasmodesmata are dynamic quasi-organelles whose conductivity can be regulated by environmental and developmental signals. New findings suggest that signalling mechanisms exist which allow the plasmodesmatal pore to dilate to allow macromolecular transport. Plant viruses spread from cell to cell via plasmodesmata. Two distinct movement mechanisms have been elucidated. One movement mechanism involves the movement of the complete virus particle along virus-induced tubular structures within a modified plasmodesma. Apparently two virus-coded movement proteins are involved. A second movement mechanism involves the movement of a non-virion form through existing plasmodesmata. In this mechanism, the viral movement protein causes a rapid dilation of existing plasmodesmata to facilitate protein and nucleic acid movement. Techniques for the isolation of plasmodesmata have been developed and information on plasmodesma-associated proteins is now becoming available. New evidence is reviewed which suggests that plasmodesmatal composition and regulation may differ in different cells and tissues.     

Sending out molecules from the TGN

The sorting of secreted cargo proteins and their export from the trans-Golgi network (TGN) remains an enigma in the field of membrane trafficking; although the sorting mechanisms of many transmembrane proteins have been well described. The sorting of secreted proteins at the TGN is crucial for the release of signaling factors, as well as extracellular matrix proteins. These proteins are required for cell–cell communication and integrity of an organism. Missecretion of these factors can cause diseases such as neurological disorders, autoimmune disease, or cancer. The major open question is how soluble proteins that are not associated with the membrane are packed into TGN derived transport carriers to facilitate their transport to the plasma membrane. Recent investigations have identified novel types of protein and lipid machinery that facilitate the packing of these molecules into a TGN derived vesicle. In addition, novel research has uncovered an exciting link between cargo sorting and export in which TGN structure and dynamics, as well as TGN/endoplasmic reticulum contact sites, play a significant role. Here, we have reviewed the progress made in our understanding of these processes.