胰瘘发生假说到捆绑式胰肠吻合的临床运用

为避免术后胰瘘的发生,在过去的100年间提出了多种胰肠吻合重建方式,但哪种方法最好一直备受争议.胰肠吻合后吻合针距间存在可能的间隙,这个问题或许成为胰肠吻合口瘘的爆发点,而且存在贯穿浆肌层缝合的胰腺表面外露的吻合针眼,如果缝针贯穿胰管小分支,胰液可能从针眼流出.这一假说构成了捆绑式胰肠吻合的基础.捆绑式胰肠吻合是一种安全、有效的预防术后胰瘘的吻合方式.     

Sequential potassium binding at the extracellular side of the Na,K-Pump

Ion binding at the extracellular face of the Na,K-ATPase is electrogenic and can be monitored by the styryl dye RH 421 in membrane fragments containing a high density of the Na,K-pumps. The fluorescent probe is noncovalently bound to the membrane and responds to changes of the local electric field generated by binding or release of cations inside the protein. Due to the fact that K⁺ binding from the extracellular side is an electrogenic reaction, it is possible to detect the amount of ions bound to the pump as function of the aqueous concentration. The results are in contradiction to a second order reaction, i.e., a simultaneous binding of two K⁺ ions. A mathematical model is presented to discuss the nature of the two step binding process. On the basis of this model the data allow a quantitative distinction between binding of the first and the second K⁺ ion. The temperature dependence of ion binding has been investigated. At low temperatures the apparent dissociation constants differ significantly. In the temperature range above 20°C the resulting apparent dissociation constants for both K⁺ ions merge and have values between 0.2 and 0.3 mm, which is consistent with previous experiments. The activation energy for the half saturating concentration of K⁺ is 22 kJ/mol. Additional analysis of the titration curve of K⁺ binding to the state P — E₂ by the Hill equation yields a Hill coefficient, n_Hill, of 1.33, which is in agreement with previously published data.The authors would like to thank G. Witz for technical assistance. This work has been financially supported by the Deutsche Forschungsgemeinschaft (SFB 156).     

On the interpretation of binding isotherms in complex biological systems: Apparent homogeneity of some heterogeneous systems

A simple treatment of the effect of site heterogeneity upon binding isotherms is presented, which is applicable to the analysis of data obtained from measurements of hormone, drug, or lectin binding to membranes and cell surfaces. Using this treatment, isotherms corresponding to various distributions of binding constants have been fitted to examples of experimental binding data ordinarily interpreted in the context of a homogeneous binding site model. It is found that these data do not permit one to exclude the alternate possibility of a broad distribution of the binding constant $\text{K}$. If a homogeneous binding site model can be satisfactorily fitted to the data, it is probable that the value of $\text{K}$ obtained by this procedure is equal or nearly equal to the number average value of $\text{K}$ in the actual (unknown) distribution.     

Optimizing the affinity and specificity of ligand binding with the inclusion of solvation effect

Solvation effect is an important factor for protein–ligand binding in aqueous water. Previous scoring function of protein–ligand interactions rarely incorporates the solvation model into the quantification of protein–ligand interactions, mainly due to the immense computational cost, especially in the structure‐based virtual screening, and nontransferable application of independently optimized atomic solvation parameters. In order to overcome these barriers, we effectively combine knowledge‐based atom–pair potentials and the atomic solvation energy of charge‐independent implicit solvent model in the optimization of binding affinity and specificity. The resulting scoring functions with optimized atomic solvation parameters is named as specificity and affinity with solvation effect (SPA‐SE). The performance of SPA‐SE is evaluated and compared to 20 other scoring functions, as well as SPA. The comparative results show that SPA‐SE outperforms all other scoring functions in binding affinity prediction and “native” pose identification. Our optimization validates that solvation effect is an important regulator to the stability and specificity of protein–ligand binding. The development strategy of SPA‐SE sets an example for other scoring function to account for the solvation effect in biomolecular recognitions. Proteins 2015; 83:1632–1642. © 2015 Wiley Periodicals, Inc.     

Prediction and validation of the unexplored RNA‐binding protein atlas of the human proteome

Detecting protein‐RNA interactions is challenging both experimentally and computationally because RNAs are large in number, diverse in cellular location and function, and flexible in structure. As a result, many RNA‐binding proteins (RBPs) remain to be identified. Here, a template‐based, function‐prediction technique SPOT‐Seq for RBPs is applied to human proteome and its result is validated by a recent proteomic experimental discovery of 860 mRNA‐binding proteins (mRBPs). The coverage (or sensitivity) is 42.6% for 1217 known RBPs annotated in the Gene Ontology and 43.6% for 860 newly discovered human mRBPs. Consistent sensitivity indicates the robust performance of SPOT‐Seq for predicting RBPs. More importantly, SPOT‐Seq detects 2418 novel RBPs in human proteome, 291 of which were validated by the newly discovered mRBP set. Among 291 validated novel RBPs, 61 are not homologous to any known RBPs. Successful validation of predicted novel RBPs permits us to further analysis of their phenotypic roles in disease pathways. The dataset of 2418 predicted novel RBPs along with confidence levels and complex structures is available at http://sparks-lab.org (in publications) for experimental confirmations and hypothesis generation. Proteins 2014; 82:640–647. © 2013 Wiley Periodicals, Inc.     

Discovery of receptor-ligand interfaces in the immunoglobulin superfamily

Cell-surface-anchored immunoglobulin superfamily (IgSF) proteins are widespread throughout the human proteome, forming crucial components of diverse biological processes including immunity, cell-cell adhesion, and carcinogenesis. IgSF proteins generally function through protein-protein interactions carried out between extracellular, membrane-bound proteins on adjacent cells, known as trans-binding interfaces. These protein-protein interactions constitute a class of pharmaceutical targets important in the treatment of autoimmune diseases, chronic infections, and cancer. A molecular-level understanding of IgSF protein-protein interactions would greatly benefit further drug development. A critical step toward this goal is the reliable identification of IgSF trans-binding interfaces. We propose a novel combination of structure and sequence information to identify trans-binding interfaces in IgSF proteins. We developed a structure-based binding interface prediction approach that can identify broad regions of the protein surface that encompass the binding interfaces and suggests that IgSF proteins possess binding supersites. These interfaces could theoretically be pinpointed using sequence-based conservation analysis, with performance approaching the theoretical upper limit of binding interface prediction accuracy, but achieving this in practice is limited by the current ability to identify an appropriate multiple sequence alignment for conservation analysis. However, an important contribution of combining the two orthogonal methods is that agreement between these approaches can estimate the reliability of the predictions. This approach was benchmarked on the set of 22 IgSF proteins with experimentally solved structures in complex with their ligands. Additionally, we provide structure-based predictions and reliability scores for the 62 IgSF proteins with known structure but yet uncharacterized binding interfaces.     

Solvent accessibility as a predictive tool for the free energy of inhibitor binding to the HIV-1 protease.

We have developed a simple approach for the evaluation of the free energies of inhibitor binding to the protease of the human immunodeficiency virus (HIV-1 PR). Our algorithm is based on the observation that most groups that line the binding pockets of this enzyme are hydrophobic in nature. Based on this fact, we have likened the binding of an inhibitor to this enzyme to its transfer from water to a medium of lower polarity. The resulting expression produced values for the free energy of binding of inhibitors to the HIV-1 PR that are in good agreement with experimental values. The additive nature of this approach has enabled us to partition the free energy of binding into the contributions of single fragments. The resulting analysis clearly indicates the existence of a ranking in the participation of the enzyme's subsites in binding. Although all the enzyme's pockets contribute to binding, the ones that bind the P2-P'2 span of the inhibitor are in general the most critical for high inhibitor potency. Moreover, our method has allowed us to determine the nature of the functional groups that fit into given enzyme binding pockets. Perusal of the energy contributions of single side chains has shown that a large number of hydrophobic and aromatic groups located in the central portion of the HIV-1 PR inhibitors present optimal binding. All of these observations are in agreement with experimental evidence, providing a validation for the physical relevancy of our model.     

Lipid-protein interactions. A comparative study of the binding of cardiotoxins and neurotoxins to phospholipid vesicles

It has recently been shown that cardiotoxin II from Naja mossambica mossambica specifically interacts with negatively charged phospholipids (Dufourcq, J. and Faucon, J.F. (1978) Biochemistry 17, 1170–1176). In order to investigate whether or not short neurotoxins give rise to similar interactions, four techniques have been used, namely intrinsic fluorescence, fluorescence polarization of 1,6-diphenylhexatriene, turbidity measurements and release of 6-carboxyfluorescein trapped inside single shelled vesicles.Neurotoxin III from Naja mossambica mossambica and neurotoxin I from the venom of the scorpion Androctonus australis Hector, specifically interact with negatively charged phospholipids leading to changes in tryptophan fluorescence and to a decrease of the fluidity of the bilayer. Cardiotoxin II from the same snake venom gives similar results. On the other hand, it seems that either a very weak or no interaction at all occurs in the case of neurotoxin I from the same Naja venom.There are important differences in the behaviour of cardiotoxin and neurotoxins: (i) neurotoxins lead to only weak release of 6-carboxyfluorescein from lipid vesicles, whereas cardiotoxin II induces fast and quantitative escape of the dye and then a general breakdown of the vesicular structure; (ii) binding of neurotoxins can be easily reversed by 100–200 mM NaCl or less than 1 mM Ca²⁺ and so it is essentially electrostatic, whereas binding of cardiotoxin II seems to involve some hydrophobic contribution.The short neurotoxins and cardiotoxins from snake venom having a great homology in sequence, their differences on binding properties are discussed in terms of changes in a particular area of the sequence.     

Effects of the Binding of Imipramine to Erythrocytes and Plasma Proteins on Its Transport Through the Rat Blood-Brain Barrier

Brain extraction of a tricyclic antidepressant, imipramine, was investigated using the carotid injection technique in the rat. The extent to which drug binding to plasma proteins and erythrocytes could inhibit the brain extraction was measured. Equilibrium dialysis showed that imipramine is highly bound to human serum albumin (HSA), alpha 1-acid glycoprotein (AAG), lipoproteins, and erythrocytes. The free dialyzable drug fraction was inversely related to the protein concentration. Despite this degree of binding, no significant reduction in the brain extraction of the drug was observed in the presence of HSA, lipoprotein, or erythrocytes. Only AAG reduced the brain transport of this drug in a ratio related to the protein concentration. However, the rat brain extraction was higher than expected from the in vitro measurement of the dialyzable fraction. These data indicate that the amount of circulating imipramine available for penetration in brain exceeds widely the dialyzable fraction of the drug as measured in vitro.     

The binding ability of insulin-related peptides as the clue to the search for their functional role in phylogenesis. Introduction to the problem

The common plan of structure of the main peptides of the vertebrate insulin family—insulin itself, IGF-I, IGF-II, and relaxin—has distinct structural formations. Each of the peptides performs its characteristic function. However, overlapping of insulin and IGF-I actions and its stability in the vertebrate phylogenesis have formed the concept of their regulation of growth and metabolism as a function fixed in phylogenesis for a certain type of structures. At the same time, study of insulin-related peptides in invertebrates has revealed the wider spectrum, than in vertebrates, of biological effects; this indicated that the similarity of the total structure design is not sufficient for judging about their functional role. Functional possibilities of a regulatory peptide depend fundamentally on its capability for binding to the receptor realizing its biological action. However, the binding ability has a wider significance than merely transmission of biological signals. Thus, IGF-II when interacting with receptors realizing its biological effects also binds to the IGF-2 receptor limiting its action and, besides, to the binding proteins (BP) modulating its action. The entire cycle of interactions occurs in the body at different affinity levels. Meanwhile, insulin interacts neither with IGF-2 receptor nor with BP. In this case, specificity and sequence of interaction with each of receptors or with protein are due not to the general design of the peptide structure, but rather to structure of individual submolecular determinants—binding domains. The leading role in disclosure of composition and structure of these domains is played by the “mutant-ligand” approach evaluating affinity of modified analogs. To analyze role of structural elements of the binding domains, the author proposes the system of estimation of affinity of the studied analogs. The present work, alongside with consideration of methodical aspects of the forthcoming analysis, is an introduction to the problem of organization of the binding domains connected directly with functional role of peptides of the insulin type. The proposed analysis is due to necessity of specification of this organization both in one molecule and in different molecules with a similar plan of structure on the basis of not always unanimous literature data and of clarification of principles of structure of these domains.     

Substitution of D-Trp32 in NPY Destabilizes the Binding Transition State to the Y1 Receptor Site in SK-N-MC Cell Membranes

The retention rate of the spin label 3-isothiocyanto methyl-2,2,5,5-tetramethyl-1-pyrrolidinyl oxyl spin label (proxyl) attached to the porcine N-acetyl-NPY peptide and the porcine N-acetyl-D-Trp³²-NPY peptide at Lys⁴ was investigated using SK-N-MC neuroblastoma cell membranes containing the Y1 receptor. The release rate of the spin labeled peptides was monitored by electron spin resonance and the K_D was determined by a direct radiolabeled NPY displacement binding assay. The analyses show that for the porcine [Ac-Tyr¹N⁴-proxyl]-NPY, the K_D was 8 × 10^–10 M and k_off was 2.7 × 10^–4 sec^–1 yielding a value for k_on of 3.3 × 10⁵ sec^–1 M^–1. The [Ac-Tyr¹, N⁴-proxyl,-D-Trp³²]-NPY antagonist ligand had a value of K_D equal to 1.35 × 10^–7 M and k_off was 1.7 × 10^–4 sec^–1 leading to a value for k_on of 1.2 × 10³ sec^–1 M^–1. The difference in the k_on rates of two orders of magnitude is interpreted as demonstrating the N-acetyl-N⁴ proxyl-D-Trp³²-NPY ligand binding transition state to be of higher energy then for the unmodified NPY amino acid sequence.     

Molecular dynamics simulations of ethanol binding to the transmembrane domain of the glycine receptor: implications for the channel potentiation mechanism

The glycine receptor (GlyR) is potentiated by ethanol and other anesthetics. The potentiation mechanism at the molecular level is unknown and remains elusive, but mutagenic studies have shown that ethanol and other volatile anesthetics bind to a pocket between TM1, TM2, and TM3. The present study extends previous studies (Cheng et al., Proteins 2007;68:581-593) wherein we conducted homology modeling and molecular dynamics (MD) simulations to construct models of the homopentameric alpha1 subunits of the GlyR transmembrane domain in open and closed states. To understand the potentiation of GlyR by ethanol we compare the binding of ethanol molecules to the channel in these different states. We observe that ethanol stably resides inside solvent-accessible cavities found in the open state of GlyR that are formed by I229 (of TM1) in one subunit and S267 and A288 (of TM2 and TM3, respectively) in the adjacent subunit. The volume of these putative binding pockets is state-dependent. Selective binding to the open states of receptors has been proposed to explain the potentiating actions of this class of anesthetics. In accordance with this model, our MD simulations suggest that the potentiation of ethanol on GlyR may be effected through preferential binding of ethanol molecules to an inter-subunit binding pocket in the open state.     

The effect of multiple binding modes on empirical modeling of ligand docking to proteins.

A popular approach to the computational modeling of ligand/receptor interactions is to use an empirical free energy like model with adjustable parameters. Parameters are learned from one set of complexes, then used to predict another set. To improve these empirical methods requires an independent way to study their inherent errors. We introduce a toy model of ligand/receptor binding as a workbench for testing such errors. We study the errors incurred from the two state binding assumption--the assumption that a ligand is either bound in one orientation, or unbound. We find that the two state assumption can cause large errors in free energy predictions, but it does not affect rank order predictions significantly. We show that fitting parameters using data from high affinity ligands can reduce two state errors; so can using more physical models that do not use the two state assumption. We also find that when using two state models to predict free energies, errors are more severe on high affinity ligands than low affinity ligands. And we show that two state errors can be diagnosed by systematically adding new binding modes when predicting free energies: if predictions worsen as the modes are added, then the two state assumption in the fitting step may be at fault.     

Relationships Between the Catechol Substrate Binding Site and Amphetamine, Cocaine, and Mazindol Binding Sites in a Kinetic Model of the Striatal Transporter of Dopamine In Vitro

Abstract: Experiments were conducted to determine how (−)-cocaine and S (+)-amphetamine binding sites relate to each other and to the catechol substrate site on the striatal dopamine transporter (sDAT). In controls, m -tyramine and S (+)-amphetamine caused release of dopamine from intracellular stores at concentrations ≥12-fold those observed to inhibit inwardly directed sDAT activity for dopamine. In preparations from animals pretreated with reserpine, m -tyramine and S (+)-amphetamine caused release of preloaded dopamine at concentrations similar to those that inhibit inwardly directed sDAT activity. S (+)-Amphetamine and m -tyramine inhibited sDAT activity for dopamine by competing for a common binding site with dopamine and each other, suggesting that phenethylamines are substrate analogues at the plasmalemmal sDAT. (−)-Cocaine inhibited sDAT at a site separate from that for substrate analogues. This site is mutually interactive with the substrate site ( K _int = 583 n M ). Mazindol competitively inhibited sDAT at the substrate analogue binding site. The results with (−)-cocaine suggest that the (−)-cocaine binding site on sDAT is distinct from that of hydroxyphenethylamine substrates, reinforcing the notion that an antagonist for (−)-cocaine binding may be developed to block (−)-cocaine binding with minimal effects on dopamine transporter activity. However, a strategy of how to antagonize drugs of abuse acting as substrate analogues is still elusive.     

In vitro and in vivo regulation of chJoroplast glyceraldehyde-3-phosphate dehydrogenase isozymes from Chenopodium rubrum. III. The molecular basis of the aggregation phenomenon: chloroplast glyceraldehyde-3-phosphate dehydrogenase as an ambiquitous enzyme

The nature of the aggregated form of chloroplast glyceraldehyde-3-phosphate dehydrogenase isozymes (GPD, EC 1.2.1.13) from Chenopodium rubrum leaves was investigated. After disaggregation of the isozymes in NADP ⁺ buffer, and resuspension of the disaggregated isozymes in NAD⁺ buffer, complete reaggregation could only be achieved by remixing the enzyme with a high molecular weight fraction, from which the isozymes had dissociated during the NADP⁺ filtration. After separation of the isozymes by inverse ammonium sulphate gradient solubilization, spontaneous extensive reaggregation of each isozyme was observed in NAD⁺ buffer. The high molecular weight material consisted of ribonucleoprotein, and RNase treatment impaired its ability to promote reaggregation of chloroplast GPD. It is proposed that pyridine nucleotide-controlled aggregation and binding to ribonucleoprotein in vitro are artifacts which reflect an in situ binding to cellular components. Since uncontrolled NAD⁺-linked activities of the bifunctional isozymes in the chloroplast would lead to an equalization of the NAD ⁺ and NADP ⁺ redox couples, it is suggested that the reversible binding of the isozymes forms the basis of a regulatory system in vivo.     

Characterization of endozepine-related peptides in the central nervous system and in peripheral tissues of the rat

Endozepines represent a novel family of regulatory peptides that have been isolated by their ability to displace benzodiazepines from their binding sites. All endozepines derive from an 86 amino acid precursor polypeptide called diazepam binding inhibitor (DBI), which generates, through proteolytic cleavage, several biologically active endozepines. The aim of the present study was to compare the molecular forms of endozepines present in different regions of the rat brain and in various peripheral organs using an antiserum raised against the central (biologically active) region of DBI. Combination of HPLC analysis and RIA detection revealed the existence of two major forms (peaks I and II) of endozepine-immunoreactive peptides. The retention times of the two peaks (36 and 39 min, respectively) were identical in all tissues or organs tested. Western blotting analysis of cerebral cortex extracts confirmed the existence of two immunoreactive species with apparent molecular weights 4000 and 6000 Da, which respectively correspond to peaks I and II. Tryptic digestion of peaks I and II generated a single immunoreactive peptide that coeluted with the synthetic octadecaneuropeptide ODN [DBI(33–50)]. These results show that, in different parts of the brain and in various peripheral organs, DBI is rapidly processed to generate two peptides of apparent molecular weight of 4000 and 6000 Da, which both possess the biologically active determinant of endozepines.     

Ydj1p锌指结构突变体对底物结合影响的分子动力学模拟分析

Ydj1p是酵母细胞质中一种主要的I型Hsp40分子伴侣,Ydj1p锌指结构在传递底物给Hsp70时发挥重要的作用,锌指结构域的两个锌离子结合位点区域(ZBDⅠ和ZBDⅡ)与半胱氨酸形成配位键对底物传递中维持结构稳定非常重要。本研究通过分子动力学手段对Ydj1p与各锌指结构突变体进行了模拟,分析ZBDⅠ突变体关键残基C143S、C201S,ZBDⅡ突变体关键残基C162S、C185S的突变影响Hsp40与Hsp70的底物传递。分析结果表明,当锌指部位的氨基酸发生突变,不仅能影响Ydj1p的结构稳定性,也能影响底物的传递,并且锌指结构Ⅰ突变体和锌指结构Ⅱ突变体之间也具有明显差异。通过结合能量的分析以及构象变化比对,揭示了Ydj1p以及各锌指结构突变体底物结合能力的强弱,这与生化实验研究了Ydj1p锌指结构与Hsp70合作,帮助多肽传递的功能是至关重要的结果较为相近。