蛋白质结构确定领域中的几种矩阵填充算法的对比评估

目的 目前,如何从核磁共振(nuclear magnetic resonance,NMR)光谱实验中准确地确定蛋白质的三维结构是生物物理学中的一个热门课题,因为蛋白质是生物体的重要组成成分,了解蛋白质的空间结构对研究其功能至关重要,然而由于实验数据的严重缺乏使其成为一个很大的挑战。方法 在本文中,通过恢复距离矩阵的矩阵填充(matrix completion,MC)算法来解决蛋白质结构确定问题。首先,初始距离矩阵模型被建立,由于实验数据的缺乏,此时的初始距离矩阵为不完整矩阵,随后通过MC算法恢复初始距离矩阵的缺失数据,从而获得整个蛋白质三维结构。为了进一步测试算法的性能,本文选取了4种不同拓扑结构的蛋白质和6种现有的MC算法进行了测试,探究了算法在不同的采样率以及不同程度噪声的情况下算法的恢复效果。结果 通过分析均方根偏差(root-mean-square deviation,RMSD)和计算时间这两个重要指标的平均值及标准差评估了算法的性能,结果显示当采样率和噪声因子控制在一定范围内时,RMSD值和标准差都能达到很小的值。另外本文更加具体地比较了不同算法的特点和优势,在精确采样情况下...     

Comparative analysis of membrane protein structure databases

BackgroundMembrane proteins play important roles in cell survival and cell communication, as they function as transporters, receptors, anchors and enzymes. They are also potential targets for drugs that block receptors or inhibit enzymes related to diseases. Although the number of known structures of membrane proteins is still small relative to the size of the proteome as a whole, many new membrane protein structures have been determined recently.Scope of the articleWe compared and analyzed the widely used membrane protein databases, mpstruc, Orientations of Proteins in Membranes (OPM), and PDBTM, as well as the extended dataset of mpstruc based on sequence similarity, the PDB structures whose classification field indicates that they are “membrane proteins” and the proteins with Structural Classification of Proteins (SCOP) class-f domains. We evaluated the relationships between these databases or datasets based on the overlap in their contents and the degree of consistency in the structural, topological, and functional classifications and in the transmembrane domain assignment.Major conclusionsThe membrane databases differ from each other in their coverage, and in the criteria that they use for annotation and classification. To ensure the efficient use of these databases, it is important to understand their differences and similarities. The establishment of more detailed and consistent annotations for the sequence, structure, membrane association, and function of membrane proteins is still required.General significanceConsidering the recent growth of experimentally determined structures, a broad survey and cumulative analysis of the sum of knowledge as presented in the membrane protein structure databases can be helpful to elucidate structures and functions of membrane proteins. We also aim to provide a framework for future research and classification of membrane proteins.     

Molecular Mechanics Calculations of Proteins. Comparison of Different Energy Minimization Strategies

Abstract

A general strategy for performing energy minimization of proteins using the SYBYL molecular modelling program has been developed. The influence of several variables including energy minimization procedure, solvation, dielectric function and dielectric constant have been investigated in order to develop a general method, which is capable of producing high quality protein structures. Avian pancreatic polypeptide (APP) and bovine pancreatic phospholipase A2 (BP PLA2) were selected for the calculations, because high quality X-ray structures exist and because all classes of secondary structure are represented in the structures. The energy minimized structures were evaluated relative to the corresponding X-ray structures. The overall similarity was checked by calculating RMS distances for all atom positions. Backbone conformation was checked by Ramachandran plots and secondary structure elements evaluated by the length on hydrogen bonds. The dimensions of active site in BP PLA2 is very dependent on electrostatic interactions, due to the presence of the positively charged calcium ion. Thus, the distances between calcium and the calcium-coordinating groups were used as a quality index for this protein. Energy minimized structures of the trimeric PLA2 from Indian cobra (N.n.n. PLA2) were used for assessing the impact of protein-protein interactions. Based on the above mentioned criteria, it could be concluded that using the following conditions: Dielectric constant ? = 4 or 20; a distance dependent dielectric function and stepwise energy minimization, it is possible to reproduce X-ray structures very accurately without including explicit solvent molecules.     

Structural analysis of protein–protein interactions in type I polyketide synthases

Abstract

Polyketide synthases (PKSs) are responsible for synthesizing a myriad of natural products with agricultural, medicinal relevance. The PKSs consist of multiple functional domains of which each can catalyze a specified chemical reaction leading to the synthesis of polyketides. Biochemical studies showed that protein–substrate and protein–protein interactions play crucial roles in these complex regio-/stereo-selective biochemical processes. Recent developments on X-ray crystallography and protein NMR techniques have allowed us to understand the biosynthetic mechanism of these enzymes from their structures. These structural studies have facilitated the elucidation of the sequence–function relationship of PKSs and will ultimately contribute to the prediction of product structure. This review will focus on the current knowledge of type I PKS structures and the protein–protein interactions in this system.     

Condensed Representations of Protein Secondary Structure Sequences and Their Application

Abstract

In this paper, we propose a nongraphical representation for protein secondary structures. By counting the frequency of occurrence of all possible four-tuples (i.e., four-letter words) of a protein secondary structure sequence, we construct a set of 3 × 3 matrices for the corresponding protein secondary structure sequence. Furthermore, the leading eigenvalues of these matrices are computed and considered as invariants for the protein secondary structure sequences. To illustrate the utility of our approach, we apply it to a set of real data to distinguish protein structural classes. The result indicates that it can be used to complement the classification of protein secondary structures.     

Oxygen-oxygen distances in protein-bound crystallographic water suggest the presence of protonated clusters

BackgroundThe availability of high-resolution X-ray structures has shown that proteins contain numerous water molecules, but their role is still not fully understood. Protonated and deprotonated water species are often involved in biochemical reactions. However protons are exceedingly difficult to detect directly because they are electron-poor species.MethodsThe oxygen‑oxygen distance of the crystallographic water molecules was analyzed in a large high-resolution data set. Moreover, a detailed analysis was carried out on the protein-bound water in the available structures of carbonic anhydrase II and cytochrome c oxidase, chosen as protein models in which protonated and deprotonated water species play a significant role.ResultsThe analysis shows an excess of water-water distances below the expected value for hydrogen bond. In the cavities and on the surface of the considered model proteins, clusters of water molecules are found, whose structure suggests the presence of chemical species deriving from self-ionization of water.ConclusionsThe presence of a small maximum below the hydrogen bond threshold in the oxygen‑oxygen distance distribution of crystallographic water molecules, along with the location of many of these water clusters, suggest the presence of Zundel-like structures in, or near, the proteins. Particularly significant is the presence of such structures in protein regions which have been identified as proton antennae or channels.General significanceThis work shows the possibilities, still unexplored, offered by this type of analysis in detecting in structures obtained by X-ray diffraction the presence of aqueous protons or hydroxide ions, which are chemical species as important as elusive.     

Probe into a multi-protein prokaryotic organelle using thermal scanning assay reveals distinct properties of the core and the shell

BackgroundBacterial microcompartments represent the only reported category of prokaryotic organelles that are capable of functioning as independent bioreactors. In this organelle, a biochemical pathway with all the enzyme machinery is encapsulated within an all protein shell. The shell proteins and the enzymes have distinct structural features. It is hypothesized that flat shell proteins align sideways to form extended sheets and, the globular enzymes fill up the central core of the organelle.MethodsUsing differential scanning fluorimetry, we explored the structure and functional alteration of Pdu BMC, involving tertiary or quaternary structures.ResultsOur findings exhibit that these intact BMCs as a whole behave similar to a globular protein with a rich hydrophobic core, which is exposed upon thermal insult. The encapsulated enzymes itself have a strong hydrophobic core, which is in line with the hydrophobic-collapse model of protein folding. The shell proteins, on the other hand, do not have a strong hydrophobic core and show a significant portion of exposed hydrophobic patches.ConclusionWe show for the first time the thermal unfolding profile of the BMC domain proteins and the unique exposure of hydrophobic patches in them might be required for anchoring the enzymes leading to better packaging of the micro-compartments.General significanceThese observations indicate that the genesis of these unique bacterial organelles is driven by the hydrophobic interactions between the shell and the enzymes. Insights from this work will aid in the genetic and biochemical engineering of thermostable efficient enzymatic biomaterials.     

The ammonia-lyases: enzymes that use a wide range of approaches to catalyze the same type of reaction

Abstract

The paradigm that protein structure determines protein function has been clearly established. What is less clear is whether a specific protein structure is always required to carry out a specific function. Numerous cases are now known where there is no apparent connection between the biological function of a protein and the other members of its structural class, and where functionally related proteins can have quite diverse structures. A set of enzymes with these diverse properties, the ammonia-lyases, will be examined in this review. These are a class of enzymes that catalyze a relatively straightforward deamination reaction. However, the individual enzymes of this class possess a wide variety of different structures, utilize a diverse set of cofactors, and appear to catalyze this related reaction through a range of different mechanisms. This review aims to address a basic question: if there is not a specific protein structure and active site architecture that is both required and sufficient to define a catalyst for a given chemical reaction, then what factor(s) determine the structure and the mechanism that is selected to catalyze a particular reaction?     

Energy Minimization for Tertiary Structure Prediction of Homologous Proteins: α1-purothionin and Viscotoxin A3 Models from Crambin

Abstract

Homologous proteins may fold into similar three-dimensional structures. Spectroscopic evidence suggests this is true for the cereal grain thionins, the mistletoe toxins, and for crambin, three classes of plant proteins. We have combined primary sequence homology and energy minimization to predict the structures α₁-purothionin (from Durum wheat) and viscotoxin A3 (from Viscum album, European mistletoe) from the high resolution (0.945 Å) crystal structure of crambin (from Crambe abyssinica). Our predictions will be verifiable because we have diffraction-quality crystals of α₁-purothionin whose structure we are have predicted. The potential energy minimizations for each protein were performed both with and without harmonic constraints to its initial backbone to explore the existence of local minima for the predicted proteins. Crambin was run as a control to examine the effects of the potential energy minimization on a protein with a well-known structure. Only α₁-purothionin which has one fewer residue in a turn region shows a significant difference for the two minimization paths. The results of these predictions suggest that α₁-purothionin and viscotoxin are amphipathic proteins, and this character may relate to the mechanism of action for these proteins. Both are mildly membrane-active and their amphipathic character is well suited for interaction with a lipid bilayer.     

Structure and Dynamics of Elastin Building Blocks. Boc-LG-OEt,Boc-VG-OEt,Boc-VGG-OH

Abstract

Short di- and tripeptides such as Boc-LG-OEt, Boc-VG-OEt and Boc-VGG-OH, corresponding to abundant repetitive sequences in elastin, have been extensively studied both in solid state, by X-ray diffraction, and in solution by circular dicroism and nuclear magnetic resonance. Furthermore, theoretical procedures such as simulated annealing and molecular dynamics were also performed on these peptides.

In general, the results indicate that no one single structure (be folded or extended) could be representative for these sequences in the protein, but rather that a multiplicity of interconverting conformers, ranging from folded to extended structures, should be considered. In any case, these structures, e.g. β-turns, polyglycine II and β-conformations, are those previously suggested to participate to conformational equilibria of elastin.     

Splitting statistical potentials into meaningful scoring functions: Testing the prediction of near-native structures from decoy conformations

Background  

Recent advances on high-throughput technologies have produced a vast amount of protein sequences, while the number of high-resolution structures has seen a limited increase. This has impelled the production of many strategies to built protein structures from its sequence, generating a considerable amount of alternative models. The selection of the closest model to the native conformation has thus become crucial for structure prediction. Several methods have been developed to score protein models by energies, knowledge-based potentials and combination of both.     

Inter-chain Proline: Proline Contacts Contribute to the Stability of the Triple Helical Conformation

Abstract

The triple helical conformation observed in the collagen group of proteins is related to the presence of large numbers of imino residues and is derived from the stereochemical properties of these residues. The triple helix is stabilized by increasing numbers of these residues. Hydrogen bonds are usually considered to be a major factor in the formation and stability of protein conformation, however, imino residues are not hydrogen bond donors. We have evaluated the role of these residues in stabilizing the triple helix by re-examining two X-ray based structures of the triple helical polypeptide (Pro-Pro- Gly)₁₀ using molecular mechanics calculations. The two minimized structures are comparable in energy and have helical parameters close to the starting values for each starting structure. Our studies suggest that clusters of close van der Waals contacts between proline residues in adjacent chains contribute significantly to the stability of the triple helix. Preliminary NMR studies support this concept. We propose that non-bonded interactions between proline residues may be a significant stabilizing force in the triple helix generated by (Pro-Pro-Gly)₁₀.     

α-casein micelles-membranes interaction: Flower-like lipid protein coaggregates formation

BackgroundEnvironmental conditions regulate the association/aggregation states of proteins and their action in cellular compartments. Analysing protein behaviour in presence of lipid membranes is fundamental for the comprehension of many functional and dysfunctional processes. Here, we present an experimental study on the interaction between model membranes and α-casein. α-casein is the major component of milk proteins and it is recognised to play a key role in performing biological functions. The conformational properties of this protein and its capability to form supramolecular structures, like micelles or irreversible aggregates, are key effectors in functional and pathological effects.MethodsBy means of quantitative fluorescence imaging and complementary spectroscopic methods, we were able to characterise α-casein association state and the course of events induced by pH changes, which regulate the interaction of this molecule with membranes.ResultsThe study of these complex dynamic events revealed that the initial conformation of the protein critically regulates the fate of α-casein, size and structure of the newly formed aggregates and their effect on membrane structures. Disassembly of micelles due to modification in electrostatic interactions results in increased membrane structure rigidity which accompanies the formation of protein lipid flower-like co-aggregates with protein molecules localised in the external part.General significanceThese results may contribute to the comprehension of how the initial state of a protein establishes the course of events that occur upon changes in the molecular environment. These events which may occur in cells may be essential to functional, pathological or therapeutical properties specifically associated to casein proteins.     

The study of the conformation and interaction of two tachykinin peptides in membrane mimicking systems by NMR spectroscopy and pulsed field gradient diffusion

Pulsed‐field gradient diffusion has been used to study the binding of two tachykinin peptides, [Tyr⁸]‐substance P (SP) and [Tyr⁰]‐neurokinin A (NKA) to two membrane‐mimicking micelles, dodecylphosphocholine, and sodium dodecylsulfate. The structure of these peptides bound to the micelles have also been studied by using two‐dimensional nmr and restrained simulated annealing calculations. No major difference in the structures of each peptide in the two micellar media was found. The difference between the micelle‐bound structure of [Tyr⁸]SP and that of SP was also minor. The longer helical conformation on the C‐terminus for [Tyr⁰]NKA was observed, compared with that for NKA. The relationship between the difference in the biological potencies of [Tyr⁸]SP and SP and the differences in their structure, especially the interaction of the side chains of the two aromatic residues, and the difference in their binding affinities to membrane was discussed. In addition, differences between the result of restrained molecular dynamics simulations of [Tyr⁸]SP in the presence of an explicit micelle and the present results were observed and discussed. © 1999 John Wiley & Sons, Inc. Biopoly 50: 555–568, 1999     

Insights into the structure–function relationship of both wild and mutant zinc transporter ZnT8 in human: a computational structural biology approach

Abstract

Polymorphism rs13266634 in SLC30A8 causes abnormal synthesis, maturation and secretion of insulin, resulting in decrease in efficiency of glucose metabolism and diabetes. SLC30A8 encodes Zinc transporter 8 protein (ZnT8). Due to lack of NMR/crystal structures of complete ZnT8 transporter, insights into the structure, function and its interaction with different drugs is still not known. Therefore, in-silico methods were adopted in the present studies for predicting three-dimensional structure of ZnT8 transporter via comparative modelling approach and studying the impact of mutation (p.ARG325TRP) on architecture and function via simulation studies. Wild-type protein comprises 15 α-helix and 3 β-strands, while mutant consists of 12 α-helix and 2 β-strands, respectively. Interaction studies of mutant ZnT8 transporter with phytochemicals/drugs screened the best phytochemicals, which can retain the wild-type property. Molecular docking studies reveal that mutant proteins have better binding energy with ligands of LY-2608204, Roseoside, and Luzonoid B. Further molecular dynamic simulation analysis exhibited a strong binding of these ligands with mutant protein and displaying similar behaviour as that of wild type. ALA79, ILE80, and ARG215 are the common interacting amino acids with ligand in all three complexes. As the ligands passed ADMET tests, these may be utilized as anti-diabetic drugs in near future. Although earlier studies have reported anti-diabetic property of LY-2608204 and Roseoside, for the first time, this study reporting Luzonoid B may have anti-diabetic property besides elucidating the structure and functions of ZnT8 transporter.     

Human disease glycomics: technology advances enabling protein glycosylation analysis – part 1

Introduction: Protein glycosylation is recognized as an important post-translational modification, with specific substructures having significant effects on protein folding, conformation, distribution, stability and activity. However, due to the structural complexity of glycans, elucidating glycan structure-function relationships is demanding. The fine detail of glycan structures attached to proteins (including sequence, branching, linkage and anomericity) is still best analysed after the glycans are released from the purified or mixture of glycoproteins (glycomics). The technologies currently available for glycomics are becoming streamlined and standardized and many features of protein glycosylation can now be determined using instruments available in most protein analytical laboratories.

Areas covered: This review focuses on the current glycomics technologies being commonly used for the analysis of the microheterogeneity of monosaccharide composition, sequence, branching and linkage of released N- and O-linked glycans that enable the determination of precise glycan structural determinants presented on secreted proteins and on the surface of all cells.

Expert commentary: Several emerging advances in these technologies enabling glycomics analysis are discussed. The technological and bioinformatics requirements to be able to accurately assign these precise glycan features at biological levels in a disease context are assessed.     

Protein Interactions and Fluctuations in a Proteomic Network using an Elastic Network Model

Abstract

A set of protein conformations are analyzed by normal mode analysis. An elastic network model is used to obtain fluctuation and cooperativity of residues with low amplitude fluctuations across different species. Slow modes that are associated with the function of proteins have common features among different protein structures. We show that the degree of flexibility of the protein is important for proteins to interact with other proteins and as the species gets more complex its proteins become more flexible. In the complex organism, higher cooperativity arises due to protein structure and connectivity.     

An Improved Computational Prediction Model for Lysine Succinylation Sites Mapping on Homo sapiens by Fusing Three Sequence Encoding Schemes with the Random Forest Classifier

Background Lysine succinylation is one of the reversible protein post-translational modifications (PTMs), which regulate the structure and function of proteins. It plays a significant role in various cellular physiologies including some diseases of human as well as many other organisms. The accurate identification of succinylation site is essential to understand the various biological functions and drug development.Methods In this study, we developed an improved method to predict lysine succinylation sites mapping on Homo sapiens by the fusion of three encoding schemes such as binary, the composition of k-spaced amino acid pairs (CKSAAP) and amino acid composition (AAC) with the random forest (RF) classifier. The prediction performance of the proposed random forest (RF) based on the fusion model in a comparison of other candidates was investigated by using 20-fold cross-validation (CV) and two independent test datasets were collected from two different sources.Results The CV results showed that the proposed predictor achieves the highest scores of sensitivity (SN) as 0.800, specificity (SP) as 0.902, accuracy (ACC) as 0.919, Mathew correlation coefficient (MCC) as 0.766 and partial AUC (pAUC) as 0.163 at a false-positive rate (FPR) = 0.10 and area under the ROC curve (AUC) as 0.958. It achieved the highest performance scores of SN as 0.811, SP as 0.902, ACC as 0.891, MCC as 0.629 and pAUC as 0.139 and AUC as 0.921 for the independent test protein set-1 and SN as 0.772, SP as 0.901, ACC as 0.836, MCC as 0.677 and pAUC as 0.141 at FPR = 0.10 and AUC as 0.923 for the independent test protein set-2. It also outperformed all the other existing prediction models.Conclusion The prediction performances as discussed in this article recommend that the proposed method might be a useful and encouraging computational resource for lysine succinylation site prediction in the case of human population.     

Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study

BackgroundIn protein crystals, flexible loops are frequently deformed by crystal contacts, whereas in solution, the large motions result in the poor convergence of such flexible loops in NMR structure determinations. We need an experimental technique to characterize the structural and dynamic properties of intrinsically flexible loops of protein molecules.MethodsWe designed an intended crystal contact-free space (CCFS) in protein crystals, and arranged the flexible loop of interest in the CCFS. The yeast Tim 21 protein was chosen as the model protein, because one of the loops (loop 2) is distorted by crystal contacts in the conventional crystal.ResultsYeast Tim21 was fused to the MBP protein by a rigid α-helical linker. The space created between the two proteins was used as the CCFS. The linker length provides adjustable freedom to arrange loop 2 in the CCFS. We re-determined the NMR structure of yeast Tim21, and conducted MD simulations for comparison. Multidimensional scaling was used to visualize the conformational similarity of loop 2. We found that the crystal contact-free conformation of loop 2 is located close to the center of the ensembles of the loop 2 conformations in the NMR and MD structures.ConclusionsLoop 2 of yeast Tim21 in the CCFS adopts a representative, dominant conformation in solution.General significanceNo single powerful technique is available for the characterization of flexible structures in protein molecules. NMR analyses and MD simulations provide useful, but incomplete information. CCFS crystallography offers a third route to this goal.     

Crystal structure of a dimerization domain of human Caprin-2: similar overall dimeric fold but different molecular surface properties to that of human Caprin-1

Abstract

Human Caprin-1 and Caprin-2 are prototypic members of the caprin (cytoplasmic activation/proliferation-associated protein) protein family. Vertebrate caprin proteins contain two highly conserved homologous regions (HR1 and HR2) and C-terminal RGG motifs. Drosophila caprin (dCaprin) shares HR1 and RGG motifs but lacks HR2. Caprin-1 and Caprin-2 have important and non-redundant functions. The detailed molecular mechanisms of their actions remain largely unknown. Previously, we determined the crystal structure of a ～120-residue fragment of Caprin-1 within the HR1 region. The structure has a novel all α-helical fold that self-associates to form a homodimer. In this study, the crystal structure of a corresponding fragment from Caprin-2 is reported. The Caprin-2 fragment has similar protein fold and dimeric structure as that of the Caprin-1 fragment. Structural comparison reveals that the molecular interactions mediating homodimerization of Caprin-1 and Caprin-2 are largely conserved in the two systems. Structural-modelling study of the corresponding dCaprin fragment indicates that dCaprin may also adopt a similar dimeric structure. The presence of a dimerization domain within HR1 may represent an evolutionarily conserved feature of the caprin protein family. Interestingly, while Caprin-1 and Caprin-2 adopt similar overall dimeric structures, the two structures have quite different molecular surface properties. In the Caprin-1 dimeric structure, some of the surface areas are known or suspected to function as binding sites for Carpin-1-interacting proteins. The different surface properties of the caprin dimeric structures may dictate their intermolecular interaction with specific protein partners.

Communicated by Ramaswamy H. Sarma.