Current Protein & Peptide Science

ISSN: 1389-2042

Current Protein and Peptide Science
Volume 8, Number 3, June 2007

Contents


Recent Progress in Measuring Structural Similarity Between Proteins Pp. 219-241
Oliviero Carugo
[Abstract]


Bioinformatics Approaches for Disulfide Connectivity Prediction Pp. 243-260
Chi-Hung Tsai, Chen-Hsiung Chan, Bo-Juen Chen, Cheng-Yan Kao, Hsuan-Liang Liu and Jyh-Ping Hsu
[Abstract]


Glycoprotein Targeting and Other Applications of Lectins in Biotechnology Pp. 261-271
Aabgeena Naeem, M. Saleemuddin and Rizwan Hasan Khan
[Abstract]


Enzymes Catalyzing Protein Folding and Their Cellular Functions Pp. 273-282
Natalya Nagradova
[Abstract]


Structure-Function Relation of Somatotropin with Reference to Molecular Modeling Pp. 283-292
Amtul Jamil Sami
[Abstract]


The PYRIN Domain in Signal Transduction Pp. 293-310
Christian Stehlik
[Abstract]




Abstracts


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Recent Progress in Measuring Structural Similarity Between Proteins
Oliviero Carugo

Surprisingly, after at least two decades of researches focused on the analysis of the similarity between protein three-dimensional structures, several new comparison methods were proposed during the last few years. These are briefly summarized and commented below. Some of the newly developed techniques are fast and were designed to handle large amounts of data and vast structural databases. Other methods are much slower and were developed to gain biological information by comparing distantly related protein structures. Additional studies were devoted to the problem of the multiple structural alignments and to strategies of comparison between alternative structural alignments.


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Bioinformatics Approaches for Disulfide Connectivity Prediction
Chi-Hung Tsai, Chen-Hsiung Chan, Bo-Juen Chen, Cheng-Yan Kao, Hsuan-Liang Liu and Jyh-Ping Hsu

Protein structure prediction with computational methods has gained much attention in the research fields of protein engineering and protein folding studies. Due to the vastness of conformational space, one of the major tasks is to restrain the flexibility of protein structure and reduce the search space. Many studies have revealed that, with the information of disulfide connectivity available, the search in conformational space can be dramatically reduced and lead to significant improvements in the prediction accuracy. As a result, predicting disulfide connectivity using bioinformatics approaches is of great interest nowadays.

In this mini-review, the prediction of disulfide connectivity in proteins will be discussed in four aspects: (1) how the problem formulated and the computational techniques used in the literatures; (2) the effects of the features adopted to encode the information and the biological meanings implied; (3) the problems encountered and limitations of disulfide connectivity prediction; and (4) the practical usages of predicted disulfide bond information in molecular simulation and the prospects in the future.


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Glycoprotein Targeting and Other Applications of Lectins in Biotechnology
Aabgeena Naeem, M. Saleemuddin and Rizwan Hasan Khan

Glycoconjugates comprise a variety of structures, include glycoproteins and glycolipids and are found on the surfaces of animal and plant cells, as well as on the surface of microorganisms. Determination of the structure and the distribution of glycoconjugates on cell surfaces are important for the understanding their biological function. Lectins are useful to investigate protein-carbohydrate interactions, because they have specificity for defined carbohydrate structure. They have been implicated in cell-to-cell recognition and signaling, blood group typing, in immune recognition process, and various other biological processes, such as viral, bacterial, mycoplasmal and parasitic infections, fertilization, cancer metastasis, growth and differentiation. Once thought to be confined to plant seeds, lectins are now recognized as ubiquitous in virtually all living systems, ranging from viruses and bacteria to animals. Plant lectins provide a rich source of carbohydrate-recognizing protein reagents for glycobiologists and biotechnologists. Biotechnology offers the therapeutic use of lectin against certain life threatening diseases such as human immunodeficiency virus and cancer. This review presents a comprehensive summary of research efforts that focus on the actual and potential uses and advantages of using lectins to target glycoproteins and also glycoproteins to target lectins.


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Enzymes Catalyzing Protein Folding and Their Cellular Functions
Natalya Nagradova

In live cells, protein folding often cannot occur spontaneously, but requires the participation of helper proteins – molecular chaperones and foldases. The mechanisms employed by chaperones markedly increase the effectiveness of protein folding, but have no bearing on the rate of this process, whereas foldases actually accelerate protein folding by exerting a direct influence on the rate-limiting steps of the overall reaction. Two types of foldases are known, using different principles of action. Peptidyl-prolyl cis/trans isomerase and protein-disulfide isomerase catalyze the folding of every protein that needs isomerization of prolyl peptide bonds or formation and isomerization of disulfide bonds for proper folding. By contrast, some foldases operating in the periplasm of bacterial cells are specifically designed to help in the folding of substrate proteins whose primary structure does not contain sufficient information for correct folding. In this review, we discuss recent data on the catalytic mechanisms of both types of foldases, focusing specifically on how a catalyst provides the structural information required for the folding of a target protein. Comparative analysis of the mechanisms employed by two different periplasmic foldases is used to substantiate the notion that combinations of a protein which is unable to fold independently and a specific catalyst delivering the necessary steric information are probably designed to achieve some particular biological purposes. The review also covers the problem of participation of peptidyl-prolyl cis/trans isomerase in different cellular functions, highlighting the role of this enzyme in conformational rearrangements of folded native proteins.


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Structure-Function Relation of Somatotropin with Reference to Molecular Modeling
Amtul Jamil Sami

Somatotropin, commonly known as growth hormone (GH) is a polypeptide chain containing about 190 amino acid residues, produced by the pituitary gland in mammals and is responsible for a number of anabolic processes. It has two disulphide bridges, with 4 alpha helices arranged in anti-paralel distinctive manner. GH molecule binds with two receptor molecules to exhibit its full biological activity. In this review, the information regarding charecterization, structure and function is updated. A number of human growth hormone variants (naturally occuring and poduced by recombinant DNA- technology) are visualised, and structure related functions are revealed. 1) The di-sulphide bridges are not essential for the biological activity of the molecule. The two chain variants of GH are able to show full biological activity. 2) The different domains of GH could be related to its functions 3) N-terminus of the molecule is involved in the galactopoietic activity of the molecule. 4) A single amio acid residue at a particular position could determine the magnitude of hormone receptor binding. 5) Role of Trp 86 is critical in packing of the apha helices bundles of the molecule. 6) Hydrophobic cores are essential for the stability of GH molecule 7) Salt bridges and hydrogen bonds are also important for the binding of the molecule with its receptors. 8) GH molecule has two binding sites for receptor molecules, SiteI and Site II which are sterically coupled. The placental growth hormone has also been discussed and compared with the pituitary derived GH for its structure and function.


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The PYRIN Domain in Signal Transduction
Christian Stehlik

The Death Domain Fold superfamily of evolutionarily conserved protein-protein interaction domains consists of 4 subfamilies: the death domain, the death effector domain, the caspase recruitment domain, and the PYRIN domain. Interaction of Death Domain Fold containing proteins modulates the activity of several downstream effectors, such as caspases and transcription factors. Recent studies provide evidence for not only homotypic-, but also heterotypic interactions among different sub-families, and even unconventional non-death domain fold interactions. As the number of potential protein associations among Death Domain Fold containing proteins expands and their influence on cellular responses increases, a challenging field for new investigations opens up. This review will focus on PYRIN domain-containing proteins and discuss the recent advances that provide strong evidence that PYRIN domain-mediated signal transduction has broad implications on cellular functions, including innate immunity, inflammation, differentiation, apoptosis, and cancer.