Search results for: protein-protein-and-domain-domain-interactions

Protein Protein and Domain Domain Interactions

Author : Pandjassarame Kangueane
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This book illustrates the importance and significance of the molecular (physical and chemical) and evolutionary (gene fusion) principles of protein-protein and domain-domain interactions towards the understanding of cell division, disease mechanism and target definition in drug discovery. It describes the complex issues associated with this phenomenon using cutting edge advancement in Bioinformatics and Bioinformation Discovery. The chapters provide current information pertaining to the types of protein-protein complexes (homodimers, heterodimers, multimer complexes) in context with various specific and sensitive biological functions. The significance of such complex formation in human biology in the light of molecular evolution is also highlighted using several examples. The chapters also describe recent advancements on the molecular principles of protein-protein interaction with reference to evolution towards target identification in drug discovery. Finally, the book also elucidates a comprehensive yet a representative description of a large number of challenges associated with the molecular interaction of proteins.

Protein protein Interactions and Networks

Author : Anna Panchenko
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The biological interactions of living organisms, and protein-protein interactions in particular, are astonishingly diverse. This comprehensive book provides a broad, thorough and multidisciplinary coverage of its field. It integrates different approaches from bioinformatics, biochemistry, computational analysis and systems biology to offer the reader a comprehensive global view of the diverse data on protein-protein interactions and protein interaction networks.

A Computational Study of the Role of Conserved Domains in Protein Interactions microform

Author : Doron Betel
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Complex organisms that are capable of inter-cellular communication and occupy various ecological niches are believed to evolve through the generation of novel cellular pathways. The myriad of processes in a cell are facilitated by proteins that form the building blocks of complex pathways through a set of carefully orchestrated interactions between functionally conserved regions in the proteins. The central notion that underlies this work is that these conserved elements of the proteins (domains) are the basic units of interaction. The objective of this thesis is to explore the role of domains in determining the interactions between proteins. The thesis outlines the necessary computational infrastructure for domain annotation and a number of computational methods that investigate the role of domains in protein interactions from visual, large-scale and individual perspectives. The first of these methods is a graphical program for the depiction of domains in a set of interacting proteins. This provides a visual tool to classify proteins and identify common elements. In the second study, protein complexes are used to identify domain pairs that co-occur in concert in a statistically significant manner. These domain co-occurrences are used to generate a network of domain correlations that represent functional networks in contrast to protein interaction networks. Such networks provide insight into new functional relationships between domains that are otherwise non-obvious and represent a first approximation of domain-domain interactions. Domain correlations are also used to analyze and compare datasets of protein complexes that are either curated or generated via high-throughput experiments. In the final study, the binding specificity of domains is inferred from a combination of protein structure complexes and other experimental interactions. The binding motifs are extracted from 3D structures with interacting domains and converted to a more informative PSSM representation by the use of the Gibbs sampling algorithm. The resulting domain binding-profiles are used to predict novel interactions for a number of proteins as well as to predict interactions within protein complexes.

Computational Prediction of Protein Protein Interaction

Author : Ranjan Kumar Barman
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Protein-protein interactions are extremely valuable towards protein functions and cellular processes or we can say that protein-protein interactions play an important role in living cells. Therefore, if we can control the interactions between proteins, as a result, we can control some functionality of cells. Main functionality of a protein is carried out by its domains. So, domain is a structural or/and functional unit of protein. Behind protein-protein interactions there exist some domain-domain interactions. Therefore, under standing protein-protein interaction at domain level gives a global view of protein-protein interaction network.In this book, we have made an attempt to infer domain-domain interactions from interacting and non-interacting protein pairs then we have predicted protein-protein interactions based on inferred domain-domain interactions.

Protein protein Interactions and Networks

Author : Anna Panchenko
File Size : 37.55 MB
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The biological interactions of living organisms, and protein-protein interactions in particular, are astonishingly diverse. This comprehensive book provides a broad, thorough and multidisciplinary coverage of its field. It integrates different approaches from bioinformatics, biochemistry, computational analysis and systems biology to offer the reader a comprehensive global view of the diverse data on protein-protein interactions and protein interaction networks.

Domain domain Interactions as Mediators of Protein Interactions Evolution Hierarchy and Dynamics

Author : Zohar Itzhaki
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Inferring Protein protein Interactions from Protein Domain Combinations

Author : Simon Kanaan
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Protein protein Interactions

Author : Erica Golemis
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Reflecting the various advances in the field, this book provides comprehensive coverage of protein-protein interactions. It presents a collection of the technical and theoretical issues involved in the study of protein associations, including biophysical approaches. It also offers a collection of computational methods for analyzing interactions.

Salt Increases the Dynamics of SH3 Domain Interactions

Author : Valeria Jaramillo Martinez
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Proteins are the workhorses of the cell and protein-protein interactions are central to almost every cellular process. Most proteins contain independently folded domains that perform a distinct function protein interaction. The most common interaction domain in animals is the SH3 domain that contains over 300 family members in humans. The SH3 domain and several other interaction domains interact with long flexible peptides (>12 residues) which do not behave like folded proteins and the molecular basis of these extended interactions is not well understood. Our goal is to characterize ApbSH3 as a model for extended peptide interactions and the subject of our directed evolution studies. To easily characterize APB1 SH3 domain (AbpSH3) of yeast and its binding partner ArkA17, we used a domain-peptide hybrid which has been optimized to solve with structure by NMR. We hypothesized high concentration of NaCl will stabilize the AbpSH3 domain by screening repulsion in the domain. The 3 salt bridges at the termini region (D24-K43, K25-E42, and K47-D44) may be destabilized by high salt, although the net -12 suggests screening repulsion outweighs destabilized salt bridges. However, we believe low concentration of NaCl will be most beneficial for peptide binding by allowing the peptide to bind and stabilize the domain through electrostatic interactions. We found with ApbSH3 domain, high NaCl increases stability but is non-specific as it does not affect the same residues in ApbSH3 involved in binding. We believe NaCl increases stability through affecting the slow-time scale dynamics as seen with peak broadening. Furthermore, in the domain, increasing the concentration of the Cl anion increases peak broadening compare to F anion. Contrarily, we found with our domain-peptide hybrid, peptide binding decreases in high NaCl, which indicates the ArkA17 peptide is strongly mediated by electrostatic interactions. ITC binding affinity confirms over a 30 fold decrease in peptide binding from no salt to 800 mM NaCl. At extreme NaCl conditions, we believe a minimally bound state exists that is made possible by our extended peptide and using binding data we can calculate the linker effect of the hybrid. Lastly, through NMR, we were able to validate our extended domain is stabilized through the extension’s interaction with the termini-distal region. Also, in our extended hybrid, the peptide extension helps stabilize the complex by interacting with a region just beyond Surface II. NMR gives us a molecular view of our various hybrids in different NaCl conditions and will provide valuable knowledge for future structural and functional studies in the SH3 domain family.

Modular Protein Domains

Author : Giovanni Cesareni
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Since the full functionality of any given protein can only be understood in terms of its interaction with other, often regulatory proteins, this unique reference source covers all relevant protein domains, including SH2, SH3, PDZ, WW, PTB, EH, PH and PX. Its user-oriented concept combines broad coverage with easy retrieval of essential information, and includes a special section on Web-based tools and databases covering protein modules and functional peptide motifs. Essential for the study of protein-protein interactions in vivo or in silico, and a prerequisite for successful functional proteomics studies. With a prologue by Sir Tom Blundell.