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| Author | : Joseph Edward Amos |
| Publisher | : |
| Total Pages | : 58 |
| Release | : 2001 |
| Genre | : |
| ISBN | : |
| Author | : Bruce Alberts |
| Publisher | : |
| Total Pages | : 0 |
| Release | : 2002 |
| Genre | : Cytology |
| ISBN | : 9780815332183 |
| Author | : |
| Publisher | : |
| Total Pages | : 318 |
| Release | : 2007 |
| Genre | : Genetic regulation |
| ISBN | : |
Protein-protein interactions are central to their biological functions in cells. Many approaches have been applied to study protein-protein interactions in a genomic-scale. In an attempt to develop new strategies to study protein-protein interactions, FRET by using ECFP and EYFP as the donor and receptor was evaluated for possible application in protein-protein interaction study in a high-throughput fashion. Due to the intrinsic properties of ECFP and EYFP, FRET-based protein-protein interaction assay is not suitable for large-scale studies. Instead, tandem affinity purification coupled with mass spectrometry approach proved to be a useful strategy to identify protein interacting partners. Several transcription factor complexes in yeast were successfully purified and novel components in the complexes were identified by combining a shotgun mass spectrometry approach and a differential analysis of the mass spectrometry data. In particular, a negative regulator of G1 to S phase transition during cell cycle, Whi5p, was identified to be a component of SBF complex; a regulator of nitrogen metabolism, Gln3p, was identified to be a component of Hap2/3/5 complex that regulates carbon metabolism, suggesting a crosstalk between nitrogen and carbon metabolism. Additionally, one-step purification coupled with shotgun mass spectrometry analysis was applied to simplify and improve the affinity purification approach used for protein-protein interaction studies. In order to map protein complexes in their native state, a sucrose density gradient was used to separate protein complexes in cells. The proteins within each fraction from the sucrose density gradient were analyzed and quantified with mass spectrometry to obtain the protein abundance profiles across the gradient. The known protein complexes were identified by clustering the protein abundance profiles. This method could possibly be improved to become a generic approach to mapping protein complexes. The goal of protein-protein interaction studies is to determine the protein functions. In an effort to identify ribosome biogenesis genes from a yeast gene network reconstructed from diverse large-scale interaction data sets, at least 25 new ribosome biogenesis genes were confirmed by extensive experimental validations, underscoring the value of proteinprotein interaction studies and gene interaction network.
| Author | : Robyn Midori Kaake |
| Publisher | : |
| Total Pages | : 191 |
| Release | : 2013 |
| Genre | : |
| ISBN | : 9781303161513 |
Essential cellular processes are carried out by assemblies of protein molecules that interact and form multi-subunit protein complexes and signaling pathways which act in concert to maintain normal cell homeostasis and respond to external stimuli and stress. The ubiquitin proteasome system (UPS) is the degradation machinery of the cell involved in various essential biological processes including apoptosis, cell cycle control, differentiation, metabolism, and DNA damage repair. Not surprisingly, disruption of normal UPS signaling is correlated with human diseases such as cancer and neurodegenerative disorders. Thus, components of the UPS represent drugable targets for therapeutic intervention of these diseases. Therefore, better understanding of UPS components is needed for future therapeutic design. Here I focus on two protein complexes involved in UPS signaling and regulation, the 26S proteasome, and the Cop9 signalosome (CSN). The 26S proteasome is the degradation machine of the UPS and plays an essential role during the eukaryotic cell cycle by degrading cell cycle regulators to ensure unidirectional progression through well-defined cell cycle phases. Previous studies have demonstrated that many regulatory interacting proteins are transient or weak in nature. Therefore, in order to capture and identify cell cycle specific proteasome interacting proteins of all natures, including weakly- and transiently-associated, we employed a novel cross-linking mass spectrometry (XL-MS) technique developed in our lab termed QTAX for quantitative analysis of tandem affinity purified cross-linked protein complexes. Using QTAX we were able to comprehensively map yeast 26S proteasome interaction networks throughout the cell cycle. The CSN is importantly involved in the regulation of a specific type of ubiquitin ligases known as cullin-RING ligases (CRLs). While some information about CSN activity is available, limited information is known about CSN interacting partners. Furthermore, it is known that various functional sub-complexes can exist in cells and therefore probing CSN interaction networks is not straightforward. In order to address this need, we developed a novel label-free multiple-bait QTAX platform for the comprehensive mapping of CSN interaction networks. Finally, in order to capture protein-protein interactions from their native biological system, we have designed and developed a revolutionary and novel XL-MS approach for de novo interactome mapping.
| Author | : Sahu Indrajit |
| Publisher | : Meem Publishers |
| Total Pages | : 0 |
| Release | : 2023-07-29 |
| Genre | : Health & Fitness |
| ISBN | : 9789631635829 |
Aims to unravel the functional importance of protein interaction networks facilitated by the 19S regulatory particle of the proteasome. The proteasome is a crucial cellular machinery responsible for protein degradation, playing a vital role in maintaining cellular homeostasis and regulating various cellular processes. The 19S regulatory particle is a key component that recognizes and processes ubiquitinated proteins, guiding them to the core proteolytic chamber for degradation. In this research, the scientists investigate the specific protein-protein interactions that occur with the 19S regulatory particle. By elucidating these interactions, the researchers seek to understand how the 19S particle regulates and selects target proteins for degradation, shedding light on the underlying molecular mechanisms. To achieve this, the study likely involves a combination of experimental techniques such as co-immunoprecipitation, yeast two-hybrid assays, mass spectrometry, and advanced computational approaches for data analysis. Through these methods, the researchers can identify the proteins that directly interact with the 19S regulatory particle and form complex networks within the cell. The findings of this research have the potential to provide valuable insights into the complex regulation of protein degradation and its implications in various cellular processes, including cell cycle control, DNA repair, immune response, and protein quality control. Moreover, a deeper understanding of these protein interaction networks could pave the way for the development of targeted therapies to manipulate proteasomal activity, potentially offering new treatment strategies for various diseases, including cancer and neurodegenerative disorders.
| Author | : Gabrielle Nina Thibodeaux |
| Publisher | : |
| Total Pages | : 310 |
| Release | : 2009 |
| Genre | : |
| ISBN | : |
Protein-protein interactions are of great importance to a number of essential biological processes including cell cycle regulation, cell-cell interactions, DNA replication, transcription and translation. Thus, an understanding of protein-protein interactions is critical for understanding many facets of cell function. Unfortunately, the tools and methods currently in use to identify and study protein-protein interactions focus largely on high affinity, stable interactions. However, the majority of the protein-protein interactions involved in regulatory processes have weak affinities and are transient in nature. Therefore, it is important to develop new biotechnology capable of detecting weak and/or transient protein-protein interactions in vivo. Here, we describe four new methods that allow for the identification and study of weak and/or transient protein-protein interactions in vivo. First, we developed a rapid method to convert Escherichia coli orthogonal tRNA/synthetase pairs into an orthogonal system for mammalian cells in order to site-specifically incorporate unnatural amino acids into any gene of interest using stop codon suppression. This method will allow the expression and purification of proteins that carry normally transient post-translational modifications. Second, we successfully employed site-specific unnatural amino acid incorporation to chemically cross-link a known homodimer, Sortase A, in vivo. Third, we developed a novel tetracycline repressor-based mammalian two-hybrid system and successfully detected homo- and hetero-dimers that are known to have weak binding constants. Finally, a synthetic antibody (termed a synbody) that binds weakly to the SH3 domain of the proto-oncogene Abelson tyrosine kinase was developed. The synbody can potentially be used as a first generation drug and/or biomarker. We hope that the methods developed in this dissertation will enable the scientific community to better understand weak/transient protein-protein interactions in vivo.
| Author | : Weibo Cai |
| Publisher | : BoD – Books on Demand |
| Total Pages | : 488 |
| Release | : 2012-03-30 |
| Genre | : Science |
| ISBN | : 9535103970 |
Proteins are indispensable players in virtually all biological events. The functions of proteins are coordinated through intricate regulatory networks of transient protein-protein interactions (PPIs). To predict and/or study PPIs, a wide variety of techniques have been developed over the last several decades. Many in vitro and in vivo assays have been implemented to explore the mechanism of these ubiquitous interactions. However, despite significant advances in these experimental approaches, many limitations exist such as false-positives/false-negatives, difficulty in obtaining crystal structures of proteins, challenges in the detection of transient PPI, among others. To overcome these limitations, many computational approaches have been developed which are becoming increasingly widely used to facilitate the investigation of PPIs. This book has gathered an ensemble of experts in the field, in 22 chapters, which have been broadly categorized into Computational Approaches, Experimental Approaches, and Others.
| Author | : Yuen Ho |
| Publisher | : |
| Total Pages | : 0 |
| Release | : 1999 |
| Genre | : |
| ISBN | : |
Entry into the mitotic cell cycle is a highly regulated event which integrates both extra- and intracellular signal inputs. In the budding yeast, ' Saccharomyces cerevisiae', entry and commitment into the mitotic cell cycle is marked by the Start transition point in late G1. It is likely that entry into the cell cycle at Start is catalyzed by a subset of genes that are transcriptionally induced at the Start transition. In budding yeast, two transcription factor complexes are known to regulate transcription at Start: the SBF and MBF complexes. SBF and M13F are heterodimers that respectively contain the Swi4 and Mbp1 DNA binding subunits. Swi6 is a common subunit in both complexes and likely plays a regulatory role. In this thesis, I describe my approach to studying the regulation of transcription at Start through studying the Swi6 subunit. The presence of protein-protein interaction motifs in Swi6, with no attributable function, prompted me to study Swi6 regulation through identifying novel proteins that physically interact with Swi6. In this thesis, I describe two interacting proteins, Hrr25 and Stb1, and the significance of their interactions with Swi6. In Chapter 2, I describe the interaction between the Hrr25 and Swi6 proteins. I show that this interaction may reflect a role for Hrr25 in phosphorylating Swi6. I describe experiments which suggest that Hrr25 may regulate Swi6 to induce repair genes in response to DNA damage. In Chapter 3, I describe the interaction between Stb1 and Swi6. I show evidence to suggest that this interaction reflects a role for 'STB1 ' in transcriptional induction at Start. Stb1 is a substrate for the Cdk, Cdc28, associated with the Cln G1 cyclin regulatory subunits. I suggest that phosphorylation of Stb1 by Cln-associated kinases activates ' STB1'-dependent transcription at Start.
| Author | : Dirk Inzé |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 240 |
| Release | : 2011-06-27 |
| Genre | : Science |
| ISBN | : 9401009368 |
In recent years, the study of the plant cell cycle has become of major interest, not only to scientists working on cell division sensu strictu , but also to scientists dealing with plant hormones, development and environmental effects on growth. The book The Plant Cell Cycle is a very timely contribution to this exploding field. Outstanding contributors reviewed, not only knowledge on the most important classes of cell cycle regulators, but also summarized the various processes in which cell cycle control plays a pivotal role. The central role of the cell cycle makes this book an absolute must for plant molecular biologists.
| Author | : Stefan Canzar |
| Publisher | : Humana |
| Total Pages | : 0 |
| Release | : 2019-10-04 |
| Genre | : Science |
| ISBN | : 9781493998722 |
This volume explores techniques that study interactions between proteins in different species, and combines them with context-specific data, analysis of omics datasets, and assembles individual interactions into higher-order semantic units, i.e., protein complexes and functional modules. The chapters in this book cover computational methods that solve diverse tasks such as the prediction of functional protein-protein interactions; the alignment-based comparison of interaction networks by SANA; using the RaptorX-ComplexContact webserver to predict inter-protein residue-residue contacts; the docking of alternative confirmations of proteins participating in binary interactions and the visually-guided selection of a docking model using COZOID; the detection of novel functional units by KeyPathwayMiner and how PathClass can use such de novo pathways to classify breast cancer subtypes. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary hardware- and software, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Protein-Protein Interaction Networks: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in learning more about this evolving field.
