Search Results - "proteins"

Protein-protein interaction networks

Table of Contents: “…Contents: General features of networks -- Creative network nodes -- Overview of cellular networks -- Definition and databases of protein-protein interaction networks -- Main methods to identify protein interaction data and their quality -- Small worldness, hubs (date and party hubs, rich clubs) and modules of protein-protein interaction networks -- Change of modular overlaps as an efficient method of adaptation.…”
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Inhibiting protein-protein interactions part 1 of 2 /

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Inhibiting protein-protein interactions part 2 of 2 /

Table of Contents: “…Contents: A different view of druggability -- Five propositions about the druggability of PPI targets -- Protein-ligand binding energy -- Ligand efficiency and drug-target binding -- ADME & druglikeness considerations -- Conventional view of druglikeness -- Druggability and chemical space -- Targeting low druggability PPI -- Macrocycles -- Covalent inhibitors -- Foldamers.…”
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Protein phosphorylation and the control of protein synthesis

Table of Contents: “…Contents: Protein synthesis -- Key step in gene expression that must be tightly controlled -- Signaling pathways regulate phosphorylation and activity of translation factor proteins -- Important in regulation of cell growth and division -- Defective control linked to human diseases such as cancer and cardiac hypertrophy.…”
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Fuzzy protein theory for disordered proteins

Table of Contents: “…Contents: Intelligent decision-making mechanisms -- Structural disorder is maintained in protein assemblies -- Mechanisms and biological consequences of fuzziness -- Conformational diversity and context-dependence -- Fuzziness in cell differentiation and transcription factor evolution -- Material state and regulation of higher-order assemblies.…”
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Protein degradation

Table of Contents: “…Contents: Protein levels in cells are regulated by their rates of synthesis and degradation -- Regulatory proteins are rapidly degraded by the ubiquitin-proteasome pathway -- Examples include many oncogenes, transcription factors and cyclins which control progress through the cell cycle -- NF-kappa B activation in disease depends on degradation of the inhibitor, I-kappa B -- Misfolded or mutant proteins are rapidly degraded -- Neurodegenerative and protein folding diseases -- Two major proteolytic pathways exist in mammalian cells -- Many acid hydrolases exist in lysosomes -- Endocytosed proteins and those in autophagic vacuoles are degraded in lysosomes -- The ubiquitin-proteasome pathway -- 3D structure of ubiquitin -- Formation of the isopeptide bonds during ubiquitin conjugation to proteins -- The ubiquitin-proteasome pathway -- Proteasome function is linked to ATP hydrolysis -- Proteasomes unfold proteins and translocate them into 20S particles -- Three types of peptidase sites -- Proposed mechanism of proteasome inhibitors -- Therapeutic applications of proteasome inhibitors -- Two systems for protein breakdown function in the two pathways for antigen presentation -- Changes in proteasome subunits induced by interferon -- Steps involved in generating antigenic peptides.…”
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Protein crystallography

Table of Contents: “…Contents: Protein crystallography -- Protein crystallization methods -- Crystal symmetry -- X-ray intensity data collection -- Electron density equation -- The Patterson function -- Multiple isomorphous replacement phasing -- Fitting the electron density with a model -- Refinement of the model -- Estimating quality of the model.…”
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Protein folding

Table of Contents: “…Contents: Introduction to principles of protein structure -- The basic facts about protein folding -- Cooperativity of protein structure formation -- Necessary and sufficient conditions for protein sequences to fold -- Concept of energy gap -- Protein folding kinetics -- Intermediates and transition state ensembles -- Allatom folding simulations -- Understanding protein folding pathways at atomic detail.…”
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Protein oxidation and removal of oxidized proteins by proteolysis

Table of Contents: “…Contents: Oxidized proteins -- Intracellular proteases -- The 20S core proteasome -- Proteasomal particles -- The proteasome-ubiquitin system -- Protein oxidation and proteasome -- Degradation of oxidized proteins and protein function -- Protein surface hydrophobicity -- Unfolding of oxidized proteins -- Stability of the 20S proteasome towards oxidation -- Oxidative stress and protein turnover -- Oxidation-induced proteolysis -- Degradation of oxidized proteins in cells -- What happens if degradation fails? …”
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The pharmacokinetics of therapeutic proteins

Table of Contents: “…Contents: Differences in the pharmacokinetics of therapeutic proteins compared to small molecule drugs -- Classes of therapeutic proteins -- Central paradigm of clinical pharmacology -- Distribution and tissue penetration of mAbs and proteins -- Three methods of renal protein metabolism -- Hepatic protein metabolism -- Target-mediated drug disposition -- Immunogenicity: general considerations and contributing factors -- Neutralizing, clearing and sustaining anti-drug antibodies.…”
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Probing protein-protein interactions with peptide libraries and arrays

Table of Contents: “…Contents: Protein-protein interactions as key to understanding signaling pathways -- Signaling through tyrosine phosphorylation -- Using peptide libraries to study specificities of protein modules -- Peptide library arrays (OPAL) -- OPAL strategies, examples and advantages.…”
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The structural basis for the modulation of protein function by protein phosphorylation

Table of Contents: “…Contents: Physical-chemical basis for phosphorylation -- Discovery -- Glycogen phosphorylase -- Signaling from adrenaline to phosphorylase -- Phosphorylase kinase still a challenge -- Regulation of the cell cycle by phosphorylation -- Cyclin dependent protein kinase 2 activation and inhibition -- Rb the guardian of the genome -- Control by p27 and cyclin E -- Summary of the structural consequences of phosphorylation.…”
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Elongation of protein synthesis structural basis of the process of decoding /

Table of Contents: “…Contents: Fidelity in biological processes -- Elongation step of protein synthesis -- Ribosome structures -- Ribosomes from different organisms -- Errors in protein synthesis -- The decoding problem -- Kinetic proof-reading -- Kinetic model of tRNA selection -- Role of induced fit in tRNA selection -- Recognition of codon-anticodon complexes by the 30S ribosomal subunit -- Local and global conformational changes of the 30S subunit -- Interactions of tRNA during decoding -- Active role of tRNA -- SelB and delivery of Sec-tRNA to the ribosome -- Accommodation of tRNA in the A site.…”
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Series (From DNA to proteins)
Series (Mechanisms of ribosome function)

Protein import into chloroplasts

Table of Contents: “…Contents: The endosymbiotic origin of chloroplasts -- Protein import as a result of genome rearrangements -- Different targeting pathways -- The general import pathway -- Properties of the targeting process -- Cytosolic components -- Components of the Toc and Tic translocon -- Stromal components -- Phylogenetic origin of the import apparatus.…”
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Elongation of protein synthesis structural basis of the peptide bond /

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From DNA to proteins the multiple levels of regulation /

Table of Contents: “…Contents: General ideas behind DNA association with: histones, replication, transcription, splicing, RNA modifications, protein synthesis and death and global gene expression analysis.…”
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Protein folding and misfolding from theory to therapy /

Table of Contents: “…Contents: Protein nature, folding and complexity -- Folding in a cellular environment -- The underlying principles of folding -- Native and transition states -- Exploring the energy surface -- The folding of lysozyme -- The consequences of protein misfolding -- The relationship between folding and disease -- Protein deposition diseases -- Protein aggregates in amyloid diseases -- Amyloidogenic mutations of lysozyme -- Mechanism of amyloid formation -- Structure of the amyloidogenic intermediate -- Amyloid formation by lysozyme in vivo -- SH3 domain of PI3 kinase -- Model of an amyloid fibril -- The underlying origins of amyloid disease -- Generic toxicity of amyloid aggregates -- Cellular defences against aggregation -- Evolutionary design of proteins -- "Post-evolutionary" diseases.…”
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Gene and protein microarrays tools for gene discovery and function /

Table of Contents: “…Contents: High-throughput methods to examine global gene expression -- Understanding interactions in a given cell, tissue and organism under normal and disease state conditions -- Application of high throughput methods used in genomics and proteomics -- Use of DNA and protein microarrays for gene discovery and function -- Background information and terminology used in genomics and proteomics -- How DNA and protein microarrays are carried out -- Predicted future direction of genomics and proteomics microarray technologies.…”
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Protein synthesis in plastids

Table of Contents: “…Contents: Plastids have complete protein synthesis machinery -- Most plastid ribosomal proteins, ribosomal RNAs, translation factors and cisacting translational regulatory elements are homologous to components of bacterial protein synthesis -- Plastid-specific components have been identified -- Proteins are targeted to thylakoid membranes during their synthesis by plastid ribosomes.…”
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Chemical protein synthesis total synthesis of proteins for biological research /

Table of Contents: “…Contents: HIV-1 protease -- Electronic properties of the catalytic apparatus -- Defining the 'aspartyl proteases' -- 'Backbone engineering' HIV-1 PR -- The alpha-helix -- Ubiquitin (76 aa) -- Conformation vs. solvation effects -- Global and local structures are highly conserved -- Stability measurements of [Aaa35] ubiquitins -- Energetic contributions at helix C' position -- Erythropoietin (Epo) -- Synthetic erythropoiesis protein -- Synthetic 'glycan mimetic' -- Glycoprotein synthesis -- Molecular basis of protein function -- The synthetic challenge -- Classical solution synthesis -- Stepwise solid-phase synthesis -- Chemical protein synthesis -- Unprotected peptides -- Principles of chemical ligation -- Thioester-forming ligation -- Total synthesis of D- & L-HIV-1 protease -- Crystal structure of D-HIV-1 protease -- Native chemical ligation -- Crambin (46 aa; 6 Cys) -- CPS: current challenges.…”
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