Computational Approaches for Studying Enzyme Mechanism, Part B is the first of two volumes in the Methods in Enzymology series that focuses on computational approaches for studying enzyme mechanism. The serial achieves the critically acclaimed gold standard of laboratory practices and remains one of the most highly respected publications in the molecular biosciences. Each volume is eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 550 volumes, the series remains a prominent and essential publication for researchers in all fields of the life sciences and biotechnology, including biochemistry, chemical biology, microbiology, synthetic biology, cancer research, genetics, and other fields of study. - Focuses on computational approaches for studying enzyme mechanism - Continues the legacy of this premier serial with quality chapters authored by leaders in the field - Covers research methods in intermediate filament associated proteins, and contains sections on such topics as lamin-associated proteins, intermediate filament-associated proteins and plakin, and other cytoskeletal cross-linkers

Computational Approaches for Studying Enzyme Mechanism Part A, is the first of two volumes in the Methods in Enzymology series, focusses on computational approaches for studying enzyme mechanism. The serial achieves the critically acclaimed gold standard of laboratory practices and remains one of the most highly respected publications in the molecular biosciences. Each volume is eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 550 volumes, the series remains a prominent and essential publication for researchers in all fields of life sciences and biotechnology, including biochemistry, chemical biology, microbiology, synthetic biology, cancer research, and genetics to name a few. - Focuses on computational approaches for studying enzyme mechanism - Continues the legacy of this premier serial with quality chapters authored by leaders in the field - Covers research methods in intermediate filament associated proteins, and contains sections on such topics as lamin-associated proteins, intermediate filament-associated proteins and plakin, and other cytoskeletal cross-linkers

Computational Approaches for Studying Enzyme Mechanism, Part B is the first of two volumes in the Methods in Enzymology series that focuses on computational approaches for studying enzyme mechanism. The serial achieves the critically acclaimed gold standard of laboratory practices and remains one of the most highly respected publications in the molecular biosciences. Each volume is eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 550 volumes, the series remains a prominent and essential publication for researchers in all fields of the life sciences and biotechnology, including biochemistry, chemical biology, microbiology, synthetic biology, cancer research, genetics, and other fields of study.

This thorough volume explores protocols of proteome- and metabolome-wide strategies for the identification of protein-small molecule complexes in different organisms, in order to shed light on these important regulatory interactions. Experimental and computational strategies to characterize protein-metabolite interactions are discussed, and recent advances in enabling technologies are featured as well. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice to ensure success in future research. Authoritative and practical, Cell-Wide Identification of Metabolite-Protein Interactions will aid researchers seeking a better understanding of the mechanisms of signal transduction occurring in the cell and assessing the effect of complex formation on cell physiology.

A quantitative description of the action of enzymes and other biological systems is both a challenge and a fundamental requirement for further progress in our und- standing of biochemical processes. This can help in practical design of new drugs and in the development of artificial enzymes as well as in fundamental understanding of the factors that control the activity of biological systems. Structural and biochemical st- ies have yielded major insights about the action of biological molecules and the mechanism of enzymatic reactions. However it is not entirely clear how to use this - portant information in a consistent and quantitative analysis of the factors that are - sponsible for rate acceleration in enzyme active sites. The problem is associated with the fact that reaction rates are determined by energetics (i. e. activation energies) and the available experimental methods by themselves cannot provide a correlation - tween structure and energy. Even mutations of specific active site residues, which are extremely useful, cannot tell us about the totality of the interaction between the active site and the substrate. In fact, short of inventing experiments that allow one to measure the forces in enzyme active sites it is hard to see how can one use a direct experimental approach to unambiguously correlate the structure and function of enzymes. In fact, in view of the complexity of biological systems it seems that only computers can handle the task of providing a quantitative structure-function correlation.

Coenzyme B12 Enzymes, Part B, Volume 169 in the Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on Structural characterization of cobalamin-dependent radical SAM methylases, Purification and characterization of sequential cobalamin-dependent radical SAM methylases ThnK and TokK in -lactam antibiotic biosynthesis, Characterization of the cobalamin-dependent radical S-adenosyl-L-methionine enzyme C-methyltransferase Fom3 in fosfomycin biosynthesis, Studies of OxsB and GenK, two B12-dependent radical SAM enzymes involved in natural product biosynthesis, Purification and structural elucidation of the cobalamin-dependent radical SAM enzyme OxsB, and more. Other chapters discuss Methods for studying the mechanisms of B12 enzymes, Computational investigations of B12 dependent enzymatic reactions, Using kinetic isotope effects to probe the mechanisms of adenosylcobalamin-dependent enzymes, Steady-state and pre-steady state kinetic analysis of ornithine 4,5-aminomutase, and more. - Provides the authority and expertise of leading contributors from an international board of authors - Presents the latest release in Methods in Enzymology series - Includes the latest information on B12 Enzymes

This thesis reports studies on the substrate specificity of crucial ketosynthase (KS) domains from trans-AT Polyketide Synthases (PKSs). Using a combination of electrospray ionisation-mass spectrometry (ESI-MS) and simple N-acetyl cysteamine (SNAC) substrate mimics, the specificity of a range of KS domains from the bacillaene and psymberin PKSs have been succsessfully studied with regard to the initial acylation step of KS-catalysis. In addition, the ability to alter the substrate tolerance of KS domains by simple point mutations in the active site has been demonstrated. A series of acyl-ACPs have been synthesised using a novel methodology and employed to probe the substrate specificity of both KS domains and the previously uncharcterised acyl hydrolase domain, PedC. KS-catalysed chain elongation reactions have also been conducted and monitored by ESI-MS/MS. All KS domains studied exhibited higher substrate specificity at the elongation step than in the preceeding acylation step. Furthermore, a mechanism of reversible acylation is proposed using the PsyA ACP1-KS1 di-domain. The findings in this thesis provide important insights into mechanisms of KS specificity and show that mutagenesis can be used to expand the repertoire of acceptable substrates for future PKS engineering.

The critically acclaimed laboratory standard for more than forty years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 400 volumes (all of them still in print), the series contains much material still relevant today—truly an essential publication for researchers in all fields of life sciences. Methods in Enzymology is now available online at ScienceDirect — full-text online of volumes 1 onwards. For more information about the Elsevier Book Series on ScienceDirect Program, please visit: http://www.info.sciencedirect.com/bookseries/ This volume is the second of two planned volumes on the topic of globin and other nitric oxide-reactive proteins.

A comprehensive overview of current empirical valence bond (EVB) theory and applications, one of the most powerful tools for studying chemical processes in the condensed phase and in enzymes. Discusses the application of EVB models to a broad range of molecular systems of chemical and biological interest, including reaction dynamics, design of artificial catalysts, and the study of complex biological problems Edited by a rising star in the field of computational enzymology Foreword by Nobel laureate Arieh Warshel, who first developed the EVB approach