Author: Stephan WarnkePublisher:
ISBN: 9783863876913
Category :
Languages : en
Pages : 0
Book Description
A Gas-phase Approach to Biomolecular Structure
Author: Stephan WarnkePublisher:
ISBN: 9783863876913
Category :
Languages : en
Pages : 0
Book Description
Biomolecular Structure and Dynamics
Author: G. VergotenPublisher: Springer Science & Business Media
ISBN: 9401154848
Category : Science
Languages : en
Pages : 327
Book Description
Biomolecular Structure and Dynamics describes recent fundamental advances in the experimental and theoretical study of molecular dynamics and stochastic dynamic simulations, X-ray crystallography and NMR of biomolecules, the structure of proteins and its prediction, time resolved Fourier transform IR spectroscopy of biomolecules, the computation of free energy, applications of vibrational CD of nucleic acids, and solid state NMR. Further presentations include recent advances in UV resonance Raman spectroscopy of biomolecules, semiempirical MO methods, empirical force fields, quantitative studies of the structure of proteins in water by Fourier transform IR, and density functional theory. Metal-ligand interactions, DFT treatment of organometallic and biological systems, and simulation vs. X-ray and far IR experiments are also discussed in some detail. The book provides a broad perspective of the current theoretical aspects and recent experimental findings in the field of biomolecular dynamics, revealing future research trends, especially in areas where theoreticians and experimentalists could fruitfully collaborate.
Structural Elucidation of Biomolecular Ions in the Gas Phase Using Novel Mass Spectrometric and Computational Methods
Author: Yang LiuPublisher:
ISBN:
Category :
Languages : en
Pages : 194
Book Description
Biological molecules such as protein and DNA play critical roles in various cellular reactions and carry out essential biological functions. But the mechanisms of these reactions, and the essential molecular structures to facilitate them are often poorly understood. Many efforts have been applied to these problems, but due to their complexity and various limitations of existing methods, the elucidation of biological reaction mechanisms and biological molecule or complex structures is still considered a challenge today. Therefore, the scientific community has been highly motivated to invent new methods to tackle these problems devise new angles of approach to grain insights into biomolecular structure. This dissertation summarizes some recent work in characterizing cation-radical reactions, and structures of gas-phase molecular complexes using novel mass spectrometry methods in combination with theoretical computational modeling. The novel mass spectrometric methods presented in this work are gas-phase photo-dissociative crosslinking techniques and UV-visible photodissociation action spectroscopy. They have several unique advantages in tackling structure elucidation of weakly bound complexes and transient radical species. 1) The mass spectrometer (MS) is a universal detector which is widely used to characterize various kinds of biological molecules. 2) MS works with ions of interest that are generated and stored in the gas phase at low pressure of an inert gas (He). It is the perfect system to study reaction mechanisms because of low interference from the ambient environment, such as solvent, counterions, surfaces, etc. 3) Methods exist to generate cation radicals in the gas phase, and thanks to the low pressure inside a mass spectrometer, the produced species are kinetically stable on the experimental time scale of several milliseconds. 4) MS is a perfect tool for conducting gas-phase reactions because it allows one to manipulate the ion population and select and focus the ions. It is advantageous for crosslinking reactions that often suffer from low concentrations of reactants when the reaction is attempted in condensed phase. 5) The experimental action spectra can be interpreted using sophisticated computational techniques providing vibronic transitions of multiple isomeric candidates. The new data generated with these new mass spectrometry methods offer unique insights, but also pose challenges to experimental data interpretation. Various computational approaches are used to supplement the experimental data, and the results from the computations are used to guide the interpretation. This dissertation also includes several novel approaches on the computational front, introducing the customized modeling pipeline with a combination of Born-Oppenheimer dynamics, density functional theory calculations, and machine learning techniques. The first chapter introduces some basic terms and outlines the background for the topic of study, including a quick review of the current challenges and techniques in the field of structure elucidation of biomolecules. Also introduced are the fundamentals of mass spectrometer, commonly used and newly developed ion activation methods, and computational modeling. This chapter lays the foundation of the work described in later chapters. A small neuroprotective peptide Cys-Ala-Gln-Lys (CAQK) has recently been discovered to mitigate adverse effects of brain trauma in mice, possibly because of specific interactions with yet-to-be identified proteins. In Chapter 2, an application of photo-crosslinking is described to study the noncovalent interactions of CAQK with several model target peptide motifs. The experimental results in combination with Born-Oppenheimer molecular dynamics revealed the structural preferences for binding to the amino acid residues of potential target peptides. In Chapter 3, inspired by the biological significance of CAQK, we employed the photo-dissociative crosslinking techniques to probe its interactions with several dinucleotides as structure motifs of nuclear DNA. This lysine-containing peptide can be viewed as a simplified surrogate of a histone interacting with DNA. We were able to show that in interactions with CAQK ions, even simple dinucleotides differ in their binding efficiency and stereochemistry. We provided structures of selected complexes obtained by electronic structure theory calculations using density functional theory (DFT). UV and energetic particle radiation can ionize DNA creating electron deficiency (hole) at nucleobases. These holes can migrate along the strand, leading to lesions and DNA damage by follow up radical reactions. Chapter 4 and chapter 5 are focused on the characterization of DNA cation radicals in the guanine and cytosine containing dinucleotide as model systems in probing the electron transfer mechanisms in DNA radiation damage. Experimental action spectra were obtained for these small nucleotides and the absorption bands were interpreted by finding the closest match from the calculated spectra. The last chapter features an ongoing project in which we have made an attempt, using photo-crosslinking techniques, to probe noncovalent interactions within a complex consisting of a chiral agonist and its binding motifs. The experimental results revealed high binding affinity of the native agonist regardless of chirality, however the crosslinking fragment was not observed. Several DFT optimized low energy structure had shown a consistently low "contact" rate of the phototag with the target peptide. A further characterization of ion structures will be complemented from the collisional cross section analysis by ion mobility (IM) measurements.
Nucleic Acids in the Gas Phase
Author: Valérie GabelicaPublisher: Springer
ISBN: 3642548423
Category : Science
Languages : en
Pages : 297
Book Description
This book gives physical chemists a broader view of potential biological applications of their techniques for the study of nucleic acids in the gas phase. It provides organic chemists, biophysicists, and pharmacologists with an introduction to new techniques they can use to find the answers to yet unsolved questions. Laboratory sciences have bloomed with a variety of techniques to decipher the properties of the molecules of life. This volume introduces techniques used to investigate the properties of nucleic acids in the absence of solvent. It highlights the specificities pertaining to the studies of nucleic acids, although some of the techniques can similarly be applied to the study of other biomolecules, like proteins. The first part of the book introduces the techniques, from the transfer of nucleic acids to the gas-phase, to their detailed physico-chemical investigation. Each chapter is devoted to a specific molecular property, and illustrates how various approaches (experimental and theoretical) can be combined for the interpretation. The second part of the book is devoted to applying the gas-phase approaches to solve specific questions related to the biophysics, biochemistry or pharmacology of nucleic acids.
Biomolecular Structure and Function
Author: Paul AgrisPublisher: Elsevier
ISBN: 0323144128
Category : Science
Languages : en
Pages : 641
Book Description
Biomolecular Structure and Function covers the proceedings of the 1977 ?Cellular Function and Molecular Structure: Biophysical Approaches to Biological Problems? symposium. It summarizes the application of several biophysical techniques to molecular research in biology. This book starts by describing the use of deuterium-labeled lipids, as monitors of the degree of organization of membrane lipids. It also describes the use of carbon-13-labeled lipids, as indicators of molecular mobility. It explains the lipid-protein interactions involving two integral membrane proteins, mitochondrial cytochrome oxidase and calcium-dependent ATPase of muscle sarcoplasmic reticulum. The book goes on to present NMR studies on the organization and conformation of phospholipids, chloroplast membranes, and erythrocyte membranes. It also presents the ESR study of spectrin-phospholipid associations. It discusses the use of fluorescence probes, electrokinetics, neutron diffraction and ion theory studies of phospholipid-protein association, hormone disease, and senescence effects on prokaryotic and eukaryotic cells. Moreover, this book presents the experiments and phosphorus-31 NMR methodology to simultaneously monitor the intracellular pH and phosphate metabolism in a beating heart, functioning kidney, or an intact living microorganism. This book then describes physical probing of intracellular fluidity and structural changes attending tissue or cell cycles. It also relates relatively narrow lines in the hydrogen-1 NMR spectrum of the extremely viscous complex of the muscle protein troponin and highly polymerized tropomyosin. Structure-function studies of fibrous proteins, such as collagen, actin, and myosin, and active site analysis of enzymes are also presented. Finally, a wide variety of methodologies and technologies is exemplified. This includes proton, carbon, fluorine, phosphorus, and lithium NMR spectroscopy; spin labeling and EPR spectroscopy; chemical studies; light scattering and fluorescence; and electron microscopy.
Biomolecules and Their Noncovalent Complexes in the Gas Phase
Author: Rebecca Ann JockuschPublisher:
ISBN:
Category :
Languages : en
Pages : 538
Book Description
Solution Versus Gas Phase Biomolecule Structure
Author: Evan WilliamsMolecular Recognition of Biomolecules in the Gas Phase
Author: Ryan Roy JulianPublisher:
ISBN:
Category : Electronic dissertations
Languages : en
Pages : 498
Book Description
Gas Phase Reactions in Organic Synthesis
Author: Yannick ValleePublisher: CRC Press
ISBN: 9789056990817
Category : Science
Languages : en
Pages : 322
Book Description
Flash Vacuum Thermolysis (FVT) techniques have become well-established methods and occupy an increasingly important place in synthesis. Gas Phase Reactions in Organic Synthesis is a complete review of the applications of flash vacuum thermolysis in organic chemistry; it features new developments in FVT, flow thermolysis and vacuum gas-solid reactions which have appeared in scientific literature since 1980.
Advances in Gas Phase Ion Chemistry
Author: Publisher: Elsevier
ISBN: 0080550886
Category : Science
Languages : en
Pages : 281
Book Description
Advances in Gas Phase Ion Chemistry