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Molecular Dynamics Studies Of The Protein Bacteriorhodopsin
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Book Synopsis Molecular Dynamics Studies of the Protein Bacteriorhodopsin by : William Fowler Humphrey
Download or read book Molecular Dynamics Studies of the Protein Bacteriorhodopsin written by William Fowler Humphrey and published by . This book was released on 1996 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular dynamics (MD) simulations are employed to study the structure and function of the protein bacteriorhodopsin (bR), a 26 kD protein which residues in the purple membrane of the bacterium Halobacterium halobium. Bacteriorhodopsin undergoes a light-driven cyclic process, which pumps protons across the membrane, in order to maintain a proton gradient necessary for ATP synthesis. The cycle is initiated through a $transto cis$ isomerization of the chromophore retinal, which is bound to a lysine residue via a protonated Schiff base linkage. The study of bR is facilitated through development of the program VMD for visualization of the simulation results, and the program NAMD for MD calculations on parallel computers. Initially, MD simulations are used to develop a refined three-dimensional structure of the protein, using the experimentally determined electron-microscopy structure of bR as a basis, and to determine equilibrium positions for several water molecules within the protein interior. MD simulations are then used to model the early isomerization reaction events in the bR photocycle, for both the native (wild-type) system and several bR mutants. The simulations reveal the possibility for bR to form two or three unique photoproducts, distinguished by the retinal isomeric state and the orientation of the Schiff base proton relative to nearby water molecules and negatively charged aspartic acids. One particular photoproduct is suggested to lead to successful proton pump activity, while the remaining structures return back to the initial state; this result is supported by simulations of non-functional bR mutants, which do not exhibit formation of the suggested functional photoproduct. The very fast initial retinal photoexcitation and subsequent isomerization reaction are also examined in detail using a combined quantum/classical simulation technique, in which the evolution of the density matrix for the retinal isomerization degree of freedom is computed using the Liouville-von Neumann equation. The simulations result in wild-type bR exhibiting a non-adiabatic crossing between excited states after 500 fs, while the computed excited-state lifetimes for mutants D85N and D212N are an order of magnitude longer. The results compare well with recent femtosecond spectroscopy data for these systems and demonstrate that the lifetime of the excited state is controlled by the position and slope of the first potential energy surface crossing point.
Book Synopsis Molecular Dynamics and Quantum Chemistry Studies of the Protein Bacteriorhodopsin by : Ilya Logunov
Download or read book Molecular Dynamics and Quantum Chemistry Studies of the Protein Bacteriorhodopsin written by Ilya Logunov and published by . This book was released on 1998 with total page 318 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Study of Bacteriorhodopsin in a Controlled Lipid Environment by : Vivien Yeh
Download or read book Study of Bacteriorhodopsin in a Controlled Lipid Environment written by Vivien Yeh and published by Springer. This book was released on 2018-10-26 with total page 151 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on the study of how the properties of nanodiscs, such as lipid composition and size, influence the function of the embedding integral membrane protein, bacteriorhodopsin. The author performed systematic studies to show that the lipid composition and the charge of the hydrophobic head and the structure of hydrophilic tails affect the photocycle pathway of bacteriorhodopsin, which is closely associated with its proton-pumping activity. Furthermore, the author demonstrated a highly efficient method for extracting membrane proteins directly from the biological membrane, preserving protein conformation, function and essential native lipids. This book demonstrates optimization and sample preparation, and presents practical methods of preparing membrane protein-embedded nanodisc samples for biophysical studies, which benefit structural and functional studies in the field of membrane protein characterization, both.
Book Synopsis Biophysical Analysis of Membrane Proteins by : Eva Pebay-Peyroula
Download or read book Biophysical Analysis of Membrane Proteins written by Eva Pebay-Peyroula and published by John Wiley & Sons. This book was released on 2008-06-25 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: Meeting the need for a book on developing and using new methods to investigate membrane proteins, this is the first of its kind to present the full range of novel techniques in one resource. Top researchers from around the world focus on the physical principles exploited in the different techniques, and provide examples of how these can bring about important new insights. Following an introduction, further sections discuss structural approaches, molecular interaction and large assemblies, dynamics and spectroscopies, finishing off with an exploration of structure-function relationships in whole cells.
Book Synopsis Spectral Signatures of the Pentagonal Water Cluster in Bacteriorhodopsin by :
Download or read book Spectral Signatures of the Pentagonal Water Cluster in Bacteriorhodopsin written by and published by . This book was released on 2008 with total page 13 pages. Available in PDF, EPUB and Kindle. Book excerpt: The exchange of protons between basic and acidic groups within proteins often involves transient protonation of amino acids and water molecules embedded in the protein matrix. One of the best studied proteins in this respect is Bacteriorohodopsin (BR), which works in the membrane of Halobacterium salinarium as a light-driven proton pump. The pumping process is triggered in the initial bR state by a photon absorption of an all-trans retinylidene chromophore, which is linked via a protonated Schiff base (pRSB) to the sidechain of Lys216. The subsequent photocycle comprises a series of intermediate states J, K, L, M, N and O, which are characterized by conformational and absorbance changes of the chromophore accompanying several elementary proton transfer processes. Upon completion of the photocycle one net proton has been transferred from the cyctoplasmic to the extracellular side against the proton gradient across the membrane. These proton exchange reactions can be monitored by time resolved infrared (IR) spectroscopy of the BR wild type and site specific mutants, which allow the localization of absorbance changes within the protein. Furthermore, these measurements have revealed the fundamental importance of internal water molecules in these processes as supported by recent large-scale QM/MM molecular dynamics studies of anharmonic IR spectra.
Book Synopsis Computational Molecular Dynamics: Challenges, Methods, Ideas by : Peter Deuflhard
Download or read book Computational Molecular Dynamics: Challenges, Methods, Ideas written by Peter Deuflhard and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 500 pages. Available in PDF, EPUB and Kindle. Book excerpt: On May 21-24, 1997 the Second International Symposium on Algorithms for Macromolecular Modelling was held at the Konrad Zuse Zentrum in Berlin. The event brought together computational scientists in fields like biochemistry, biophysics, physical chemistry, or statistical physics and numerical analysts as well as computer scientists working on the advancement of algorithms, for a total of over 120 participants from 19 countries. In the course of the symposium, the speakers agreed to produce a representative volume that combines survey articles and original papers (all refereed) to give an impression of the present state of the art of Molecular Dynamics. The 29 articles of the book reflect the main topics of the Berlin meeting which were i) Conformational Dynamics, ii) Thermodynamic Modelling, iii) Advanced Time-Stepping Algorithms, iv) Quantum-Classical Simulations and Fast Force Field and v) Fast Force Field Evaluation.
Book Synopsis Biomolecular Structure and Dynamics by : G. Vergoten
Download or read book Biomolecular Structure and Dynamics written by G. Vergoten and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 327 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Theoretical Studies on Structure, Function and Dynamics of Retinal-binding Proteins by : Jhenny Flor P. Galan
Download or read book Theoretical Studies on Structure, Function and Dynamics of Retinal-binding Proteins written by Jhenny Flor P. Galan and published by . This book was released on 2006 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: The structure, function and dynamics of the retinal-binding proteins, bacteriorhodopsin, 4-keto bacteriorhodopsin and rhodopsin are investigated by using theoretical methods. Retinal-binding proteins are composed of seven transmembrane helical domains and a retinylidene chromophore covalently attached to a lysine residue via a Schiff base linkage. A detailed discussion of the retinal-binding proteins is presented in Chapter one. Chapter two discusses the nature of the low frequency modes of bacteriorhodopsin (BR) and a variant, D96N. The low frequency modes are calculated by using normal mode analysis and molecular dynamics simulations. The calculated THz spectra are compared with available experimental data. A comparison of the two theoretical methods is also presented. Differences in the nature of the low frequency modes between the wild-type and D96N bacteriorhodopsin are studied as well. Chapter three focuses on the mechanisms of spectral tuning of an analog of BR, 4-keto bacteriorhodopsin. This pigment exhibits an abnormally blue-shifted absorption spectrum relative to wild-type BR. Wavelength selection in bacteriorhodopsin is affected by chromophore conformation and the interaction of the chromophore with the surrounding residues. These factors are investigated in Chapter 3 to explain the blue-shift in 4-keto BR. The energies of different models of 4-keto BR with different chromophore conformations and orientation of the Arg 82 residue are compared. Chapter four investigates the protonation states of important residues in the visual pigment, rhodopsin. This study is focused on the protonation state of Glu181, which is in the vicinity of the chromophore and is important in the activation of the protein. The pKas of the different residues are calculated by using multiconformation continuum electrostatics.
Book Synopsis Structures and Functions of Retinal Proteins by : Jean-Louis Rigaud
Download or read book Structures and Functions of Retinal Proteins written by Jean-Louis Rigaud and published by John Libbey Eurotext. This book was released on 1992 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim of the 5th International Conference on Retinal Proteins was to present the findings of the interdisciplinary fields where photochemical, biophysical, molecular biology and physiological aspects are intimately linked. This title covers nearly all the presentations given during this symposium.
Book Synopsis Structure of Partially Denatured Bacteriorhodopsin in Detergent Micelles and Structural Changes During Its Refolding by : Venkatramanan Krishnamani
Download or read book Structure of Partially Denatured Bacteriorhodopsin in Detergent Micelles and Structural Changes During Its Refolding written by Venkatramanan Krishnamani and published by . This book was released on 2010 with total page 120 pages. Available in PDF, EPUB and Kindle. Book excerpt: The partially denatured state of bacteriorhodopsin (bR), a model hepta-helical integral membrane protein that acts as a proton pump in the membranes of Halobacterium salinarum, in SDS micelles was studied to understand the sequence dependent structural perturbations. Two-frequency pulsed electron paramagnetic resonance (EPR) (double electron-electron spin resonance, DEER) investigation combined with molecular dynamics (MD) of denaturation of individual helices of bR was used in an attempt to unravel the structural details of bR in sodium dodecyl sulfate (SDS) micelles. The results from the DEER experiments reveal a discrete heterogeneous ensemble of structures of bR in the detergent. The MD simulations show the role of charged residues in unfolding and the partitioning preference of the helices in SDS micelles. The refolding kinetics from this partially denatured starting state to a functional regenerated state using stopped flow continuous wave EPR measurements revealed that the secondary structure formation is faster than 140 msec and further helix association events followed a two step process. Majority of the structural changes happen before the functional recovery of the protein in the first step with a time constant of 3-5 sec followed by minor structural changes occurring in concert with the retinal chromophore recovery with varying association time constants for each helix pair.
Book Synopsis The Biochemistry of Archaea (Archaebacteria) by : M. Kates
Download or read book The Biochemistry of Archaea (Archaebacteria) written by M. Kates and published by Elsevier. This book was released on 1993-12-13 with total page 633 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the last 10 years, considerable information has accumulated on the biochemistry of archaea. In this volume, the subject as a whole is treated in a comprehensive manner. The book brings together recent knowledge concerning general metabolism, bioenergetics, molecular biology and genetics, membrane lipid and cell-wall structural chemistry and evolutionary relations, of the three major groups of archaea: the extreme halophiles, the extreme thermophiles, and the methanogens.Subjects included are: the evolutionary relationship of these microorganisms to all other living cells; special metabolic features of archeaea; protein structural chemistry; cell envelopes; molecular biology in archaea including DNA structure and replication, transcription apparatus, translation apparatus, and ribosomal structure; and a final chapter on the molecular genetics of archaea. This comprehensive scope ensures its usefulness to researchers, and stimulates further study in this rapidly developing field.
Author :VICTORIA GARCIA SAKAI Publisher :Springer Science & Business Media ISBN 13 :1461407265 Total Pages :455 pages Book Rating :4.4/5 (614 download)
Book Synopsis Dynamics of Soft Matter by : VICTORIA GARCIA SAKAI
Download or read book Dynamics of Soft Matter written by VICTORIA GARCIA SAKAI and published by Springer Science & Business Media. This book was released on 2011-12-19 with total page 455 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dynamics of Soft Matter: Neutron Applications provides an overview of neutron scattering techniques that measure temporal and spatial correlations simultaneously, at the microscopic and/or mesoscopic scale. These techniques offer answers to new questions arising at the interface of physics, chemistry, and biology. Knowledge of the dynamics at these levels is crucial to understanding the soft matter field, which includes colloids, polymers, membranes, biological macromolecules, foams, emulsions towards biological & biomimetic systems, and phenomena involving wetting, friction, adhesion, or microfluidics. Emphasizing the complementarities of scattering techniques with other spectroscopic ones, this volume also highlights the potential gain in combining techniques such as rheology, NMR, light scattering, dielectric spectroscopy, as well as synchrotron radiation experiments. Key areas covered include polymer science, biological materials, complex fluids and surface science.
Download or read book Cumulated Index Medicus written by and published by . This book was released on 1996 with total page 1340 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Kinetic Studies of the Folding of the Membrane Protein Bacteriorhodopsin by :
Download or read book Kinetic Studies of the Folding of the Membrane Protein Bacteriorhodopsin written by and published by . This book was released on 1998 with total page 522 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Statistical Mechanics, Protein Structure, and Protein Substrate Interactions by : Sebastian Doniach
Download or read book Statistical Mechanics, Protein Structure, and Protein Substrate Interactions written by Sebastian Doniach and published by Springer Science & Business Media. This book was released on 2013-11-22 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: A number of factors have come together in the last couple of decades to define the emerging interdisciplinary field of structural molecular biology. First, there has been the considerable growth in our ability to obtain atomic-resolution structural data for biological molecules in general, and proteins in particular. This is a result of advances in technique, both in x-ray crystallography, driven by the development of electronic detectors and of synchrotron radiation x-ray sources, and by the development ofNMR techniques which allow for inference of a three-dimensional structure of a protein in solution. Second, there has been the enormous development of techniques in DNA engineering which makes it possible to isolate and clone specific molecules of interest in sufficient quantities to enable structural measurements. In addition, the ability to mutate a given amino acid sequence at will has led to a new branch of biochemistry in which quantitative measurements can be made assessing the influence of a given amino acid on the function of a biological molecule. A third factor, resulting from the exponential increase in computing power available to researchers, has been the emergence of a growing body of people who can take the structural data and use it to build atomic-scale models of biomolecules in order to try and simulate their motions in an aqueous environment, thus helping to provide answers to one of the most basic questions of molecular biology: the relation of structure to function.
Book Synopsis Kinetic Studies of the Folding of the Protein Bacteriorhodopsin by : Amjad Farood
Download or read book Kinetic Studies of the Folding of the Protein Bacteriorhodopsin written by Amjad Farood and published by . This book was released on 1998 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Protein Structure and Engineering by : O. Jardetsky
Download or read book Protein Structure and Engineering written by O. Jardetsky and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 383 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proceedings of the Tenth Course of the International School of Pure and Applied Biostructure (Erice, Italy, June 1989). Knowledge of protein structure and of design and manufacture methods has made it possible to produce proteins of any desired sequence, but progress is limited by inability to predi
