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1 Velmurugu, Yogambigai Dynamics and Mechanism of DNA-Bending Proteins in Binding Site Recognition I10294 2017 eBook  
2 Fern??ndez, Ariel Physics at the Biomolecular Interface I09945 2016 eBook  
3 Scherer, Philipp O.J Theoretical Molecular Biophysics I09798 2017 eBook  
4 Popot, Jean-Luc Membrane Proteins in Aqueous Solutions I09698 2018 eBook  
5 Nakasako, Masayoshi X-Ray Diffraction Imaging of Biological Cells I09683 2018 eBook  
6 Joo, Chirlmin Biophysics of RNA-Protein Interactions I09182 2019 eBook  
7 Likhtenshtein, Gertz I Nitroxides I08904 2020 eBook  
8 Koshlan, Tatiana Mathematical Modeling of Protein Complexes I08862 2018 eBook  
9 Ashrafuzzaman, Mohammad Membrane Biophysics I08181 2013 eBook  
10 Kr??mer, Reinhard Membrane Transport Mechanism I07955 2014 eBook  
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TitleDynamics and Mechanism of DNA-Bending Proteins in Binding Site Recognition
Author(s)Velmurugu, Yogambigai
PublicationCham, 1. Imprint: Springer 2. Springer International Publishing, 2017.
DescriptionXXI, 199 p. 112 illus., 105 illus. in color : online resource
Abstract NoteUsing a novel approach that combines high temporal resolution of the laser T-jump technique with unique sets of fluorescent probes, this study unveils previously unresolved DNA dynamics during search and recognition by an architectural DNA bending protein and two DNA damage recognition proteins. Many cellular processes involve special proteins that bind to specific DNA sites with high affinity. How these proteins recognize their sites while rapidly searching amidst ~3 billion nonspecific sites in genomic DNA remains an outstanding puzzle. Structural studies show that proteins severely deform DNA at specific sites and indicate that DNA deformability is a key factor in site-specific recognition. However, the dynamics of DNA deformations have been difficult to capture, thus obscuring our understanding of recognition mechanisms. The experiments presented in this thesis uncover, for the first time, rapid (~100-500 microseconds) DNA unwinding/bending attributed to nonspecific interrogation, prior to slower (~5-50 milliseconds) DNA kinking/bending/nucleotide-flipping during recognition. These results help illuminate how a searching protein interrogates DNA deformability and eventually ???stumbles??? upon its target site. Submillisecond interrogation may promote preferential stalling of the rapidly scanning protein at cognate sites, thus enabling site-recognition. Such multi-step search-interrogation-recognition processes through dynamic conformational changes may well be common to the recognition mechanisms for diverse DNA-binding proteins.
ISBN,Price9783319451299
Keyword(s)1. Biological and Medical Physics, Biophysics 2. BIOLOGICAL PHYSICS 3. BIOPHYSICS 4. EBOOK 5. EBOOK - SPRINGER 6. MICROSCOPY 7. Protein-Ligand Interactions 8. Proteins?? 9. SPECTROSCOPY 10. Spectroscopy and Microscopy
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TitlePhysics at the Biomolecular Interface : Fundamentals for Molecular Targeted Therapy
Author(s)Fern??ndez, Ariel
PublicationCham, 1. Imprint: Springer 2. Springer International Publishing, 2016.
DescriptionXV, 483 p. 295 illus., 208 illus. in color : online resource
Abstract NoteThis book focuses primarily on the role of interfacial forces in understanding biological phenomena at the molecular scale. By providing a suitable statistical mechanical apparatus to handle the biomolecular interface, the book becomes uniquely positioned to address core problems in molecular biophysics. It highlights the importance of interfacial tension in delineating a solution to the protein folding problem, in unravelling the physico-chemical basis of enzyme catalysis and protein associations, and in rationally designing molecular targeted therapies. Thus grounded in fundamental science, the book develops a powerful technological platform for drug discovery, while it is set to inspire scientists at any level in their careers determined to address the major challenges in molecular biophysics. The acknowledgment of how exquisitely the structure and dynamics of proteins and their aqueous environment are related attests to the overdue recognition that biomolecular phenomena cannot be effectively understood without dealing with interfacial behaviour. There is an urge to grasp how biologically relevant behaviour is shaped by the structuring of biomolecular interfaces and how interfacial tension affects the molecular events that take place in the cell. This book squarely addresses these needs from a physicist perspective. The book may serve as a monograph for practitioners and, alternatively, as an advanced textbook. Fruitful reading requires a background in physical chemistry and some basics in biophysics. The selected problems at the end of the chapters and the progression in conceptual difficulty make it a suitable textbook for a graduate level course or an elective course for seniors majoring in chemistry, physics, biomedical engineering or related disciplines
ISBN,Price9783319308524
Keyword(s)1. Biological and Medical Physics, Biophysics 2. BIOLOGICAL PHYSICS 3. BIOPHYSICS 4. COMPLEX SYSTEMS 5. DYNAMICAL SYSTEMS 6. EBOOK 7. EBOOK - SPRINGER 8. MOLECULAR BIOLOGY 9. Molecular Medicine 10. Pharmaceutical Sciences/Technology 11. Pharmaceutical technology 12. PHYSICAL CHEMISTRY 13. Protein Structure 14. Proteins?? 15. STATISTICAL PHYSICS
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TitleTheoretical Molecular Biophysics
Author(s)Scherer, Philipp O.J;Fischer, Sighart F
PublicationBerlin, Heidelberg, 1. Imprint: Springer 2. Springer Berlin Heidelberg, 2017.
DescriptionXVI, 513 p. 226 illus., 27 illus. in color : online resource
Abstract NoteThis book gives an introduction to molecular biophysics. It starts from material properties at equilibrium related to polymers, dielectrics and membranes. Electronic spectra are developed for the understanding of elementary dynamic processes in photosynthesis including proton transfer and dynamics of molecular motors. Since the molecular structures of functional groups of bio-systems were resolved, it has become feasible to develop a theory based on the quantum theory and statistical physics with emphasis on the specifics of the high complexity of bio-systems. This introduction to molecular aspects of the field focuses on solvable models. Elementary biological processes provide as special challenge the presence of partial disorder in the structure which does not destroy the basic reproducibility of the processes. Apparently the elementary molecular processes are organized in a way to optimize the efficiency. Learning from nature by means exploring the relation between structure and function may even help to build better artificial solar cells. The reader is exposed to basic concepts in modern biophysics, such as entropic forces, phase separation, potential of mean force, electron and proton transfer, heterogeneous reactions, coherent and incoherent energy transfer as well as molecular motors. Basic knowledge in classical and Quantum mechanics, electrostatics and statistical physics is desirable. Simplified models are presented which can be solved in limited cases analytically from the guiding lines to generate the basis for a fundamental understanding of the more complex biophysical systems. Chapters close with challenging problems whose solutions are provided at the end of the book to complete the pedagogical treatment in the book. To the second edition several new chapters were added. The medium polarization is treated self-consistently using basic elements of polaron theory and more advanced nonlinear Schr??dinger equations to describe the dynamics of solvation. Ion transport through a membrane was extended by the discussion of cooperative effects. Intramolecular transitions are now discussed in the new edition in much more detail, including also radiationless transitions. Very recent developments in spectroscopy are included, especially two-dimensional and hole-burning spectroscopy. The discussion of charge transfer processes was extended by including recent results of hole transfer in DNA in connection with the super-exchange mechanism. The chapter on molecular motors was rewritten to include the most recent developments of new models. The book is a useful text for students and researchers wanting to go through the mathematical derivations in the theories presented. This book attracts a group of applied mathematically oriented students and scholars to the exciting field of molecular biophysics.??
ISBN,Price9783662556719
Keyword(s)1. Biochemical engineering 2. Biological and Medical Physics, Biophysics 3. BIOLOGICAL PHYSICS 4. BIOMATHEMATICS 5. Biomedical engineering 6. Biomedical Engineering and Bioengineering 7. BIOPHYSICS 8. EBOOK 9. EBOOK - SPRINGER 10. Mathematical and Computational Biology 11. Protein Science 12. Proteins??
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TitleMembrane Proteins in Aqueous Solutions : From Detergents to Amphipols
Author(s)Popot, Jean-Luc
PublicationCham, 1. Imprint: Springer 2. Springer International Publishing, 2018.
DescriptionXXVII, 708 p. 437 illus., 266 illus. in color : online resource
Abstract NoteMembrane proteins represent about one third of the proteins encoded in a cell's genome, and, because of their key physiological roles, more than half of drug targets. Detergents are traditionally used to extract proteins from membranes in order to make them amenable to the tools of biochemistry and biophysics. However, detergent-solubilized proteins are generally unstable. This has led to the development of alternative, non-conventional surfactants, such as bicelles, nanodiscs, amphipathic peptides, fluorinated surfactants, and specially designed amphipathic polymers called 'amphipols'. These novel tools, mainly developed over the past 20 years, are revolutionizing handling membrane proteins in vitro for basic and applied research, as well as for such biomedical applications as drug screening or vaccination. This book, written by a specialist of membrane proteins and one of the creators of amphipols, describes the properties and uses of these novel molecules. It opens with general introductions on membrane proteins and their natural environment, detergents, the current status of membrane protein in vitro studies, a broad panorama of non-conventional surfactants and a discussion of their respective advantages and limitations, and the preparation and properties of amphipols and membrane protein/amphipol complexes. Topical chapters cover in vitro folding, cell-free synthesis and stabilization of membrane proteins, and such biophysical and biochemical applications as electron microscopy, Xray diffraction, NMR, optical spectroscopy, mass spectrometry, the whole range of solutions studies, proteomics, and such practical applications as membrane protein immobilization and drug screening and the use of amphipols in vivo for vaccination and drug delivery. Each topical chapter is introduced with a concise, up-to-date overview of how membrane proteins are currently studied using each individual technique, before offering an exhaustive coverage and in-depth discussion of the contribution of amphipols, and concluding with hands-on protocols written by everyday practitioners of each application. In addition to a comprehensive coverage of the properties and uses of non-conventional surfactants, this book therefore also offers a concise, accessible introduction to membrane protein biochemistry and biophysics. It is meant to be used both in basic and applied research laboratories and as a teaching help
ISBN,Price9783319731483
Keyword(s)1. Biological and Medical Physics, Biophysics 2. BIOLOGICAL PHYSICS 3. BIOPHYSICS 4. EBOOK 5. EBOOK - SPRINGER 6. Medicinal chemistry 7. Pharmaceutical Sciences/Technology 8. Pharmaceutical technology 9. PHYSICAL CHEMISTRY 10. Polymer Sciences 11. Polymers???? 12. Protein Science 13. Proteins??
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TitleX-Ray Diffraction Imaging of Biological Cells
Author(s)Nakasako, Masayoshi
PublicationTokyo, 1. Imprint: Springer 2. Springer Japan, 2018.
DescriptionXX, 228 p. 96 illus., 89 illus. in color : online resource
Abstract NoteIn this book, the author describes the development of the experimental diffraction setup and structural analysis of non-crystalline particles from material science and biology. Recent advances in X-ray free electron laser (XFEL)-coherent X-ray diffraction imaging (CXDI) experiments allow for the structural analysis of non-crystalline particles to a resolution of 7 nm, and to a resolution of 20 nm for biological materials. Now XFEL-CXDI marks the dawn of a new era in structural analys of non-crystalline particles with dimensions larger than 100 nm, which was quite impossible in the 20th century. To conduct CXDI experiments in both synchrotron and XFEL facilities, the author has developed apparatuses, named KOTOBUKI-1 and TAKASAGO-6 for cryogenic diffraction experiments on frozen-hydrated non-crystalline particles at around 66 K. At the synchrotron facility, cryogenic diffraction experiments dramatically reduce radiation damage of specimen particles and allow tomography CXDI experiments. In addition, in XFEL experiments, non-crystalline particles scattered on thin support membranes and flash-cooled can be used to efficiently increase the rate of XFEL pulses. The rate, which depends on the number density of scattered particles and the size of X-ray beams, is currently 20-90%, probably the world record in XFEL-CXDI experiments. The experiment setups and results are introduced in this book. The author has also developed software suitable for efficiently processing of diffraction patterns and retrieving electron density maps of specimen particles based on the diffraction theory used in CXDI
ISBN,Price9784431566182
Keyword(s)1. Characterization and Evaluation of Materials 2. CRYSTALLOGRAPHY 3. Crystallography and Scattering Methods 4. EBOOK 5. EBOOK - SPRINGER 6. LASERS 7. MATERIALS SCIENCE 8. Measurement Science and Instrumentation 9. Measurement?????? 10. Optics, Lasers, Photonics, Optical Devices 11. PHOTONICS 12. PHYSICAL MEASUREMENTS 13. Protein Structure 14. Proteins??
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TitleBiophysics of RNA-Protein Interactions : A Mechanistic View
Author(s)Joo, Chirlmin;Rueda, David
PublicationNew York, NY, 1. Imprint: Springer 2. Springer New York, 2019.
DescriptionVII, 249 p. 77 illus., 74 illus. in color : online resource
Abstract NoteRNA molecules play key roles in all aspects of cellular life, but to do so efficiently, they must work in synergism with proteins. This book addresses how proteins and RNA interact to carry out biological functions such as protein synthesis, regulation of gene expression, genome defense, liquid phase separation and more. The topics addressed in this volume will appeal to researchers in biophysics, biochemistry and structural biology. The book is a useful resource for anybody interested in elucidating the molecular mechanisms and discrete properties of RNA-protein complexes. Included are reviews of key systems such as microRNA and CRISPR/Cas that exemplify how RNA and proteins work together to perform their biological function. Also covered are techniques ranging from single molecule fluorescence and force spectroscopy to crystallography, cryo-EM microscopy, and kinetic modeling
ISBN,Price9781493997268
Keyword(s)1. Analytical chemistry 2. Biochemical engineering 3. Biological and Medical Physics, Biophysics 4. BIOLOGICAL PHYSICS 5. BIOPHYSICS 6. EBOOK 7. EBOOK - SPRINGER 8. Protein Science 9. Proteins??
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TitleNitroxides : Brief History, Fundamentals, and Recent Developments
Author(s)Likhtenshtein, Gertz I
PublicationCham, 1. Imprint: Springer 2. Springer International Publishing, 2020.
DescriptionXI, 316 p : online resource
Abstract NoteWritten by a pioneer in the development of spin labeling in biophysics, this expert book covers the fundamentals of nitroxide spin labeling through cutting-edge applications in chemistry, physics, materials science, molecular biology, and biomedicine. Nitroxides have earned their place as one of the most popular organic paramagnets due to their suitability as inhibitors of oxidative processes, as a means to polarize magnetic nuclei, and, in molecular biology, as probes and labels to understand molecular structures and dynamics as drags for cancer and other diseases. Beginning with an overview of the basic methodology and nitroxides??? 145-year history, this book equips students with necessary background and techniques to undertake original research and industry work in this growing field
ISBN,Price9783030348229
Keyword(s)1. Biological and Medical Physics, Biophysics 2. BIOLOGICAL PHYSICS 3. BIOPHYSICS 4. EBOOK 5. EBOOK - SPRINGER 6. Electronic materials 7. MAGNETIC MATERIALS 8. MAGNETISM 9. Magnetism, Magnetic Materials 10. Optical and Electronic Materials 11. OPTICAL MATERIALS 12. Pharmaceutical Sciences/Technology 13. Pharmaceutical technology 14. Polymer Sciences 15. Polymers???? 16. Protein Science 17. Proteins??
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TitleMathematical Modeling of Protein Complexes
Author(s)Koshlan, Tatiana;Kulikov, Kirill
PublicationCham, 1. Imprint: Springer 2. Springer International Publishing, 2018.
DescriptionXIV, 367 p. 65 illus., 48 illus. in color : online resource
Abstract NoteThis book is devoted to the physical and mathematical modeling of the formation of complexes of protein molecules. The models developed show remarkable sensitivity to the amino acid sequences of proteins, which facilitates experimental studies and allows one to reduce the associated costs by reducing the number of measurements required according to the developed criteria. These models make it possible to reach a conclusion about the interactions between different amino acid chains and to identify more stable sites on proteins. The models also take the phosphorylation of amino acid residues into account. At the end of the book, the authors present possible directions of application of their physical and mathematical models in clinical medicine
ISBN,Price9783319983042
Keyword(s)1. Biological and Medical Physics, Biophysics 2. BIOLOGICAL PHYSICS 3. BIOMATHEMATICS 4. Biomedical engineering 5. Biomedical Engineering and Bioengineering 6. BIOPHYSICS 7. EBOOK 8. EBOOK - SPRINGER 9. Mathematical and Computational Biology 10. Numerical and Computational Physics, Simulation 11. PHYSICS 12. Protein Structure 13. Proteins??
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TitleMembrane Biophysics
Author(s)Ashrafuzzaman, Mohammad;Tuszynski, Jack A
PublicationBerlin, Heidelberg, 1. Imprint: Springer 2. Springer Berlin Heidelberg, 2013.
DescriptionXIV, 182 p : online resource
Abstract NotePhysics, mathematics and chemistry all play a vital role in understanding the true nature and functioning of biological membranes, key elements of living processes. Besides simple spectroscopic observations and electrical measurements of membranes we address in this book the phenomena of coexistence and independent existence of different membrane components using various theoretical approaches. This treatment will be helpful for readers who want to understand biological processes by applying both simple observations and fundamental scientific analysis. It provides a deep understanding of the causes and effects of processes inside membranes, and will thus eventually open new doors for high-level pharmaceutical approaches towards fighting membrane- and cell-related diseases
ISBN,Price9783642161056
Keyword(s)1. Biological and Medical Physics, Biophysics 2. BIOLOGICAL PHYSICS 3. BIOPHYSICS 4. Cell membranes?? 5. EBOOK 6. EBOOK - SPRINGER 7. Membrane Biology 8. Nanoscale science 9. Nanoscale Science and Technology 10. NANOSCIENCE 11. Nanostructures 12. Numerical and Computational Physics, Simulation 13. PHYSICAL CHEMISTRY 14. PHYSICS 15. Protein-Ligand Interactions 16. Proteins??
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TitleMembrane Transport Mechanism : 3D Structure and Beyond
Author(s)Kr??mer, Reinhard;Ziegler, Christine
PublicationBerlin, Heidelberg, 1. Imprint: Springer 2. Springer Berlin Heidelberg, 2014.
DescriptionXII, 272 p. 65 illus., 56 illus. in color : online resource
Abstract NoteThis book provides a molecular view of membrane transport by means of numerous biochemical and biophysical techniques. The rapidly growing number of atomic structures of transporters in different conformations and the constant progress in bioinformatics have recently added deeper insights. ?? The unifying mechanism of energized solute transport across membranes is assumed to consist of the conformational cycling of a carrier protein to provide access to substrate binding sites from either side of a cellular membrane. Due to the central role of active membrane transport there is considerable interest in deciphering the principles of one of the most fundamental processes in nature: the alternating access mechanism. ?? This book brings together particularly significant structure-function studies on a variety of carrier systems from different transporter families: Glutamate symporters, LeuT-like fold transporters, MFS transporters and SMR (RND) exporters, as well as ABC-type importers. ?? The selected examples impressively demonstrate how the combination of functional analysis, crystallography, investigation of dynamics and computational studies has made it possible to create a conclusive picture, or, more precisely, ???a molecular movie???. Although we are still far from a complete molecular description of the alternating access mechanism, remarkable progress has been made from static snapshots towards membrane transport dynamics
ISBN,Price9783642538391
Keyword(s)1. BIOINFORMATICS 2. Biological and Medical Physics, Biophysics 3. BIOLOGICAL PHYSICS 4. BIOPHYSICS 5. Cell membranes?? 6. Computational Biology/Bioinformatics 7. CRYSTALLOGRAPHY 8. Crystallography and Scattering Methods 9. EBOOK 10. EBOOK - SPRINGER 11. Membrane Biology 12. Protein Structure 13. Proteins??
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