Download or read book Dissecting Structure function Relationships in Molecular Motors Using Protein Engineering and Single molecule Methods written by Athena Ierokomos and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological cells can harness the free energy of ATP hydrolysis to perform mechanical tasks using molecular motor proteins. These nanoscale machines are able to generate directional motion through mechanochemical cycles which rely on allosteric communication and large rearrangements of protein domains. In studies of molecular motors, protein engineering allows us to test our understanding of relationships between structure and function, while single-molecule methods allow us to directly observe motor dynamics. Here we consider two systems which undergo large conformational changes: cytoplasmic dynein and DNA gyrase. We use protein engineering to investigate structural features that contribute to dynein velocity and processivity. Building on our initial findings, we are able to design dynein motors that change speed in response to light. The speed and controllability of future designs may be improved with further engineering, in order to generate light-activatable, dynein-based tools which can be used to study transport functions in vivo. In the second half of this dissertation, we consider a single-molecule technique for multimodal measurements of mechanics and fluorescence in DNA and DNA:protein complexes. Mechanical measurements based on magnetic tweezers are combined with simultaneous fluorescence imaging that can report on macromolecular binding and local conformational changes. We outline how this method can be applied to study the mechanism of DNA gyrase, a motor which introduces negative supercoils by coordinating protein domain motions and ATP hydrolysis with DNA cleavage and religation. We observe binding coincident with mechanics and report on challenges in using FRET-labeled enzymes to correlate domain motions with mechanical substeps. We anticipate that correlative multimodal measurements will be valuable tools for characterizing the dynamics of DNA gyrase and other large nucleoprotein machines.
Download or read book Dissecting the Coordinated Transport of Molecular Motors a Single Molecule Approach Towards Studying Bidirectional Motion written by Abdullah Chaudhary and published by . This book was released on 2020 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: "Many cellular processes are driven by the collective action of motors working in teams. One such example of this type of phenomenon is intracellular transport -- the transport of cargoes carried out by teams of similar or opposite polarity motors (kinesin and dynein). In most cells, long-range transport occurs along microtubules that are oriented with their plus ends towards the cell periphery, and minus ends towards the cell body. Despite the presence of opposite polarity motors, the mechanism by which cargoes are directed to specific locations in the cell is not well understood. A set of microtubule-associated proteins (MAPs) and scaffolding molecules have been shown to have some effect on motility and cargo directionality, but the mechanism by which these molecules tune motor specific processivity is not well understood. Defects in intracellular trafficking can result in severe developmental and neurodegenerative diseases. One prominent example is Huntington’s disease (HD), which is an autosomal dominant neurodegenerative disorder caused by an extension of the CAG repeat region in the N-terminus of the huntingtin gene. Though it is clear that wild-type huntingtin plays a role in intracellular trafficking by interacting with motor and motor-associated proteins, it is unclear how post-translational modifications (PTMs) modulate the activity of motor proteins and the specific biophysical mechanism behind this activity. In HD, mutated huntingtin aggregates in neurons, disrupting cargo transport. Disruption in vesicle transport results in abnormal cell signaling and impaired clearance of damaged proteins and organelles. This suggests a mechanism where defects in transport are due to misregulation of motor protein activity by vesicle-bound huntingtin.In addition to scaffolding molecules like huntingtin, transport is also regulated by microtubule-associated proteins (MAPs) that bind along the microtubule surface. Tau is a neuronal MAP that stabilizes axonal microtubules by crosslinking them into bundles. It also indirectly modulates cargo motility by serving as a roadblock to motors. Misregulation of tau leads to a range of neurodegenerative diseases known as tauopathies, including Alzheimer’s disease (AD). In AD, tau hyperphosphorylation leads to the development of fibrillary bodies that aggregate to form neurofibrillary tangles (NFTs). Varying concentration of tau inhibits single motor and multiple motor activity. Yet, despite the presence of tau in healthy neurons, teams of motors are still able to navigate efficiently over long distances in the axon without being inhibited. Similar to tau, MAP7 (ensconsin) also binds along microtubules and stabilizes them. It organizes the microtubule cytoskeleton in mitosis and neuronal branching. MAP7 not only promotes the interaction of kinesin-1 to microtubules but also competes with tau for binding along microtubules to regulate kinesin transport. Since bidirectional motility is a hallmark of intracellular transport, understanding how MAPs regulate teams of kinesin and dynein motors will provide insight into how transport is regulated"--
Download or read book Molecular Motors written by Ann O. Sperry and published by Humana. This book was released on 2010-11-19 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular motor proteins produce force for movement in an incredibly wide variety of cellular processes. This volume explores the extreme functional and structural diversity of molecular motors and presents methods relevant to each motor family. In addition, it describes techniques directed at motors that fall outside of the three characterized families: dynamin and F1ATPase.
Download or read book Engineering Cytoskeletal Motors written by Lu Chen and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Cytoskeletal motors convert chemical energy into work and are involved in a wide range of cellular processes, including motility, contractility and cargo transport. Engineering the motility of these molecular machines provides insights into structural-functional relationships, components for driving transport in microscale devices, and tools for controlling cellular processes that depend on these motors. I have engineered motors with novel functions that provide new levels of control over nanoscale motion, including myosin motors that can be chemically signaled to switch their direction of motion, and kinesins with light-activated gearshifts. Myosin motors generate directed motion using a powerstroke mechanism, in which a conformational change in the catalytic head domain is amplified by a rigid geometric element called the lever arm. Our controllable motor designs are based on introducing dynamic changes in lever arm geometry. I designed myosin VI variants with chimeric lever arms composed of a three-helix bundle fused to two or more calmodulin-binding IQ repeats. In low concentrations of calcium, these engineered motors move toward the ( - ) end of actin filaments; in high concentrations of calcium, the motors are (+) end directed. I confirmed the designed behavior using in vitro assays of myosin function, including single-molecule measurements. To further adapt these controllable engineered motors to future applications, it is desirable to have 1) high processivity and 2) optical control. Processivity is a requirement for building nanoscale devices that harness the transport capabilities of molecular motors, and light is a more versatile control signal than calcium concentration because it can be precisely modulated in space and time, and is generally orthogonal to cellular signaling. I have collaborated with other members of the Bryant laboratory to develop controllable processive walkers, and to characterize myosin motors that reversibly change gears -- speed up, slow down, or switch directions -- when exposed to blue light. Finally, I expanded the toolbox of engineered motors to include microtubule-based motors. Microtubules and actin filaments are used for different sets of cellular functions, and have different properties that can be exploited for building tracks or shuttles in nanoscale device applications. Optimizing properties and controllability of both sets of motors enhances our ability to select the best motor for specific applications in vivo and in vitro. I have created microtubule-based motors that can reversibly change gears in response to blue light, by porting gearshift designs from our controllable myosins to class 14 kinesins, which have a myosin-like swinging lever arm mechanism. As part of this work, in collaboration with the Nogales laboratory at Berkeley, I have started to add cryo-EM structural data to our design cycle. We have successfully reconstructed two engineered kinesins and confirmed that the structures of engineered elements are in agreement with our structural designs based on rigid recombination of modular protein domains. I have developed a set of controllable cytoskeletal motors with novel functions. With further refinements, the engineered motors described here may be useful in diagnostic devices that harness active transport, as well as for in vivo investigations of cellular processes.
Download or read book Single molecule Force Manipulation and Nanoscopic Imaging of Protein Structure dynamics function Relationship written by Susovan Roy Chowdhury and published by . This book was released on 2021 with total page 141 pages. Available in PDF, EPUB and Kindle. Book excerpt: The anisotropic nature of the force fluctuation inside cells makes it very biologically relevant to study the dynamics of the structure-function relationship of protein molecules under force. The ability to manipulate individual molecules under near-physiological conditions makes the Atomic force microscope a very widely used technique. Force applied by AFM can be either compressive force or pulling force. Here in the thesis, we have explored the compressive force response of the protein molecules and the impact of the compressive force using AFM.The abrupt ruptures of protein native structures under compressive force were demonstrated by single-molecule AFM-FRET spectroscopic nanoscopy. The simultaneous measurement of the force curve and the FRET efficiency showed a temporal correlation between the compressive force drop and the FRET efficiency drop which indicated a spontaneous and abrupt rupture of the protein native tertiary structure.Furthermore, a similar compressive force experiment was done on targeted calmodulin molecules to characterize two different forms of CaM, the Ca2+-ligated activated form, and the Ca2+ free non-activated form (Apo-Calmodulin). A sudden and spontaneous rupture of Apo-CaM molecules was observed under the compressive force applied by an AFM tip, though no such events were recorded in the case of the Ca2+-ligated form.To further prove that this kind of compressive force rupture of Apo-CaM can trigger new chemistry inside the cell, a similar experiment was carried out where we observed compressive force rupture of apo-CaM molecules and successive binding of C28W peptide to the ruptured protein, a typical protein signaling activity that only a Ca2+-activated CaM has. This observation demonstrates that both chemical activation and force activation can play a vital role in biology, such as cell-signaling protein dynamics and function.Lastly, we further explored the entangled protein state formed following the events of the multiple and simultaneous tau protein ruptures under crowding. Crowded proteins simultaneously rupture and then spontaneously refold to an entangled folding state, different from either folded or unfolded states of the tau protein, which can be a plausible pathway for the tau protein aggregation that is related to several neurodegenerative diseases like Alzheimer's disease and Parkinson's disease.
Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Dissertation Abstracts International written by and published by . This book was released on 2005 with total page 796 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Molecular Machines and Motors written by J.-P. Sauvage and published by Springer Science & Business Media. This book was released on 2001-07-03 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt: This series presents critical reviews of the present position and future trends in modern chemical research. It consists of short and concise reports on chemistry, each written by the world’s renowned experts, and still valid and useful after 5 or 10 years.
Download or read book Advanced Techniques in Biophysics written by José Luis R. Arrondo and published by Springer Science & Business Media. This book was released on 2007-04-21 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt: Technical advancements are basic elements in our life. In biophysical studies, new applications and improvements in well-established techniques are being implemented every day. This book deals with advancements produced not only from a technical point of view, but also from new approaches that are being taken in the study of biophysical samples, such as nanotechniques or single-cell measurements. This book constitutes a privileged observatory for reviewing novel applications of biophysical techniques that can help the reader enter an area where the technology is progressing quickly and where a comprehensive explanation is not always to be found.
Download or read book Macromolecular Protein Complexes III Structure and Function written by J. Robin Harris and published by Springer Nature. This book was released on 2020-11-30 with total page 580 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers important topics such as the dynamic structure and function of the 26S proteasome, the DNA replication machine: structure and dynamic function and the structural organization and protein–protein interactions in the human adenovirus capsid, to mention but a few. The 18 chapters included here, written by experts in their specific field, are at the forefront of scientific knowledge. The impressive integration of structural data from X-ray crystallography with that from cryo-electron microscopy is apparent throughout the book. In addition, functional aspects are also given a high priority. Chapter 1 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Download or read book Structural DNA Nanotechnology written by Nadrian C. Seeman and published by Cambridge University Press. This book was released on 2015 with total page 269 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by the founder of the field, this is a comprehensive and accessible introduction to structural DNA nanotechnology.
Download or read book An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation written by Gregory R. Bowman and published by Springer Science & Business Media. This book was released on 2013-12-02 with total page 148 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim of this book volume is to explain the importance of Markov state models to molecular simulation, how they work, and how they can be applied to a range of problems. The Markov state model (MSM) approach aims to address two key challenges of molecular simulation: 1) How to reach long timescales using short simulations of detailed molecular models. 2) How to systematically gain insight from the resulting sea of data. MSMs do this by providing a compact representation of the vast conformational space available to biomolecules by decomposing it into states sets of rapidly interconverting conformations and the rates of transitioning between states. This kinetic definition allows one to easily vary the temporal and spatial resolution of an MSM from high-resolution models capable of quantitative agreement with (or prediction of) experiment to low-resolution models that facilitate understanding. Additionally, MSMs facilitate the calculation of quantities that are difficult to obtain from more direct MD analyses, such as the ensemble of transition pathways. This book introduces the mathematical foundations of Markov models, how they can be used to analyze simulations and drive efficient simulations, and some of the insights these models have yielded in a variety of applications of molecular simulation.
Download or read book Research at the Intersection of the Physical and Life Sciences written by National Research Council and published by National Academies Press. This book was released on 2010-03-25 with total page 122 pages. Available in PDF, EPUB and Kindle. Book excerpt: Traditionally, the natural sciences have been divided into two branches: the biological sciences and the physical sciences. Today, an increasing number of scientists are addressing problems lying at the intersection of the two. These problems are most often biological in nature, but examining them through the lens of the physical sciences can yield exciting results and opportunities. For example, one area producing effective cross-discipline research opportunities centers on the dynamics of systems. Equilibrium, multistability, and stochastic behavior-concepts familiar to physicists and chemists-are now being used to tackle issues associated with living systems such as adaptation, feedback, and emergent behavior. Research at the Intersection of the Physical and Life Sciences discusses how some of the most important scientific and societal challenges can be addressed, at least in part, by collaborative research that lies at the intersection of traditional disciplines, including biology, chemistry, and physics. This book describes how some of the mysteries of the biological world are being addressed using tools and techniques developed in the physical sciences, and identifies five areas of potentially transformative research. Work in these areas would have significant impact in both research and society at large by expanding our understanding of the physical world and by revealing new opportunities for advancing public health, technology, and stewardship of the environment. This book recommends several ways to accelerate such cross-discipline research. Many of these recommendations are directed toward those administering the faculties and resources of our great research institutions-and the stewards of our research funders, making this book an excellent resource for academic and research institutions, scientists, universities, and federal and private funding agencies.
Download or read book Physics of Cancer written by Claudia Mierke and published by Iph001. This book was released on 2018-10-24 with total page 500 pages. Available in PDF, EPUB and Kindle. Book excerpt: This revised second edition is improved linguistically with multiple increases of the number of figures and the inclusion of several novel chapters such as actin filaments during matrix invasion, microtubuli during migration and matrix invasion, nuclear deformability during migration and matrix invasion, and the active role of the tumor stroma in regulating cell invasion.
Download or read book Ribosomes Structure Function and Dynamics written by Marina V. Rodnina and published by Springer Science & Business Media. This book was released on 2011-12-10 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ribosome is a macromolecular machine that synthesizes proteins with a high degree of speed and accuracy. Our present understanding of its structure, function and dynamics is the result of six decades of research. This book collects over 40 articles based on the talks presented at the 2010 Ribosome Meeting, held in Orvieto, Italy, covering all facets of the structure and function of the ribosome. New high-resolution crystal structures of functional ribosome complexes and cryo-EM structures of translating ribosomes are presented, while partial reactions of translation are examined in structural and mechanistic detail, featuring translocation as a most dynamic process. Mechanisms of initiation, both in bacterial and eukaryotic systems, translation termination, and novel details of the functions of the respective factors are described. Structure and interactions of the nascent peptide within, and emerging from, the ribosomal peptide exit tunnel are addressed in several articles. Structural and single-molecule studies reveal a picture of the ribosome exhibiting the energy landscape of a processive Brownian machine. The collection provides up-to-date reviews which will serve as a source of essential information for years to come.
Download or read book Innovations and Implementations of Computer Aided Drug Discovery Strategies in Rational Drug Design written by Sanjeev Kumar Singh and published by Springer Nature. This book was released on 2021-02-02 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents various computer-aided drug discovery methods for the design and development of ligand and structure-based drug molecules. A wide variety of computational approaches are now being used in various stages of drug discovery and development, as well as in clinical studies. Yet, despite the rapid advances in computer software and hardware, combined with the exponential growth in the available biological information, there are many challenges that still need to be addressed, as this book shows. In turn, it shares valuable insights into receptor-ligand interactions in connection with various biological functions and human diseases. The book discusses a wide range of phylogenetic methods and highlights the applications of Molecular Dynamics Simulation in the drug discovery process. It also explores the application of quantum mechanics in order to provide better accuracy when calculating protein-ligand binding interactions and predicting binding affinities. In closing, the book provides illustrative descriptions of major challenges associated with computer-aided drug discovery for the development of therapeutic drugs. Given its scope, it offers a valuable asset for life sciences researchers, medicinal chemists and bioinformaticians looking for the latest information on computer-aided methodologies for drug development, together with their applications in drug discovery.
Download or read book Protein Protein Interactions written by Weibo Cai and published by BoD – Books on Demand. This book was released on 2012-03-30 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are indispensable players in virtually all biological events. The functions of proteins are coordinated through intricate regulatory networks of transient protein-protein interactions (PPIs). To predict and/or study PPIs, a wide variety of techniques have been developed over the last several decades. Many in vitro and in vivo assays have been implemented to explore the mechanism of these ubiquitous interactions. However, despite significant advances in these experimental approaches, many limitations exist such as false-positives/false-negatives, difficulty in obtaining crystal structures of proteins, challenges in the detection of transient PPI, among others. To overcome these limitations, many computational approaches have been developed which are becoming increasingly widely used to facilitate the investigation of PPIs. This book has gathered an ensemble of experts in the field, in 22 chapters, which have been broadly categorized into Computational Approaches, Experimental Approaches, and Others.
