"As key effector units of the cell, understanding structure and function relationships of proteins are integral to explaining physiology and, in turn, pathophysiology. With the cost of drug development soaring and success dwindling, new ways to probe protein function will be at the forefront of innovation. A protein's function is the product of its conformational dynamics, where distinct 3-dimensional conformations of a protein dictate its various effects on the cell. Though highly valuable technologies capable of reporting on protein conformation currently exist, X-ray crystallography and nuclear magnetic resonance among others, their capacity to report on dynamic events and/or in physiologically relevant assay conditions are limited.This thesis describes the development and application of biosensors capable of reporting on protein conformation in live human cells. Biosensors were developed for two classes of protein targets, ion channels - Kir3, and G protein-coupled receptors (GPCR) - FP and AT1R, together representing the targets of a majority of current prescription drugs. The biosensor design was based on bioluminescence resonance energy transfer (BRET) and required the insertion of a bioluminescent protein and a short peptide sequences within the protein of interest. Due to the specific affinity for the peptide sequence of an organic fluorophore, fluorescein biarsenical hairpin binder (FlAsH), the latter could be used as a resonance energy transfer acceptor to probe the different conformations of the protein of interest without disrupting its function.Both panels of biosensors successfully reported on ligand-induced conformational rearrangements in the target proteins and correlated with functional effects. The GPCR biosensors were further applied to enrich our understanding of receptor dimerization and allosteric communication between proteins, in this case, the FP/AT1R heterodimer." --

This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.

Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. - Presents a thorough overview of the latest and emerging methods and technologies for protein study - Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy - Includes computational and machine learning methods - Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins

Protein Interactions as Targets in Drug Discovery, Volume 121, is dedicated to the design of therapeutics, both experimental and computational, that target protein interactions. Chapters in this new release include Trends in structure based drug design with protein targets, From fragment- to peptide-protein interaction: addressing the structural basis of binding using Supervised Molecular Dynamics (SuMD), Protein-protein and protein-ligand interactions: identification of potential inhibitors through computational analysis, Aromatic-aromatic interactions in protein-drug and protein-protein interactions, Role of protein-protein interaction in allosteric drug design within the human methyltransferome, and much more. Integrates experimental and computational methods for studying protein interactions and their modulation by potential therapeutics Contains timely chapters written by well-renown authorities in their field Covers information that is well supported by a number of high quality illustrations, figures and tables Targets a very wide audience of specialists, researchers and students

Vitamin B12, Volume 119 in the Vitamins and Hormones series, highlights new advances in the field, with this new volume presenting interesting chapters written by an international board of authors. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Vitamins and Hormones series Updated release includes the latest information on Vitamin B12

Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases

This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.

The conformational dynamics of an unfolded biopolymer such as a polypeptide or DNA has attracted a significant amount of attention in the context of protein folding and the design of biomimetic technologies. To this end, recent advances in single-molecule experiments have allowed for biomolecules to be probed with an unprecedented level of detail, shedding light on their dynamics. Motivated by the need to interpret experimental data and to help guide future studies, we use concepts from polymer physics, computer simulations, and experimental data to study the timescales in which an unfolded biopolymer undergoes conformational rearrangement. First, we examine the end-to-end loop formation time in the experimentally relevant scenario where the dynamics are probed using a fluorescence probe and quencher. We show that the loop formation time in the experimentally relevant case is quantitatively dissimilar from the predictions of previous theoretical studies that neglect the quenching kinetics, which are often used to interpret experimental data. We additionally find that the loop formation times can be re-casted in a simple, universal dependence that is characteristic of random-coils. Furthermore, deviations from this universal dependence can be used as a sensitive tool for detecting structural order in unfolded biopolymers. We also consider a surface-tethered polymer chain and investigate the rate of a reaction between the free end and the surface. We explore this rate in the reaction-controlled limit and the diffusion-controlled limit, providing evidence for near-universal dependences of the rate in the respective limits. Next, we examine the transit time of end-to-end loop formation in a case study. We find that approximating the end-to-end dynamics as diffusion in a 1D potential of mean force fails dramatically to describe the transit time. Furthermore, we find that the transit time is uninfluenced by the average entropic force imposed by the polymer chain and is well described by a simple free-diffusion model. Finally, we explore the role of internal friction in the dynamics of an unfolded protein. Using simple polymer models that incorporate internal friction as an adjustable free parameter, we mimic typical single-molecule experiments that probe the unfolded state dynamics and make several experimentally verifiable predictions.