Geometric Folding Algorithms

Geometric Folding Algorithms
Author: Erik D. Demaine
Publisher: Cambridge University Press
Total Pages: 388
Release: 2007-07-16
Genre: Computers
ISBN: 1107394090

Did you know that any straight-line drawing on paper can be folded so that the complete drawing can be cut out with one straight scissors cut? That there is a planar linkage that can trace out any algebraic curve, or even 'sign your name'? Or that a 'Latin cross' unfolding of a cube can be refolded to 23 different convex polyhedra? Over the past decade, there has been a surge of interest in such problems, with applications ranging from robotics to protein folding. With an emphasis on algorithmic or computational aspects, this treatment gives hundreds of results and over 60 unsolved 'open problems' to inspire further research. The authors cover one-dimensional (1D) objects (linkages), 2D objects (paper), and 3D objects (polyhedra). Aimed at advanced undergraduate and graduate students in mathematics or computer science, this lavishly illustrated book will fascinate a broad audience, from school students to researchers.

RNA Structure and Folding

RNA Structure and Folding
Author: Dagmar Klostermeier
Publisher: Walter de Gruyter
Total Pages: 432
Release: 2013-10-14
Genre: Science
ISBN: 3110284952

While structure-function relationships of proteins have been studied for a long time, structural studies of RNA face additional challenges. Nevertheless, with the continuous discovery of novel RNA molecules with key cellular functions and of novel pathways and interaction networks, the need for structural information of RNA is still increasing. This volume provides an introduction into techniques to assess structure and folding of RNA. Each chapter explains the theoretical background of one technique, and illustrates possibilities and limitations in selected application examples.

Protein Homeostasis Diseases

Protein Homeostasis Diseases
Author: Angel L. Pey
Publisher: Academic Press
Total Pages: 450
Release: 2020-02-13
Genre: Science
ISBN: 0128191333

Protein Homeostasis Diseases: Mechanisms and Novel Therapies offers an interdisciplinary examination of the fundamental aspects, biochemistry and molecular biology of protein homeostasis disease, including the use of natural and pharmacological small molecules to treat common and rare protein homeostasis disorders. Contributions from international experts discuss the biochemical and genetic components of protein homeostasis disorders, the mechanisms by which genetic variants may cause loss-of-function and gain-of-toxic-function, and how natural ligands can restore protein function and homeostasis in genetic diseases. Applied chapters provide guidance on employing high throughput sequencing and screening methodologies to develop pharmacological chaperones and repurpose approved drugs to treat protein homeostasis disorders. Provides an interdisciplinary examination of protein homeostasis disorders, with an emphasis on treatment strategies employing small natural and pharmacological ligands Offers applied approaches in employing high throughput sequencing and screening to develop pharmacological chaperones to treat protein homeostasis disease Gathers expertise from a range of international chapter authors who work across various biological methods and disease specific disciplines of relevance

Unfolded

Unfolded
Author: Petra Schmidt
Publisher: Walter de Gruyter
Total Pages: 256
Release: 2012-11-05
Genre: Design
ISBN: 3034609051

In Unfolded—Paper in Design, Art, Architecture and Industry paper conquers the third dimension and demonstrates the undreamed-of possibilities it holds today for lightweight construction, product design, fashion and art. From "Paper", the collection of bags by Stefan Diez, to Konstantin Grcic’s paper models and the scented paper garments of Issey Miyake, this book presents paper as a high-quality contemporary and ecological material. An enormous selection of projects, the lavish design and numerous illustrations provide designers with invaluable inspiration for their work. The content core of the book is a comprehensive list of state-of-the-art paper products and innovative paper technologies, supporting designers in their everyday work with detailed information on the "high-tech" material paper. From Japanese washi paper and paper foam, to ceramic paper and carbon fiber paper, Unfolded presents the latest in research and development, as well as the most important methods and technologies in handcrafts and industry.

Unfolded Proteins

Unfolded Proteins
Author:
Publisher: Elsevier
Total Pages: 422
Release: 2002-11-04
Genre: Science
ISBN: 0080524524

A variety of complementary techniques and approaches have been used to characterize peptide and protein unfolding induced by temperature, pressure, and solvent. Volume 62, Unfolded Proteins, assembles these complementary views to develop a more complete picture of denatured peptides and proteins. The unifying observation common to all chapters is the detection of preferred backbone confirmations in experimentally accessible unfolded states. Peptide and protein unfolding induced by temperature, pressure, and solvent Denatured peptides and proteins Detection of preferred backbone confirmations in experimentally accessible unfolded states

Unfolded Proteins

Unfolded Proteins
Author: Trevor P. Creamer
Publisher: Nova Publishers
Total Pages: 330
Release: 2008
Genre: Science
ISBN: 9781604561074

The word revolution has a number of definitions (The American Heritage Dictionary, 2006). The one most pertinent to this series and volume is 'a sudden or momentous change in a situation'. Recent years have seen an unprecedented explosion of interest in unfolded proteins in all of their various forms. Coupled with this increase in interest we have seen momentous changes in the way unfolded proteins are viewed. Two particular paradigms have come under close scrutiny: unfolded proteins are disordered random coils devoid of persistent structure, and protein function first requires protein structure. The first of these is currently a hotly debated subject. The second paradigm we can safely claim has been overturned. There is a second definition of revolution that is quite relevant to a significant portion of the work reviewed herein, in particular those chapters dealing with local and persistent structure in unfolded proteins. That definition is 'a turning or rotational motion about an axis' (The American Heritage Dictionary, 2006). About four decades ago, Charles Tanford (1968) demonstrated that highly denatured proteins possess hydrodynamic properties consistent with Paul Flory's random coil (Flory, 1969). Given that the Flory random coil definition included the stipulation that conformers making up the denatured state ensemble would differ in energy by just a few kT, there has been the assumption that denatured states must therefore be completely random in nature with no persistent structure or biases towards particular conformers. Notably however, Tanford did note the random coil-like hydrodynamic data he obtained did not necessarily rule out the presence of structure in denatured proteins (Tanford, 1968). Around the same time, Sam Krimm and M. Lois Tiffany noted that the CD spectra they obtained for proteins in the presence of high concentration of chemical denaturants had similarities to spectra obtained for homopolymers of proline, lysine, and glutamic acid in water (Tiffany and Krimm, 1968a, 1968b, 1973, 1974). Homopolymers of these residues were known to adopt the left-handed polyproline II conformation, leading Tiffany and Krimm to hypothesise that highly denatured proteins possess significant polyproline II helix content. Of these two views, that espousing the lack of structure in denatured proteins became more widely adopted and was, over time, adopted as a central paradigm in protein folding. As several of the chapters in this volume note, a Tiffany and Krimm-like view appears to be, to some extent, the more correct one. The level to which it is correct is still unknown, although it is clear that the polyproline II helical conformation is not the only, perhaps not even the most common, persistent conformation present in unfolded proteins. Thus we have come through a full circle or revolution. (from the preface)

Molecular Self-Assembly

Molecular Self-Assembly
Author: Alex Li Dequan
Publisher: CRC Press
Total Pages: 464
Release: 2012-12-20
Genre: Science
ISBN: 9814364312

In the past several decades, molecular self-assembly has emerged as one of the main themes in chemistry, biology, and materials science. This book compiles and details cutting-edge research in molecular assemblies ranging from self-organized peptide nanostructures and DNA-chromophore foldamers to supramolecular systems and metal-directed assemblies

Modern Thermodynamics for Chemists and Biochemists

Modern Thermodynamics for Chemists and Biochemists
Author: Dennis Sherwood
Publisher: Oxford University Press
Total Pages: 928
Release: 2018-05-11
Genre: Science
ISBN: 0191085820

Thermodynamics is fundamental to university and college curricula in chemistry, physics, engineering and many life sciences around the world. It is also notoriously difficult for students to understand, learn and apply. What makes this book different, and special, is the clarity of the text. The writing style is fluid, natural and lucid, and everything is explained in a logical and transparent manner. Thermodynamics is a deep, and important, branch of science, and this book does not make it "easy". But it does make it intelligible. This book introduces a new, 'Fourth Law' of Thermodynamics' based on the notion of Gibbs free energy, which underpins almost every application of thermodynamics and which the authors claim is worthy of recognition as a 'law'. The last four chapters bring thermodynamics into the twenty-first century, dealing with bioenergetics (how living systems capture and use free energy), macromolecule assembly (how proteins fold), and macromolecular aggregation (how, for example, virus capsids assemble). This is of great current relevance to students of biochemistry, biochemical engineering and pharmacy, and is covered in very few other texts on thermodynamics. The book also contains many novel and effective examples, such as the explanation of why friction is irreversible, the proof of the depression of the freezing point, and the explanation of the biochemical standard state.

Structure And Action Of Molecular Chaperones: Machines That Assist Protein Folding In The Cell

Structure And Action Of Molecular Chaperones: Machines That Assist Protein Folding In The Cell
Author: Lila M Gierasch
Publisher: World Scientific
Total Pages: 328
Release: 2016-08-08
Genre: Science
ISBN: 9814749346

This unique volume reviews the beautiful architectures and varying mechanical actions of the set of specialized cellular proteins called molecular chaperones, which provide essential kinetic assistance to processes of protein folding and unfolding in the cell. Ranging from multisubunit ring-shaped chaperonin and Hsp100 machines that use their central cavities to bind and compartmentalize action on proteins, to machines that use other topologies of recognition — binding cellular proteins in an archway or at the surface of a 'clamp' or at the surface of a globular assembly — the structures show us the ways and means the cell has devised to assist its major effectors, proteins, to reach and maintain their unique active forms, as well as, when required, to disrupt protein structure in order to remodel or degrade. Each type of chaperone is beautifully illustrated by X-ray and EM structure determinations at near- atomic level resolution and described by a leader in the study of the respective family. The beauty of what Mother Nature has devised to accomplish essential assisting actions for proteins in vivo is fully appreciable.