Download or read book A Rational Approach to Understanding the Relationship of Sequence Structure and Function in EF Hand Calcium binding Proteins written by Melanie Renee Nelson and published by . This book was released on 1999 with total page 534 pages. Available in PDF, EPUB and Kindle. Book excerpt: EF-hand calcium-binding proteins are a large and diverse family of proteins, involved in many critical biological functions. The members of this family all contain multiple copies of the helix-loop-helix EF-hand motif. How this conserved motif is adapted to a wide-range of structures is not understood, even for the relatively well-studied classical signal transducers such as calmodulin and classical signal modulators such as calbindin D 9k . Calmodulin and calbindin D9k have similar sequences and apo structures, yet respond very differently to the calcium signal. This dissertation uses site-directed mutagenesis to address the question of how two similar proteins such as these can respond so differently to the same signal. The ability of these mutagenesis studies to provide new information about how sequence determines structure in this family depends upon a careful mutant design process, which in turn relies upon the efficient use of the information already available about these proteins. Therefore, the design and implementation of a relational database to organize and interconnect information from the literature with the data about the sequences and structures of EF-hand calcium-binding proteins is presented, and a thorough analysis of the relevant protein structures is performed. Information from the database and the structural analyses is used to design limited-site mutants to test hypotheses about how specific differences in the sequences of calbindin D 9k and calmodulin dictate differences in their structures and properties. Two more extensive multiple-site mutants are also designed, with the ultimate goal of re-engineering the response of calbindin D9k to the calcium signal, and making it more similar to the response exhibited by calmodulin. A structural assay is developed to identify the mutants most likely to have significant structural effects, and the assay is applied to three of the limited-site mutants, culminating in the structure determination of the apo state of one of these mutants, F36G. The structural effects of this mutation are consistent with the hypothesis it was designed to test, but also include perturbations not predicted by the mutant design, illustrating the value of studies such as this in elucidating how the sequence of a protein determines its structure.
Download or read book Calcium Binding Proteins written by Eugene Permyakov and published by John Wiley & Sons. This book was released on 2011-03-21 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: Calcium Binding Proteins explains the unique and highly diverse functions of calcium in biology, which are realized by calcium binding proteins. The structures and physical characteristics of these calcium binding proteins are described, as well as their functions and general patterns of their evolution. Techniques that underlie the description of proteins are discussed, including NMR, circular dichroism, optical rotatory dispersion spectroscopy, calorimetry,and crystallography. The book discusses the patterns of bochmical phenomena such as calcium homeostasis, mineralization, and cell signaling that involve specific proteins. It summarizes ongoing research and presents general hypotheses that help to focus future research, and also provides a conceptual framework and a description of the underlying techniques that permits someone entering the field to become conversant.
Download or read book Calcium Binding Protein Protocols written by Hans J. Vogel and published by Springer Science & Business Media. This book was released on 2008-02-04 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt: Calcium plays an important role in a wide variety of biological processes. This divalent metal ion can bind to a large number of proteins; by doing so it modifies their biological activity or their stability. Because of its distinct che- cal properties calcium is uniquely suited to act as an on–off switch or as a light dimmer of biological activities. The two books entitled Calcium-Binding Protein Protocols (Volumes I and II) focus on modern experimental analyses and methodologies for the study of calcium-binding proteins. Both extracel- lar and intracellular calcium-binding proteins are discussed in detail. H- ever, proteins involved in calcium handling (e. g. , calcium pumps and calcium channels), fall outside of the scope of these two volumes. Also, calcium-bi- ing proteins involved in bone deposition will not be discussed, as this specific topic has been addressed previously. The focus of these two books is on studies of the calcium-binding proteins and their behavior in vitro and in vivo. The primary emphasis is on protein chemistry and biophysical methods. Many of the methods described will also be applicable to proteins that do not bind calcium. Calcium-Binding Protein Protocols is divided into three main sections. The section entitled Introduction and Reviews provides information on the role of calcium in intracellular secondary messenger activation mechanisms. Mo- over, unique aspects of calcium chemistry and the utilization of calcium in dairy proteins, as well as calcium-binding proteins involved in blood clotting, are addressed.
Download or read book A Comparison of Motif and Homology Methodologies for Protein Structure Determination written by Hooman H. Rashidi and published by . This book was released on 1998 with total page 102 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Probing Functional Diversity of EF hand Calcium Binding Proteins Through Mutant Design and Structural Analysis written by Jonathan H. Sheehan and published by . This book was released on 2006 with total page 122 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many Ca2+ signaling events in cells are mediated by EF-hand calcium-binding proteins, which can be classified as Ca2+ sensors such as calmodulin or signal modulators such as calbindin D9k. This functional categorization correlates with conformational changes upon binding Ca2+. The structural basis for the functional diversity of EF-hand protein was first investigated using centrin, a calmodulin homolog found in microtubule-organizing centers of diverse organisms. The affinities of the C-terminal domain for Ca2+ and for a peptide fragment of one of its targets, Kar1p, were characterized by fluorescence, CD, and NMR spectroscopy. The coupling of the Ca2+ binding-induced shift in the equilibrium between closed and open conformations to interaction with Kar1p suggests that centrin is constitutively bound to Kar1p through its C-terminal domain. This implies Ca2+ sensor activities are mediated by the N-terminal domain. The solution structure of the Ca 2+-loaded N-terminal domain of centrin showed it occupies an open conformation typical of EF-hand Ca2+ sensors. Comparison of the N- and C-terminal domains of centrin reveals a structural and biochemical basis for the domain specificity of interactions with its cellular targets and the distinct nature of centrin relative to other EF-hand proteins. Functional diversity of EF-hand proteins was further investigated using a protein design strategy. The objective was to create calbindomodulin (CBM-1), a calbindin D9k re-engineered with 15 mutations to respond to Ca2+ binding with a conformational change similar to that of calmodulin. Ca 2+-induced changes in CD and fluorescence, combined with the X-ray crystal structure of Ca2+-CBM-1 revealed the anticipated conformational changes with increased hydrophobic surface area relative to the wild-type protein. A nascent but occluded calmodulin-like hydrophobic docking surface was also found. Finally, a mutant incorporating a subset of 8 of the 15 CBM-1 mutations was characterized, the results from which disproved the hypothesis that preformation of the Ca2+-binding site is the discriminating characteristic between Ca2+ sensors versus signal modulators.
Download or read book American Doctoral Dissertations written by and published by . This book was released on 1998 with total page 784 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Calcium binding Proteins 1 written by Hiroshi Kawasaki and published by . This book was released on 1995 with total page 186 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Determining the Site Specific Metal Binding and Structural Properties of EF hand Protein Using Grafting Approach written by Hsiau-Wei Lee and published by . This book was released on 2007 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Calmodulin is an essential EF-hand protein with a helix-loop-helix calcium binding motif. Understanding Ca(II) dependent activation of calmodulin and other EF-hand proteins is limited by Ca(II)-induced conformational change, multiple and cooperative binding of Ca(II) ions, and interactions between the paired EF-hand motifs. The goal of this research project is to probe key determinants for calcium binding properties and pairing interactions at the site specific level using a grafting approach and high resolution NMR. An individual Ca(II) binding site of the EF-hand motifs of calmodulin was grafted into a non-calcium dependent protein, CD2, to bypass limitations associated with natural EF-hand proteins and peptide fragments. Using high resolution NMR, we have shown that the grafted EF-loop III of calmodulin in the host protein retains its native conformation with a strong loop and [beta]-conformation preference. Grafted ligand residues in the engineered protein are directly involved in binding of Ca(II) and La(III). The NMR studies support our hypothesis that both ligand arrangement and dynamic properties play essential role in tuning Ca(II) binding affinities. Using pulse-field diffusion NMR and protein engineering, we further demonstrated that grafted EF- loop remains as a monomer. Although the EF-loop with flanking helices dimerizes in the presence of Ca(II). Additionally, removal of conserved hydrophobic residues at the flanking helices of the EF-hand motif leads to be monomer in the absence and presence of metal ions. Our results suggest that conserved hydrophobic residues are essential for the pair-paired interaction in the coupled EF-hand protein. We have shown that our developed grafting approach can be applied to probe intrinsic Ca(II) binding affinities of different Ca(II) binding sites.
Download or read book Calcium Binding Proteins written by Eugene Permyakov and published by Wiley. This book was released on 2011-01-11 with total page 606 pages. Available in PDF, EPUB and Kindle. Book excerpt: Calcium Binding Proteins explains the unique and highly diverse functions of calcium in biology, which are realized by calcium binding proteins. The structures and physical characteristics of these calcium binding proteins are described, as well as their functions and general patterns of their evolution. Techniques that underlie the description of proteins are discussed, including NMR, circular dichroism, optical rotatory dispersion spectroscopy, calorimetry,and crystallography. The book discusses the patterns of bochmical phenomena such as calcium homeostasis, mineralization, and cell signaling that involve specific proteins. It summarizes ongoing research and presents general hypotheses that help to focus future research, and also provides a conceptual framework and a description of the underlying techniques that permits someone entering the field to become conversant.
Download or read book EF Hand Calcium Binding Proteins Data Library written by and published by . This book was released on with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents the EF-Hand Calcium-Binding Proteins Data Library, a collection of published sequence, structural, functional, and other information about EF-hand calcium-binding proteins and their roles in cellular signal transduction. Includes sequence and structural information and a summary of proteins included. Provides access to a picture gallery and links to related Web sites.
Download or read book Scientific Report written by Scripps Research Institute and published by . This book was released on 1995 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Calcium binding Proteins written by and published by . This book was released on 1994 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Protein Engineering written by Dale L. Oxender and published by . This book was released on 1987 with total page 388 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computational Analysis of Cadherins written by Nancy Carol Hoffman Vosnidou and published by . This book was released on 2002 with total page 422 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cellular adhesion is an essential component of tissue differentiation and maintenance, and is mediated by four major classes of proteins: integrins, selectins, adhesion molecules of the immunoglobulin superfamily and cadherins. Most cells feature a variety of adhesion molecules whose expressions are both temporally and spatially dynamic. Cadherins are a diverse, interesting class of molecules whose members include both the "classical" cadherins (homotypic, homophilic adhesion) and the "non-classical" cadherins (share many sequence and structural similarities but have more extracellular domains) for which there are only gene sequences and whose functions are unknown. The component cadherin domains of the extracellular portion of the protein resemble immunoglobulin folds but have several unique features, including areas of calcium coordination between the domains. Like other calcium-binding proteins, cadherins often exhibit an unusual seven-fold calcium coordination geometry; however, the coordinating ligands are not all part of the same secondary structure, and the binding affinities are fairly low (millimolar). If calcium is absent from the extracellular matrix, a cadherin molecule is not able to participate in cellular adhesion. The project presented in this dissertation utilized various computational methods that both described and quantified interactions postulated from structural studies, and addressed questions that were not answerable using existing experimental techniques. Sequence and structure analysis methods were used to determine relationships between whole cadherin protein sequences as well as between the individual extracellular domains. The presence or absence of key dimerization features, known from structural observations of two cadherins as well as from a Bence-Jones protein fragment, were also studied. A theoretical level dependency study was conducted to ascertain the most appropriate quantum computational method for the study of calcium coordination in cadherins. Because of the fundamental requirement of calcium binding for cadherin function, quantum computational methods were employed to define the characteristics of calcium coordination, analyze the individual calcium coordination states, determine the relative contributions of each ion and each ligand in the coordination schema, determine if there were any cooperativity effects in the calcium binding, and quantify the effects of removing a ligand (simulating a point mutation). The computational results presented in this paper illustrate a theoretical approach to determine cadherin:cadherin interactions, and demonstrate how and why cadherins interact with calcium ions.
Download or read book Rational Design of Novel Calcium binding Proteins written by Wei Yang and published by . This book was released on 2001 with total page 476 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Formalizing Life written by Håkan Viklund and published by . This book was released on 2007 with total page 55 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Calcium binding Protein Protocols written by Hans J. Vogel and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This handbook focuses on modern experimental analyses and methodologies for the study of calcium-binding proteins.
