The Experts below are selected from a list of 177 Experts worldwide ranked by ideXlab platform
Willi Hunzlker - One of the best experts on this subject based on the ideXlab platform.
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intracellular Calcium Binding proteins more sites than insights
Trends in Biochemical Sciences, 1991Co-Authors: Claus W Heizmann, Willi HunzlkerAbstract:Abstract Calcium ions as biological regulators exert their effects in part via interaction with a wide variety of intracellular Calcium-Binding proteins. One class of these proteins shares a common Calcium-Binding motif, the EF-hand. A consensus amino acid sequence for this motif has aided the identification of new members of this family of EF-hand proteins, which now has about 170 members. A few of these proteins are present in all cells, whereas the vast majority are expressed in a tissue-specific fashion. The physiological function of a few of these proteins is known to be achieved via a Calcium-dependent interaction with other proteins, thereby regulating their activity. The elucidation of the interactions and functions of the majority of these proteins remains a challenging task for the coming years.
Jenny J. Yang - One of the best experts on this subject based on the ideXlab platform.
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Analysis and Evaluation of Rational Designed Calcium Binding Sites in CD2
Peptides: The Wave of the Future, 2020Co-Authors: Wei Yang, Jenny J. YangAbstract:Calcium functions as a second messenger. It regulates different biological systems by interaction with proteins with different affinities in different biological environments. Calcium and Calcium-Binding proteins play central roles in intracellular signal transduction pathways and are associated with a wide-range of effects in health and disease [1]. To reveal the key factors for the Calcium Binding in proteins, rational design of de novo Calcium-Binding proteins has been carried out to overcome the drawbacks of natural Calcium-Binding proteins such as metal-metal interactions and conformational changes. Establishments of the parameters in programs and criteria in screening the output from the computer are the keys for successful design.
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Identifying and Designing of Calcium Binding Sites in Proteins by Computational Algorithm
Computational Studies Nanotechnology and Solution Thermodynamics of Polymer Systems, 2020Co-Authors: Wei Yang, Homme W. Hellinga, Michelle Pu, Jenny J. YangAbstract:Our studies for the identification of the natural Calcium Binding sites with both classic and pseudo EF-hand motifs in three EF-hand proteins have shown that natural Calcium Binding sites can be accurately relocated with Dezymer using a set of geometric descriptions of an ideal pentagonal bipyramid. The success of each constructed site can be ranked by the relative U(p) values. The searched native-like sites in three EF-hand proteins have the smallest deviation from the target geometry. Our work indicates that a useful method for searching Calcium-Binding sites in proteins has been established. It is possible to use established parameters to design novel Calcium Binding proteins.
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Encyclopedia of Inorganic and Bioinorganic Chemistry - Calcium-Binding Proteins
Encyclopedia of Inorganic and Bioinorganic Chemistry, 2011Co-Authors: Jenny J. Yang, Wei YangAbstract:Ca2+ is an important second messenger in the regulation of cell life cycle in addition to being an essential component in biomineralization. Ca2+ mediates its action in regulation by Binding to Ca2+ receptors/proteins that in turn regulate signal transduction, enzymatic activity, and protein stability. During the past few years, owing to the fast progress in genomic information and structural biological studies, our understanding of Calcium-Binding proteins has been greatly expanded. Since 1991, the structures of Calcium-Binding proteins have been extended to more than 1000 today and Calcium-Binding proteins are found in every cellular compartment. In this article, we will first summarize the current knowledge about the common properties of Calcium-Binding proteins. We then will highlight recent developments in structural biology and biological functions of Calcium-Binding proteins. Keywords: Calcium-Binding proteins; metalloproteins; EF-hand; calmodulin; conformational change; protein–protein interaction; extracellular Calcium-Binding proteins; Calcium signaling, Calcium homeostasis; trigger proteins; biometals; signal transduction
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Predicting Calcium-Binding sites in proteins—A graph theory and geometry approach
Proteins, 2006Co-Authors: Hai Deng, Wei Yang, Guantao Chen, Jenny J. YangAbstract:Identifying Calcium-Binding sites in proteins is one of the first steps towards predicting and understanding the role of Calcium in biological systems for protein structure and function studies. Due to the complexity and irregularity of Calcium-Binding sites, a fast and accurate method for predicting and identifying Calcium-Binding protein is needed. Here we report our development of a new fast algorithm (GG) to detect Calcium-Binding sites. The GG algorithm uses a graph theory algorithm to find oxygen clusters of the protein and a geometric algorithm to identify the center of these clusters. A cluster of four or more oxygen atoms has a high potential for Calcium Binding. High performance with about 90% site sensitivity and 80% site selectivity has been obtained for three datasets containing a total of 123 proteins. The results suggest that a sphere of a certain size with four or more oxygen atoms on the surface and without other atoms inside is necessary and sufficient for quickly identifying the majority of the Calcium-Binding sites with high accuracy. Our finding opens a new avenue to visualize and analyze Calcium-Binding sites in proteins facilitating the prediction of functions from structural genomic information.
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Obtaining site-specific Calcium-Binding affinities of calmodulin.
Protein and Peptide Letters, 2003Co-Authors: Jenny J. Yang, Amy Gawthrop, Yiming YeAbstract:Calmodulin (CaM) is an EF-hand Ca(II)-Binding protein involved in the regulation of many important biological processes. To date, there is a wealth of information available concerning studies to obtain site-specific Calcium Binding affinities of CaM, and further to estimate the cooperativity of Calcium Binding using mutational studies, peptide models, and proteolytic fragmentation. In this paper, we will discuss the energetics of Calcium Binding and the strong relationship between Calcium Binding cooperativity and conformational change. We then explain the difficulty of studying key determinants of Calcium Binding affinity of CaM due to the large change of Calcium Binding affinity upon mutation. Subsequently, we will introduce “grafting” as a novel approach to obtain the site-specific metal Binding properties of calmodulin.
Wei Yang - One of the best experts on this subject based on the ideXlab platform.
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Analysis and Evaluation of Rational Designed Calcium Binding Sites in CD2
Peptides: The Wave of the Future, 2020Co-Authors: Wei Yang, Jenny J. YangAbstract:Calcium functions as a second messenger. It regulates different biological systems by interaction with proteins with different affinities in different biological environments. Calcium and Calcium-Binding proteins play central roles in intracellular signal transduction pathways and are associated with a wide-range of effects in health and disease [1]. To reveal the key factors for the Calcium Binding in proteins, rational design of de novo Calcium-Binding proteins has been carried out to overcome the drawbacks of natural Calcium-Binding proteins such as metal-metal interactions and conformational changes. Establishments of the parameters in programs and criteria in screening the output from the computer are the keys for successful design.
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Identifying and Designing of Calcium Binding Sites in Proteins by Computational Algorithm
Computational Studies Nanotechnology and Solution Thermodynamics of Polymer Systems, 2020Co-Authors: Wei Yang, Homme W. Hellinga, Michelle Pu, Jenny J. YangAbstract:Our studies for the identification of the natural Calcium Binding sites with both classic and pseudo EF-hand motifs in three EF-hand proteins have shown that natural Calcium Binding sites can be accurately relocated with Dezymer using a set of geometric descriptions of an ideal pentagonal bipyramid. The success of each constructed site can be ranked by the relative U(p) values. The searched native-like sites in three EF-hand proteins have the smallest deviation from the target geometry. Our work indicates that a useful method for searching Calcium-Binding sites in proteins has been established. It is possible to use established parameters to design novel Calcium Binding proteins.
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Encyclopedia of Inorganic and Bioinorganic Chemistry - Calcium-Binding Proteins
Encyclopedia of Inorganic and Bioinorganic Chemistry, 2011Co-Authors: Jenny J. Yang, Wei YangAbstract:Ca2+ is an important second messenger in the regulation of cell life cycle in addition to being an essential component in biomineralization. Ca2+ mediates its action in regulation by Binding to Ca2+ receptors/proteins that in turn regulate signal transduction, enzymatic activity, and protein stability. During the past few years, owing to the fast progress in genomic information and structural biological studies, our understanding of Calcium-Binding proteins has been greatly expanded. Since 1991, the structures of Calcium-Binding proteins have been extended to more than 1000 today and Calcium-Binding proteins are found in every cellular compartment. In this article, we will first summarize the current knowledge about the common properties of Calcium-Binding proteins. We then will highlight recent developments in structural biology and biological functions of Calcium-Binding proteins. Keywords: Calcium-Binding proteins; metalloproteins; EF-hand; calmodulin; conformational change; protein–protein interaction; extracellular Calcium-Binding proteins; Calcium signaling, Calcium homeostasis; trigger proteins; biometals; signal transduction
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Predicting Calcium-Binding sites in proteins—A graph theory and geometry approach
Proteins, 2006Co-Authors: Hai Deng, Wei Yang, Guantao Chen, Jenny J. YangAbstract:Identifying Calcium-Binding sites in proteins is one of the first steps towards predicting and understanding the role of Calcium in biological systems for protein structure and function studies. Due to the complexity and irregularity of Calcium-Binding sites, a fast and accurate method for predicting and identifying Calcium-Binding protein is needed. Here we report our development of a new fast algorithm (GG) to detect Calcium-Binding sites. The GG algorithm uses a graph theory algorithm to find oxygen clusters of the protein and a geometric algorithm to identify the center of these clusters. A cluster of four or more oxygen atoms has a high potential for Calcium Binding. High performance with about 90% site sensitivity and 80% site selectivity has been obtained for three datasets containing a total of 123 proteins. The results suggest that a sphere of a certain size with four or more oxygen atoms on the surface and without other atoms inside is necessary and sufficient for quickly identifying the majority of the Calcium-Binding sites with high accuracy. Our finding opens a new avenue to visualize and analyze Calcium-Binding sites in proteins facilitating the prediction of functions from structural genomic information.
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Rational design of a Calcium-Binding protein
Journal of the American Chemical Society, 2003Co-Authors: Wei Yang, Lisa M. Jones, Leanne Isley, Yiming Ye, Anna L. Wilkins, Homme W. Hellinga, Russell Malchow, Mohammed GhaziAbstract:Calcium ions play key roles as structural components in biomineralization and as a second messenger in signaling pathways. We have introduced a de novo designed Calcium-Binding site into the framework of a non-Calcium-Binding protein, domain 1 of CD2. The resulting protein selectively binds Calcium over magnesium with Calcium-Binding affinity comparable to that of natural extracellular Calcium-Binding proteins (Kd of 50 μM). This experiment is the first successful metalloprotein design that has a high coordination number (seven) metal-Binding site constructed into a β-sheet protein. Our results demonstrate the feasibility of designing a single Calcium-Binding site into a host protein, taking into account only local properties of a Calcium-Binding site obtained by a survey of natural Calcium-Binding proteins and chelators. The resulting site exhibits strong metal selectivity, suggesting that it should now be feasible to understand and manipulate signaling processes by designing novel Calcium-modulated prot...
Claus W Heizmann - One of the best experts on this subject based on the ideXlab platform.
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intracellular Calcium Binding proteins more sites than insights
Trends in Biochemical Sciences, 1991Co-Authors: Claus W Heizmann, Willi HunzlkerAbstract:Abstract Calcium ions as biological regulators exert their effects in part via interaction with a wide variety of intracellular Calcium-Binding proteins. One class of these proteins shares a common Calcium-Binding motif, the EF-hand. A consensus amino acid sequence for this motif has aided the identification of new members of this family of EF-hand proteins, which now has about 170 members. A few of these proteins are present in all cells, whereas the vast majority are expressed in a tissue-specific fashion. The physiological function of a few of these proteins is known to be achieved via a Calcium-dependent interaction with other proteins, thereby regulating their activity. The elucidation of the interactions and functions of the majority of these proteins remains a challenging task for the coming years.
Arthur S. Polans - One of the best experts on this subject based on the ideXlab platform.
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[7] Calcium-Binding proteins and their assessment in ocular diseases
Methods in Enzymology, 2020Co-Authors: Arthur S. Polans, Teresa M. Walker, Paul R. Van GinkelAbstract:Publisher Summary Calcium-Binding proteins play critical roles in the normal function and assorted pathologies of many cells including those of ocular origin. Interpretation of the vast array of Calcium signals impinging on the cell depends on spatiotemporal information about the sources of the signals as well as the localization of specific target molecules. Often these cellular targets are Calcium-Binding proteins that alter their configuration on the chelation of Calcium and in turn bind to and alter the activity of other biologically relevant molecules such as enzymes or ion channels. As the concentration of intracellular Calcium diminishes on illumination, guanylate cyclase-activating protein 1 (GCAP1) stimulates guanylate cyclase to synthesize cyclic GMP, thus opening cation channels in the plasma membrane of the photoreceptor cell outer segment and reestablishing the dark resting potential of the cell. Aside from studies of phototransduction, these and other Calcium-Binding proteins are involved in ocular pathologies arising in humans. This chapter presents an assessment of these Calcium-Binding proteins and their role in ocular diseases.
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Methods for the purification and characterization of Calcium-Binding proteins from retina
Techniques in Protein Chemistry, 1995Co-Authors: Arthur S. Polans, Krzysztof Palczewski, Wojciech A. Gorczyca, John W. CrabbAbstract:Publisher Summary More than 200 EF hand Calcium-Binding proteins have been identified; however, the function of only a few is known. This chapter discusses methods that have been used for purifying and characterizing Calcium-Binding proteins from ocular tissues and for determining their Calcium Binding parameters. Several strategies have been provided for the purification and characterization of Calcium-Binding proteins of the EF hand family. Members of this family often can be enriched through Calcium-dependent Binding to a hydrophobic matrix. Although, Calbindin D-28K, for example, does not bind to phenyl-Sepharose, it can be purified through Binding to DEAE-Sepharose in low Calcium. In addition to these relatively soluble Calcium-Binding proteins, other less soluble EF hand proteins (eg. GCAP) can be purified by relatively simple procedures. Such isolation procedures will be of increasing importance for studying signal transduction pathways that involve Calcium. The chapter explains that the procedures are adaptable to a variety of tissues and hopefully will facilitate further investigations of Calcium-Binding proteins.
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Calcium-Binding Proteins in the Retina
Methods in Neurosciences, 1993Co-Authors: Arthur S. Polans, John W. Crabb, Krzysztof PalczewskiAbstract:Publisher Summary This chapter discusses the purification and characterization of some of the major retinal Calcium-Binding proteins, such as recoverin and visinin. It is a fact that Calcium has been implicated in a wide variety of physiological processes. On Binding Calcium, calmodulin becomes able to activate a diverse set of enzymes, including adenylate cyclase, protein kinases, and cyclic nucleotide phosphodiesterases. Other Binding proteins regulate the diffusion and buffering of intracellular Calcium. However, the functions of the majority of Calcium-Binding proteins are unknown. Since these proteins are expressed in a cell-specific manner, they are thought to be involved in specialized functions of the cell. The portions of their sequences not involved in Calcium Binding remain highly conserved, thus suggesting that these regions can be important for interacting with effector molecules. In the retina, Calcium is thought to act as a modulator of light adaptation. Alterations in Calcium concentration affect the recovery phase of the photoresponse as well as the sensitivity of the cell to a flash of light in the presence of background illumination.
