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Li D, Kirberger M, Qiao J, Gui Z, Xue S, Pu F, Jiang J, Xu Y, Tan S, Salarian M, Ibhagui O, Hekmatyar K, Yang JJ. Protein MRI Contrast Agents as an Effective Approach for Precision Molecular Imaging. Invest Radiol 2024; 59:170-186. [PMID: 38180819 DOI: 10.1097/rli.0000000000001057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2024]
Abstract
ABSTRACT Cancer and other acute and chronic diseases are results of perturbations of common molecular determinants in key biological and signaling processes. Imaging is critical for characterizing dynamic changes in tumors and metastases, the tumor microenvironment, tumor-stroma interactions, and drug targets, at multiscale levels. Magnetic resonance imaging (MRI) has emerged to be a primary imaging modality for both clinical and preclinical applications due to its advantages over other modalities, including sensitivity to soft tissues, nondepth limitations, and the use of nonionizing radiation. However, extending the application of MRI to achieve both qualitative and quantitative precise molecular imaging with the capability to quantify molecular biomarkers for early detection, staging, and monitoring therapeutic treatment requires the capacity to overcome several major challenges including the trade-off between metal-binding affinity and relaxivity, which is an issue frequently associated with small chelator contrast agents. In this review, we will introduce the criteria of ideal contrast agents for precision molecular imaging and discuss the relaxivity of current contrast agents with defined first shell coordination water molecules. We will then report our advances in creating a new class of protein-targeted MRI contrast agents (ProCAs) with contributions to relaxivity largely derived from the secondary sphere and correlation time. We will summarize our rationale, design strategy, and approaches to the development and optimization of our pioneering ProCAs with desired high relaxivity, metal stability, and molecular biomarker-targeting capability, for precision MRI. From first generation (ProCA1) to third generation (ProCA32), we have achieved dual high r1 and r2 values that are 6- to 10-fold higher than clinically approved contrast agents at magnetic fields of 1.5 T, and their relaxivity values at high field are also significantly higher, which enables high resolution during small animal imaging. Further engineering of multiple targeting moieties enables ProCA32 agents that have strong biomarker-binding affinity and specificity for an array of key molecular biomarkers associated with various chronic diseases, while maintaining relaxation and exceptional metal-binding and selectivity, serum stability, and resistance to transmetallation, which are critical in mitigating risks associated with metal toxicity. Our leading product ProCA32.collagen has enabled the first early detection of liver metastasis from multiple cancers at early stages by mapping the tumor environment and early stage of fibrosis from liver and lung in vivo, with strong translational potential to extend to precision MRI for preclinical and clinical applications for precision diagnosis and treatment.
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Affiliation(s)
- Dongjun Li
- From the Center for Diagnostics and Therapeutics, Advanced Translational Imaging Facility, Department of Chemistry, Georgia State University, Atlanta, GA (D.L., M.K., J.Q., Z.G., S.X., P.F., J.J., S.T., M.S., O.I., K.H., J.J.Y.); and InLighta BioSciences, LLC, Marietta, GA (Y.X., J.J.Y)
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Tang S, Deng X, Jiang J, Kirberger M, Yang JJ. Design of Calcium-Binding Proteins to Sense Calcium. Molecules 2020; 25:molecules25092148. [PMID: 32375353 PMCID: PMC7248937 DOI: 10.3390/molecules25092148] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 01/25/2023] Open
Abstract
Calcium controls numerous biological processes by interacting with different classes of calcium binding proteins (CaBP’s), with different affinities, metal selectivities, kinetics, and calcium dependent conformational changes. Due to the diverse coordination chemistry of calcium, and complexity associated with protein folding and binding cooperativity, the rational design of CaBP’s was anticipated to present multiple challenges. In this paper we will first discuss applications of statistical analysis of calcium binding sites in proteins and subsequent development of algorithms to predict and identify calcium binding proteins. Next, we report efforts to identify key determinants for calcium binding affinity, cooperativity and calcium dependent conformational changes using grafting and protein design. Finally, we report recent advances in designing protein calcium sensors to capture calcium dynamics in various cellular environments.
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Affiliation(s)
- Shen Tang
- Department of Chemistry, Center for Diagnostics and Therapeutics and Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA; (S.T.); (X.D.); (J.J.)
| | - Xiaonan Deng
- Department of Chemistry, Center for Diagnostics and Therapeutics and Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA; (S.T.); (X.D.); (J.J.)
| | - Jie Jiang
- Department of Chemistry, Center for Diagnostics and Therapeutics and Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA; (S.T.); (X.D.); (J.J.)
| | - Michael Kirberger
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA 30043, USA;
| | - Jenny J. Yang
- Department of Chemistry, Center for Diagnostics and Therapeutics and Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA; (S.T.); (X.D.); (J.J.)
- Correspondence: ; Tel.: +1-404-413-5520
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Herrera MG, Noguera ME, Sewell KE, Agudelo Suárez WA, Capece L, Klinke S, Santos J. Structure of the Human ACP-ISD11 Heterodimer. Biochemistry 2019; 58:4596-4609. [PMID: 31664822 DOI: 10.1021/acs.biochem.9b00539] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, the mammalian mitochondrial protein complex for iron-sulfur cluster assembly has been the focus of important studies. This is partly because of its high degree of relevance in cell metabolism and because mutations of the involved proteins are the cause of several human diseases. Cysteine desulfurase NFS1 is the key enzyme of the complex. At present, it is well-known that the active form of NFS1 is stabilized by the small protein ISD11. In this work, the structure of the human mitochondrial ACP-ISD11 heterodimer was determined at 2.0 Å resolution. ACP-ISD11 forms a cooperative unit stabilized by several ionic interactions, hydrogen bonds, and apolar interactions. The 4'-phosphopantetheine-acyl chain, which is covalently bound to ACP, interacts with several residues of ISD11, modulating together with ACP the foldability of ISD11. Recombinant human ACP-ISD11 was able to interact with the NFS1 desulfurase, thus yielding an active enzyme, and the NFS1/ACP-ISD11 core complex was activated by frataxin and ISCU proteins. Internal motions of ACP-ISD11 were studied by molecular dynamics simulations, showing the persistence of the interactions between both protein chains. The conformation of the dimer is similar to that found in the context of the (NFS1/ACP-ISD11)2 supercomplex core, which contains the Escherichia coli ACP instead of the human variant. This fact suggests a sequential mechanism for supercomplex consolidation, in which the ACP-ISD11 complex may fold independently and, after that, the NFS1 dimer would be stabilized.
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Affiliation(s)
- María Georgina Herrera
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Intendente Güiraldes 2160-Ciudad Universitaria , C1428EGA Buenos Aires , Argentina
| | - Martín Ezequiel Noguera
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Intendente Güiraldes 2160-Ciudad Universitaria , C1428EGA Buenos Aires , Argentina.,Instituto de Química y Fisicoquímica Biológicas , Dr. Alejandro Paladini, Universidad de Buenos Aires, CONICET , Junín 956 , C1113AAD Buenos Aires , Argentina
| | - Karl Ellioth Sewell
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Intendente Güiraldes 2160-Ciudad Universitaria , C1428EGA Buenos Aires , Argentina
| | - William Armando Agudelo Suárez
- Fundación Instituto de Inmunología de Colombia (FIDIC) , Av. 50 No. 26-20 , Bogotá D.C. , Colombia.,Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE CONICET) , C1428EGA Buenos Aires , Argentina
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE CONICET) , C1428EGA Buenos Aires , Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir , IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM , Av. Patricias Argentinas 435 , C1405BWE Buenos Aires , Argentina
| | - Javier Santos
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Intendente Güiraldes 2160-Ciudad Universitaria , C1428EGA Buenos Aires , Argentina
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Reddish FN, Miller CL, Gorkhali R, Yang JJ. Calcium Dynamics Mediated by the Endoplasmic/Sarcoplasmic Reticulum and Related Diseases. Int J Mol Sci 2017; 18:E1024. [PMID: 28489021 PMCID: PMC5454937 DOI: 10.3390/ijms18051024] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 04/28/2017] [Accepted: 05/01/2017] [Indexed: 12/17/2022] Open
Abstract
The flow of intracellular calcium (Ca2+) is critical for the activation and regulation of important biological events that are required in living organisms. As the major Ca2+ repositories inside the cell, the endoplasmic reticulum (ER) and the sarcoplasmic reticulum (SR) of muscle cells are central in maintaining and amplifying the intracellular Ca2+ signal. The morphology of these organelles, along with the distribution of key calcium-binding proteins (CaBPs), regulatory proteins, pumps, and receptors fundamentally impact the local and global differences in Ca2+ release kinetics. In this review, we will discuss the structural and morphological differences between the ER and SR and how they influence localized Ca2+ release, related diseases, and the need for targeted genetically encoded calcium indicators (GECIs) to study these events.
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Affiliation(s)
- Florence N Reddish
- Department of Chemistry, Center for Diagnostics and Therapeutics (CDT), Georgia State University, Atlanta, GA 30303, USA.
| | - Cassandra L Miller
- Department of Chemistry, Center for Diagnostics and Therapeutics (CDT), Georgia State University, Atlanta, GA 30303, USA.
| | - Rakshya Gorkhali
- Department of Chemistry, Center for Diagnostics and Therapeutics (CDT), Georgia State University, Atlanta, GA 30303, USA.
| | - Jenny J Yang
- Department of Chemistry, Center for Diagnostics and Therapeutics (CDT), Georgia State University, Atlanta, GA 30303, USA.
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Tang S, Reddish F, Zhuo Y, Yang JJ. Fast kinetics of calcium signaling and sensor design. Curr Opin Chem Biol 2015; 27:90-7. [PMID: 26151819 DOI: 10.1016/j.cbpa.2015.06.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 06/11/2015] [Accepted: 06/11/2015] [Indexed: 12/25/2022]
Abstract
Fast calcium signaling is regulated by numerous calcium channels exhibiting high spatiotemporal profiles which are currently measured by fluorescent calcium sensors. There is still a strong need to improve the kinetics of genetically encoded calcium indicators (sensors) to capture calcium dynamics in the millisecond time frame. In this review, we summarize several major fast calcium signaling pathways and discuss the recent developments and application of genetically encoded calcium indicators to detect these pathways. A new class of genetically encoded calcium indicators designed with site-directed mutagenesis on the surface of beta-barrel fluorescent proteins to form a pentagonal bipyramidal-like calcium binding domain dramatically accelerates calcium binding kinetics. Furthermore, novel genetically encoded calcium indicators with significantly increased fluorescent lifetime change are advantageous in deep-field imaging with high light-scattering and notable morphology change.
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Affiliation(s)
- Shen Tang
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, United States
| | - Florence Reddish
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, United States
| | - You Zhuo
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, United States
| | - Jenny J Yang
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, United States.
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Zhang C, Zhuo Y, Moniz HA, Wang S, Moremen KW, Prestegard JH, Brown EM, Yang JJ. Direct determination of multiple ligand interactions with the extracellular domain of the calcium-sensing receptor. J Biol Chem 2014; 289:33529-42. [PMID: 25305020 DOI: 10.1074/jbc.m114.604652] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Numerous in vivo functional studies have indicated that the dimeric extracellular domain (ECD) of the CaSR plays a crucial role in regulating Ca(2+) homeostasis by sensing Ca(2+) and l-Phe. However, direct interaction of Ca(2+) and Phe with the ECD of the receptor and the resultant impact on its structure and associated conformational changes have been hampered by the large size of the ECD, its high degree of glycosylation, and the lack of biophysical methods to monitor weak interactions in solution. In the present study, we purified the glycosylated extracellular domain of calcium-sensing receptor (CaSR) (ECD) (residues 20-612), containing either complex or high mannose N-glycan structures depending on the host cell line employed for recombinant expression. Both glycosylated forms of the CaSR ECD were purified as dimers and exhibit similar secondary structures with ∼ 50% α-helix, ∼ 20% β-sheet content, and a well buried Trp environment. Using various spectroscopic methods, we have shown that both protein variants bind Ca(2+) with a Kd of 3.0-5.0 mm. The local conformational changes of the proteins induced by their interactions with Ca(2+) were visualized by NMR with specific (15)N Phe-labeled forms of the ECD. Saturation transfer difference NMR approaches demonstrated for the first time a direct interaction between the CaSR ECD and l-Phe. We further demonstrated that l-Phe increases the binding affinity of the CaSR ECD for Ca(2+). Our findings provide new insights into the mechanisms by which Ca(2+) and amino acids regulate the CaSR and may pave the way for exploration of the structural properties of CaSR and other members of family C of the GPCR superfamily.
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Affiliation(s)
- Chen Zhang
- From the Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303
| | - You Zhuo
- From the Department of Chemistry
| | - Heather A Moniz
- the Department of Biochemistry and Molecular Biology and the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, and
| | - Shuo Wang
- the Department of Biochemistry and Molecular Biology and the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, and
| | - Kelley W Moremen
- the Department of Biochemistry and Molecular Biology and the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, and
| | - James H Prestegard
- the Department of Biochemistry and Molecular Biology and the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, and
| | - Edward M Brown
- the Department of Medicine, Division of Endocrinology, Brigham and Women's Hospital, Boston, Massachusetts 02115
| | - Jenny J Yang
- From the Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303,
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7
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Myoplasmic resting Ca2+ regulation by ryanodine receptors is under the control of a novel Ca2+-binding region of the receptor. Biochem J 2014; 460:261-71. [PMID: 24635445 PMCID: PMC4019983 DOI: 10.1042/bj20131553] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Passive SR (sarcoplasmic reticulum) Ca2+ leak through the RyR (ryanodine receptor) plays a critical role in the mechanisms that regulate [Ca2+]rest (intracellular resting myoplasmic free Ca2+ concentration) in muscle. This process appears to be isoform-specific as expression of either RyR1 or RyR3 confers on myotubes different [Ca2+]rest. Using chimaeric RyR3–RyR1 receptors expressed in dyspedic myotubes, we show that isoform-dependent regulation of [Ca2+]rest is primarily defined by a small region of the receptor encompassing amino acids 3770–4007 of RyR1 (amino acids 3620–3859 of RyR3) named as the CLR (Ca2+ leak regulatory) region. [Ca2+]rest regulation by the CLR region was associated with alteration of RyRs’ Ca2+-activation profile and changes in SR Ca2+-leak rates. Biochemical analysis using Tb3+-binding assays and intrinsic tryptophan fluorescence spectroscopy of purified CLR domains revealed that this determinant of RyRs holds a novel Ca2+-binding domain with conformational properties that are distinctive to each isoform. Our data suggest that the CLR region provides channels with unique functional properties that modulate the rate of passive SR Ca2+ leak and confer on RyR1 and RyR3 distinctive [Ca2+]rest regulatory properties. The identification of a new Ca2+-binding domain of RyRs with a key modulatory role in [Ca2+]rest regulation provides new insights into Ca2+-mediated regulation of RyRs. This paper reports the finding of a new class of Ca2+-binding domain of intracellular Ca2+ channels from muscle cells. This domain provides channels with distinctive properties that result in channel-specific modulation of the intracellular resting Ca2+ concentration.
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Xue S, Qiao J, Pu F, Cameron M, Yang JJ. Design of a novel class of protein-based magnetic resonance imaging contrast agents for the molecular imaging of cancer biomarkers. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2013; 5:163-79. [PMID: 23335551 DOI: 10.1002/wnan.1205] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Magnetic resonance imaging (MRI) of disease biomarkers, especially cancer biomarkers, could potentially improve our understanding of the disease and drug activity during preclinical and clinical drug treatment and patient stratification. MRI contrast agents with high relaxivity and targeting capability to tumor biomarkers are highly required. Extensive work has been done to develop MRI contrast agents. However, only a few limited literatures report that protein residues can function as ligands to bind Gd(3+) with high binding affinity, selectivity, and relaxivity. In this paper, we focus on reporting our current progress on designing a novel class of protein-based Gd(3+) MRI contrast agents (ProCAs) equipped with several desirable capabilities for in vivo application of MRI of tumor biomarkers. We will first discuss our strategy for improving the relaxivity by a novel protein-based design. We then discuss the effect of increased relaxivity of ProCAs on improving the detection limits for MRI contrast agent, especially for in vivo application. We will further report our efforts to improve in vivo imaging capability and our achievement in molecular imaging of cancer biomarkers with potential preclinical and clinical applications.
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Affiliation(s)
- Shenghui Xue
- Departments of Chemistry and Biology, Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, GA, USA
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Wei L, Li S, Yang J, Ye Y, Zou J, Wang L, Long R, Zurkiya O, Zhao T, Johnson J, Qiao J, Zhou W, Castiblanco A, Maor N, Chen Y, Mao H, Hu X, Yang JJ, Liu ZR. Protein-based MRI contrast agents for molecular imaging of prostate cancer. Mol Imaging Biol 2011; 13:416-423. [PMID: 20574851 DOI: 10.1007/s11307-010-0342-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE The purpose of this study was to demonstrate a novel protein-based magnetic resonance imaging (MRI) contrast agent that has the capability of targeting prostate cancer and which provides high-sensitivity MR imaging in tumor cells and mouse models. PROCEDURE A fragment of gastrin-releasing peptide (GRP) was fused into a protein-based MRI contrast agent (ProCA1) at different regions. MR imaging was obtained in both tumor cells (PC3 and H441) and a tumor mouse model administrated with ProCA1.GRP. RESULTS PC3 and DU145 cells treated with ProCA1.GRPs exhibited enhanced signal in MRI. Intratumoral injection of ProCA1.GRP in a PC3 tumor model displayed enhanced MRI signal. The contrast agent was retained in the PC3 tumor up to 48 h post-injection. CONCLUSIONS Protein-based MRI contrast agent with tumor targeting modality can specifically target GRPR-positive prostate cancer. Intratumoral injection of the ProCA1 agent in the prostate cancer mouse model verified the targeting capability of ProCA1.GRP and showed a prolonged retention time in tumors.
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Affiliation(s)
- Lixia Wei
- Department of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Shunyi Li
- Department of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Jianhua Yang
- Department of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Yiming Ye
- Biotechnology Core Facility Branch, Center for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Jin Zou
- Department of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Liya Wang
- Department of Radiology, Emory University, Atlanta, GA, 30322, USA
| | - Robert Long
- Department of Radiology, Emory University, Atlanta, GA, 30322, USA
| | - Omar Zurkiya
- Department of Biomedical Engineering, Emory University, Atlanta, GA, 30322, USA
| | - Tiejun Zhao
- Department of Biomedical Engineering, Emory University, Atlanta, GA, 30322, USA
| | - Julian Johnson
- Department of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Jingjuan Qiao
- Department of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Wangda Zhou
- Department of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Adriana Castiblanco
- Department of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Natalie Maor
- Department of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Yanyi Chen
- Department of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Hui Mao
- Department of Radiology, Emory University, Atlanta, GA, 30322, USA
| | - Xiaoping Hu
- Department of Biomedical Engineering, Emory University, Atlanta, GA, 30322, USA
| | - Jenny J Yang
- Department of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA.
| | - Zhi-Ren Liu
- Department of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA
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Kirberger M, Wang X, Zhao K, Tang S, Chen G, Yang JJ. Integration of Diverse Research Methods to Analyze and Engineer Ca-Binding Proteins: From Prediction to Production. Curr Bioinform 2010; 5:68-80. [PMID: 20802832 PMCID: PMC2927018 DOI: 10.2174/157489310790596358] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In recent years, increasingly sophisticated computational and bioinformatics tools have evolved for the analyses of protein structure, function, ligand interactions, modeling and energetics. This includes the development of algorithms to recursively evaluate side-chain rotamer permutations, identify regions in a 3D structure that meet some set of search parameters, calculate and minimize energy values, and provide high-resolution visual tools for theoretical modeling. Here we discuss the interdependency between different areas of bioinformatics, the evolution of different algorithm design approaches, and finally the transition from theoretical models to real-world design and application as they relate to Ca(2+)-binding proteins. Within this context, it has become evident that significant pre-experimental design and calculations can be modeled through computational methods, thus eliminating potentially unproductive research and increasing our confidence in the correlation between real and theoretical models. Moving from prediction to production, it is anticipated that bioinformatics tools will play an increasingly significant role in research and development, improving our ability to both understand the physiological roles of Ca(2+) and other metals and to extend that knowledge to the design of function-specific synthetic proteins capable of fulfilling different roles in medical diagnostics and therapeutics.
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Affiliation(s)
- Michael Kirberger
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
| | - Xue Wang
- Department of Computer Science, Georgia State University, Atlanta, Georgia
| | - Kun Zhao
- Department of Mathematics and Statistics, Georgia State University, Atlanta, Georgia, USA
| | - Shen Tang
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
| | - Guantao Chen
- Department of Computer Science, Georgia State University, Atlanta, Georgia
- Department of Mathematics and Statistics, Georgia State University, Atlanta, Georgia, USA
| | - Jenny J. Yang
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
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Maniccia AW, Yang W, Johnson JA, Li S, Tjong H, Zhou HX, Shaket LA, Yang JJ. Inverse tuning of metal binding affinity and protein stability by altering charged coordination residues in designed calcium binding proteins. PMC BIOPHYSICS 2009; 2:11. [PMID: 20025729 PMCID: PMC2816670 DOI: 10.1186/1757-5036-2-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 12/21/2009] [Indexed: 11/10/2022]
Abstract
Ca(2+ )binding proteins are essential for regulating the role of Ca(2+ )in cell signaling and maintaining Ca(2+ )homeostasis. Negatively charged residues such as Asp and Glu are often found in Ca(2+ )binding proteins and are known to influence Ca(2+ )binding affinity and protein stability. In this paper, we report a systematic investigation of the role of local charge number and type of coordination residues in Ca(2+ )binding and protein stability using de novo designed Ca(2+ )binding proteins. The approach of de novo design was chosen to avoid the complications of cooperative binding and Ca(2+)-induced conformational change associated with natural proteins. We show that when the number of negatively charged coordination residues increased from 2 to 5 in a relatively restricted Ca(2+)-binding site, Ca(2+ )binding affinities increased by more than 3 orders of magnitude and metal selectivity for trivalent Ln(3+ )over divalent Ca(2+ )increased by more than 100-fold. Additionally, the thermal transition temperatures of the apo forms of the designed proteins decreased due to charge repulsion at the Ca(2+ )binding pocket. The thermal stability of the proteins was regained upon Ca(2+ )and Ln(3+ )binding to the designed Ca(2+ )binding pocket. We therefore observe a striking tradeoff between Ca(2+)/Ln(3+ )affinity and protein stability when the net charge of the coordination residues is varied. Our study has strong implications for understanding and predicting Ca(2+)-conferred thermal stabilization of natural Ca(2+ )binding proteins as well as for designing novel metalloproteins with tunable Ca(2+ )and Ln(3+ )binding affinity and selectivity.PACS codes: 05.10.-a.
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Affiliation(s)
- Anna Wilkins Maniccia
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
| | - Wei Yang
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Renmin Road 5625, Changchun, Jilin 130022, PR China
| | - Julian A Johnson
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
| | - Shunyi Li
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
| | - Harianto Tjong
- Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Lev A Shaket
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
| | - Jenny J Yang
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
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Li S, Yang W, Maniccia AW, Barrow D, Tjong H, Zhou HX, Yang JJ. Rational design of a conformation-switchable Ca2+- and Tb3+-binding protein without the use of multiple coupled metal-binding sites. FEBS J 2008; 275:5048-61. [PMID: 18785925 DOI: 10.1111/j.1742-4658.2008.06638.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Ca2+, as a messenger of signal transduction, regulates numerous target molecules via Ca2+-induced conformational changes. Investigation into the determinants for Ca2+-induced conformational change is often impeded by cooperativity between multiple metal-binding sites or protein oligomerization in naturally occurring proteins. To dissect the relative contributions of key determinants for Ca2+-dependent conformational changes, we report the design of a single-site Ca2+-binding protein (CD2.trigger) created by altering charged residues at an electrostatically sensitive location on the surface of the host protein rat Cluster of Differentiation 2 (CD2).CD2.trigger binds to Tb3+ and Ca2+ with dissociation constants of 0.3 +/- 0.1 and 90 +/- 25 microM, respectively. This protein is largely unfolded in the absence of metal ions at physiological pH, but Tb3+ or Ca2+ binding results in folding of the native-like conformation. Neutralization of the charged coordination residues, either by mutation or protonation, similarly induces folding of the protein. The control of a major conformational change by a single Ca2+ ion, achieved on a protein designed without reliance on sequence similarity to known Ca2+-dependent proteins and coupled metal-binding sites, represents an important step in the design of trigger proteins.
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Affiliation(s)
- Shunyi Li
- Department of Chemistry, Center of Drug Design and Biotechnology, Georgia State University, Atlanta, GA, USA
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Statistical analysis of structural characteristics of protein Ca2+-binding sites. J Biol Inorg Chem 2008; 13:1169-81. [PMID: 18594878 DOI: 10.1007/s00775-008-0402-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Accepted: 06/17/2008] [Indexed: 10/21/2022]
Abstract
To better understand the biological significance of Ca(2+), we report a comprehensive statistical analysis of calcium-binding proteins from the Protein Data Bank to identify structural parameters associated with EF-hand and non-EF-hand Ca(2+)-binding sites. Comparatively, non-EF-hand sites utilize lower coordination numbers (6 +/- 2 vs. 7 +/- 1), fewer protein ligands (4 +/- 2 vs. 6 +/- 1), and more water ligands (2 +/- 2 vs. 1 +/- 0) than EF-hand sites. The orders of ligand preference for non-EF-hand and EF-hand sites, respectively, were H(2)O (33.1%) > side-chain Asp (24.5%) > main-chain carbonyl (23.9%) > side-chain Glu (10.4%), and side-chain Asp (29.7%) > side-chain Glu (26.6%) > main-chain carbonyl (21.4%) > H(2)O (13.3%). Less formal negative charge was observed in the non-EF-hand than in the EF-hand binding sites (1 +/- 1 vs. 3 +/- 1). Additionally, over 20% of non-EF-hand sites had formal charge values of zero due to increased utilization of water and carbonyl oxygen ligands. Moreover, the EF-hand sites presented a narrower range of ligand distances and bond angles than non-EF-hand sites, possibly owing to the highly conserved helix-loop-helix motif. Significant differences between ligand types (carbonyl, side chain, bidentate) demonstrated that angles associated with each type must be classified separately, and the EF-hand side-chain Ca-O-C angles exhibited an unusual bimodal quality consistent with an Asp distribution that differed from the Gaussian model observed for non-EF-hand proteins. The results of this survey more accurately describe differences between EF-hand and non-EF-hand proteins and provide new parameters for the prediction and design of different classes of Ca(2+)-binding proteins.
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Yang JJ, Yang J, Wei L, Zurkiya O, Yang W, Li S, Zou J, Zhou Y, Maniccia ALW, Mao H, Zhao F, Malchow R, Zhao S, Johnson J, Hu X, Krogstad E, Liu ZR. Rational design of protein-based MRI contrast agents. J Am Chem Soc 2008; 130:9260-7. [PMID: 18576649 DOI: 10.1021/ja800736h] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe the rational design of a novel class of magnetic resonance imaging (MRI) contrast agents with engineered proteins (CAi.CD2, i = 1, 2,..., 9) chelated with gadolinium. The design of protein-based contrast agents involves creating high-coordination Gd(3+) binding sites in a stable host protein using amino acid residues and water molecules as metal coordinating ligands. Designed proteins show strong selectivity for Gd(3+) over physiological metal ions such as Ca(2+), Zn(2+), and Mg(2+). These agents exhibit a 20-fold increase in longitudinal and transverse relaxation rate values over the conventional small-molecule contrast agents, e.g., Gd-DTPA (diethylene triamine pentaacetic acid), used clinically. Furthermore, they exhibit much stronger contrast enhancement and much longer blood retention time than Gd-DTPA in mice. With good biocompatibility and potential functionalities, these protein contrast agents may be used as molecular imaging probes to target disease markers, thereby extending applications of MRI.
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Affiliation(s)
- Jenny J Yang
- Department of Chemistry, Center for Drug Design and Advanced Biotechnology, Georgia State University, Atlanta, Georgia 30303, USA.
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Zhou Y, Tzeng WP, Yang W, Zhou Y, Ye Y, Lee HW, Frey TK, Yang J. Identification of a Ca2+-binding domain in the rubella virus nonstructural protease. J Virol 2007; 81:7517-28. [PMID: 17475644 PMCID: PMC1933374 DOI: 10.1128/jvi.00605-07] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The rubella virus (RUB) nonstructural protein (NS) open reading frame (ORF) encodes a polypeptide precursor that is proteolytically self cleaved into two replicase components involved in viral RNA replication. A putative EF-hand Ca(2+)-binding motif that was conserved across different genotypes of RUB was predicted within the nonstructural protease that cleaves the precursor by using bioinformatics tools. To probe the metal-binding properties of this motif, we used an established grafting approach and engineered the 12-residue Ca(2+)-coordinating loop into a non-Ca(2+)-binding scaffold protein, CD2. The grafted EF-loop bound to Ca(2+) and its trivalent analogs Tb(3+) and La(3+) with K(d)s of 214, 47, and 14 microM, respectively. Mutations (D1210A and D1217A) of two of the potential Ca(2+)-coordinating ligands in the EF-loop led to the elimination of Tb(3+) binding. Inductive coupled plasma mass spectrometry was used to confirm the presence of Ca(2+) ([Ca(2+)]/[protein] = 0.7 +/- 0.2) in an NS protease minimal metal-binding domain, RUBCa, that spans the EF-hand motif. Conformational studies on RUBCa revealed that Ca(2+) binding induced local conformational changes and increased thermal stability (Delta T(m) = 4.1 degrees C). The infectivity of an RUB infectious cDNA clone containing the mutations D1210A/D1217A was decreased by approximately 20-fold in comparison to the wild-type (wt) clone, and these mutations rapidly reverted to the wt sequence. The NS protease containing these mutations was less efficient at precursor cleavage than the wt NS protease at 35 degrees C, and the mutant NS protease was temperature sensitive at 39 degrees C, confirming that the Ca(2+)-binding loop played a structural role in the NS protease and was specifically required for optimal stability under physiological conditions.
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Affiliation(s)
- Yubin Zhou
- Department of Chemistry, Georgia State University, 50 Decatur St., Atlanta, GA 30303, USA
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