51
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Giegé R. What macromolecular crystallogenesis tells us - what is needed in the future. IUCRJ 2017; 4:340-349. [PMID: 28875021 PMCID: PMC5571797 DOI: 10.1107/s2052252517006595] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 05/02/2017] [Indexed: 05/05/2023]
Abstract
Crystallogenesis is a longstanding topic that has transformed into a discipline that is mainly focused on the preparation of crystals for practising crystallo-graphers. Although the idiosyncratic features of proteins have to be taken into account, the crystallization of proteins is governed by the same physics as the crystallization of inorganic materials. At present, a diversified panel of crystallization methods adapted to proteins has been validated, and although only a few methods are in current practice, the success rate of crystallization has increased constantly, leading to the determination of ∼105 X-ray structures. These structures reveal a huge repertoire of protein folds, but they only cover a restricted part of macromolecular diversity across the tree of life. In the future, crystals representative of missing structures or that will better document the structural dynamics and functional steps underlying biological processes need to be grown. For the pertinent choice of biologically relevant targets, computer-guided analysis of structural databases is needed. From another perspective, crystallization is a self-assembly process that can occur in the bulk of crowded fluids, with crystals being supramolecular assemblies. Life also uses self-assembly and supramolecular processes leading to transient, or less often stable, complexes. An integrated view of supramolecularity implies that proteins crystallizing either in vitro or in vivo or participating in cellular processes share common attributes, notably determinants and antideterminants that favour or disfavour their correct or incorrect associations. As a result, under in vivo conditions proteins show a balance between features that favour or disfavour association. If this balance is broken, disorders/diseases occur. Understanding crystallization under in vivo conditions is a challenge for the future. In this quest, the analysis of packing contacts and contacts within oligomers will be crucial in order to decipher the rules governing protein self-assembly and will guide the engineering of novel biomaterials. In a wider perspective, understanding such contacts will open the route towards supramolecular biology and generalized crystallogenesis.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l’ARN, UPR 9002, Université de Strasbourg and CNRS, F-67084 Strasbourg, France
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52
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Crystal structure of the adenosine A 2A receptor bound to an antagonist reveals a potential allosteric pocket. Proc Natl Acad Sci U S A 2017; 114:2066-2071. [PMID: 28167788 DOI: 10.1073/pnas.1621423114] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The adenosine A2A receptor (A2AR) has long been implicated in cardiovascular disorders. As more selective A2AR ligands are being identified, its roles in other disorders, such as Parkinson's disease, are starting to emerge, and A2AR antagonists are important drug candidates for nondopaminergic anti-Parkinson treatment. Here we report the crystal structure of A2A receptor bound to compound 1 (Cmpd-1), a novel A2AR/N-methyl d-aspartate receptor subtype 2B (NR2B) dual antagonist and potential anti-Parkinson candidate compound, at 3.5 Å resolution. The A2A receptor with a cytochrome b562-RIL (BRIL) fusion (A2AR-BRIL) in the intracellular loop 3 (ICL3) was crystallized in detergent micelles using vapor-phase diffusion. Whereas A2AR-BRIL bound to the antagonist ZM241385 has previously been crystallized in lipidic cubic phase (LCP), structural differences in the Cmpd-1-bound A2AR-BRIL prevented formation of the lattice observed with the ZM241385-bound receptor. The crystals grew with a type II crystal lattice in contrast to the typical type I packing seen from membrane protein structures crystallized in LCP. Cmpd-1 binds in a position that overlaps with the native ligand adenosine, but its methoxyphenyl group extends to an exosite not previously observed in other A2AR structures. Structural analysis revealed that Cmpd-1 binding results in the unique conformations of two tyrosine residues, Tyr91.35 and Tyr2717.36, which are critical for the formation of the exosite. The structure reveals insights into antagonist binding that are not observed in other A2AR structures, highlighting flexibility in the binding pocket that may facilitate the development of A2AR-selective compounds for the treatment of Parkinson's disease.
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Brader ML, Baker EN, Dunn MF, Laue TM, Carpenter JF. Using X-Ray Crystallography to Simplify and Accelerate Biologics Drug Development. J Pharm Sci 2017; 106:477-494. [DOI: 10.1016/j.xphs.2016.10.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/11/2016] [Accepted: 10/13/2016] [Indexed: 02/08/2023]
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55
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Zhou RB, Cao HL, Zhang CY, Yin DC. A review on recent advances for nucleants and nucleation in protein crystallization. CrystEngComm 2017. [DOI: 10.1039/c6ce02562e] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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56
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Mrázková J, Malinovská L, Wimmerová M. Step-By-Step In Vitro Mutagenesis: Lessons From Fucose-Binding Lectin PA-IIL. Methods Mol Biol 2017; 1498:399-419. [PMID: 27709592 DOI: 10.1007/978-1-4939-6472-7_28] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Site-directed mutagenesis is a powerful technique which is used to understand the basis of interactions between proteins and their binding partners, as well as to modify these interactions. Methods of rational design that are based on detailed knowledge of the structure of a protein of interest are often used for preliminary investigations of the possible outcomes which can result from the practical application of site-directed mutagenesis. Also, random mutagenesis can be used in tandem with site-directed mutagenesis for an examination of amino acid "hotspots."Lectins are sugar-binding proteins which, among other functions, mediate the recognition of host cells by a pathogen and its adhesion to the host cell surface. Hence, lectins and their binding properties are studied and engineered using site-directed mutagenesis.In this chapter, we describe a site-directed mutagenesis method used for investigating the sugar binding pattern of the PA-IIL lectin from the pathogenic bacterium Pseudomonas aeruginosa. Moreover, procedures for the production and purification of PA-IIL mutants are described, and several basic methods for characterizing the mutants are discussed.
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Affiliation(s)
- Jana Mrázková
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská, 611 37, Brno, Czech Republic
| | - Lenka Malinovská
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Michaela Wimmerová
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37, Brno, Czech Republic. .,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská, 611 37, Brno, Czech Republic. .,Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.
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57
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Abstract
This chapter provides a review of different advanced methods that help to increase the success rate of a crystallization project, by producing larger and higher quality single crystals for determination of macromolecular structures by crystallographic methods. For this purpose, the chapter is divided into three parts. The first part deals with the fundamentals for understanding the crystallization process through different strategies based on physical and chemical approaches. The second part presents new approaches involved in more sophisticated methods not only for growing protein crystals but also for controlling the size and orientation of crystals through utilization of electromagnetic fields and other advanced techniques. The last section deals with three different aspects: the importance of microgravity, the use of ligands to stabilize proteins, and the use of microfluidics to obtain protein crystals. All these advanced methods will allow the readers to obtain suitable crystalline samples for high-resolution X-ray and neutron crystallography.
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Affiliation(s)
- Abel Moreno
- Instituto de Química, Universidad Nacional Autónoma de Mexico, Av. Universidad 3000, Cd.Mx., Mexico City, 04510, Mexico.
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58
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Pica A, Russo Krauss I, Parente V, Tateishi-Karimata H, Nagatoishi S, Tsumoto K, Sugimoto N, Sica F. Through-bond effects in the ternary complexes of thrombin sandwiched by two DNA aptamers. Nucleic Acids Res 2016; 45:461-469. [PMID: 27899589 PMCID: PMC5224481 DOI: 10.1093/nar/gkw1113] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 10/20/2016] [Accepted: 10/29/2016] [Indexed: 11/23/2022] Open
Abstract
Aptamers directed against human thrombin can selectively bind to two different exosites on the protein surface. The simultaneous use of two DNA aptamers, HD1 and HD22, directed to exosite I and exosite II respectively, is a very powerful approach to exploit their combined affinity. Indeed, strategies to link HD1 and HD22 together have been proposed in order to create a single bivalent molecule with an enhanced ability to control thrombin activity. In this work, the crystal structures of two ternary complexes, in which thrombin is sandwiched between two DNA aptamers, are presented and discussed. The structures shed light on the cross talk between the two exosites. The through-bond effects are particularly evident at exosite II, with net consequences on the HD22 structure. Moreover, thermodynamic data on the binding of the two aptamers are also reported and analyzed.
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Affiliation(s)
- Andrea Pica
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, I-80126 Naples, Italy.,Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone, 16, I-80134 Naples, Italy
| | - Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, I-80126 Naples, Italy.,Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone, 16, I-80134 Naples, Italy
| | - Valeria Parente
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, I-80126 Naples, Italy
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan
| | - Satoru Nagatoishi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113- 8656, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113- 8656, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan .,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, I-80126 Naples, Italy .,Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone, 16, I-80134 Naples, Italy
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59
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Protein-RNA interactions: structural biology and computational modeling techniques. Biophys Rev 2016; 8:359-367. [PMID: 28510023 DOI: 10.1007/s12551-016-0223-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/20/2016] [Indexed: 12/30/2022] Open
Abstract
RNA-binding proteins are functionally diverse within cells, being involved in RNA-metabolism, translation, DNA damage repair, and gene regulation at both the transcriptional and post-transcriptional levels. Much has been learnt about their interactions with RNAs through structure determination techniques and computational modeling. This review gives an overview of the structural data currently available for protein-RNA complexes, and discusses the technical issues facing structural biologists working to solve their structures. The review focuses on three techniques used to solve the 3-dimensional structure of protein-RNA complexes at atomic resolution, namely X-ray crystallography, solution nuclear magnetic resonance (NMR) and cryo-electron microscopy (cryo-EM). The review then focuses on the main computational modeling techniques that use these atomic resolution data: discussing the prediction of RNA-binding sites on unbound proteins, docking proteins, and RNAs, and modeling the molecular dynamics of the systems. In conclusion, the review looks at the future directions this field of research might take.
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60
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Boyko KM, Timofeev VI, Samygina VR, Kuranova IP, Popov VO, Koval’chuk MV. Protein crystallization under microgravity conditions. Analysis of the results of Russian experiments performed on the International Space Station in 2005−2015. CRYSTALLOGR REP+ 2016. [DOI: 10.1134/s1063774516050059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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61
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Yang X, Liu H, Liu J, Li F, Li X, Shi L, Chen J. Rational Selection of the 3D Structure of Biomacromolecules for Molecular Docking Studies on the Mechanism of Endocrine Disruptor Action. Chem Res Toxicol 2016; 29:1565-70. [PMID: 27556396 DOI: 10.1021/acs.chemrestox.6b00245] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular modeling has become an essential tool in predicting and simulating endocrine disrupting effects of chemicals. A key prerequisite for successful application of molecular modeling lies in the correctness of 3D structure for biomacromolecules to be simulated. To date, there are several databases that can provide the experimentally-determined 3D structures. However, commonly, there are many challenges or disadvantageous factors, e.g., (a) lots of 3D structures for a given biomacromolecular target in the protein database; (b) the quality variability for those structures; (c) belonging to different species; (d) mutant amino acid residue in key positions, and so on. Once an inappropriate 3D structure of a target biomacromolecule was selected in molecular modeling, the accuracy and scientific nature of the modeling results could be inevitably affected. In this article, based on literature survey and an analysis of the 3D structure characterization of biomacromolecular targets belonging to the endocrine system in protein databases, six principles were proposed to guide the selection of the appropriate 3D structure of biomacromolecules. The principles include considering the species diversity, the mechanism of action, whether there are mutant amino acid residues, whether the number of protein chains is correct, the degree of structural similarity between the ligand in 3D structure and the target compounds, and other factors, e.g., the experimental pH conditions of the structure determined process and resolution.
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Affiliation(s)
- Xianhai Yang
- Nanjing Institute of Environmental Science , Ministry of Environmental Protection, Nanjing 210042, China
| | - Huihui Liu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, China
| | - Jining Liu
- Nanjing Institute of Environmental Science , Ministry of Environmental Protection, Nanjing 210042, China
| | - Fei Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences , Yantai 264003, China
| | - Xuehua Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology , Dalian 116024, China
| | - Lili Shi
- Nanjing Institute of Environmental Science , Ministry of Environmental Protection, Nanjing 210042, China
| | - Jingwen Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology , Dalian 116024, China
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62
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Vergara A. Use of Kirkwood-Buff Integrals for Extracting Distinct Diffusion Coefficients in Macromolecule-Solvent Mixtures. MACROMOL THEOR SIMUL 2016. [DOI: 10.1002/mats.201600040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alessandro Vergara
- Department of Chemical Sciences; University of Napoli “Federico II,”; Via Cinthia; Complesso di Monte S. Angelo; 80126 Napoli Italy
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63
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Kowalski AE, Huber TR, Ni TW, Hartje LF, Appel KL, Yost JW, Ackerson CJ, Snow CD. Gold nanoparticle capture within protein crystal scaffolds. NANOSCALE 2016; 8:12693-12696. [PMID: 27264210 DOI: 10.1039/c6nr03096c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA assemblies have been used to organize inorganic nanoparticles into 3D arrays, with emergent properties arising as a result of nanoparticle spacing and geometry. We report here the use of engineered protein crystals as an alternative approach to biologically mediated assembly of inorganic nanoparticles. The protein crystal's 13 nm diameter pores result in an 80% solvent content and display hexahistidine sequences on their interior. The hexahistidine sequence captures Au25(glutathione)∼17 (nitrilotriacetic acid)∼1 nanoclusters throughout a chemically crosslinked crystal via the coordination of Ni(ii) to both the cluster and the protein. Nanoparticle loading was validated by confocal microscopy and elemental analysis. The nanoparticles may be released from the crystal by exposure to EDTA, which chelates the Ni(ii) and breaks the specific protein/nanoparticle interaction. The integrity of the protein crystals after crosslinking and nanoparticle capture was confirmed by single crystal X-ray crystallography.
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Affiliation(s)
- Ann E Kowalski
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80521, USA.
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64
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65
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Gao A, Wu Q, Wang D, Ha Y, Chen Z, Yang P. A Superhydrophobic Surface Templated by Protein Self-Assembly and Emerging Application toward Protein Crystallization. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:579-87. [PMID: 26607764 DOI: 10.1002/adma.201504769] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 10/10/2015] [Indexed: 05/06/2023]
Abstract
A proteinaceous superhydrophobic material for facile protein crystallization is reported. The lysozyme phase transition is rationally manipulated to form a reliable superhydrophobic coating on virtually arbitrary material surfaces with good thermostability and mechanical robustness. Such a surface exhibits a fascinating capability to drive protein crystallization, and the protein crystal array can be facilitated in a large area at an ultralow protein concentration.
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Affiliation(s)
- Aiting Gao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Qian Wu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Dehui Wang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Yuan Ha
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Zhijun Chen
- State Key Laboratory of Supramolecular Structure, Jilin University, Changchun, 130012, China
| | - Peng Yang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
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66
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Abstract
Nucleic acid crystallization buffers contain a large variety of chemicals fitting specific needs. Among them, anions are often solely considered for pH-regulating purposes and as cationic co-salts while their ability to directly bind to nucleic acid structures is rarely taken into account. Here we review current knowledge related to the use of anions in crystallization buffers along with data on their biological prevalence. Chloride ions are frequently identified in crystal structures but display low cytosolic concentrations. Hence, they are thought to be distant from nucleic acid structures in the cell. Sulfate ions are also frequently identified in crystal structures but their localization in the cell remains elusive. Nevertheless, the characterization of the binding properties of these ions is essential for better interpreting the solvent structure in crystals and consequently, avoiding mislabeling of electron densities. Furthermore, understanding the binding properties of these anions should help to get clues related to their potential effects in crowded cellular environments.
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Affiliation(s)
- Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, UPR 9002 CNRS/Université de Strasbourg, 15, rue René Descartes, Strasbourg Cedex, 67084, France
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67
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Boyko KM, Popov VO, Kovalchuk MV. Promising approaches to crystallization of macromolecules suppressing the convective mass transport to the growing crystal. RUSSIAN CHEMICAL REVIEWS 2015. [DOI: 10.1070/rcr4557] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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68
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Qi F, Fudo S, Neya S, Hoshino T. A Dominant Factor for Structural Classification of Protein Crystals. J Chem Inf Model 2015; 55:1673-85. [DOI: 10.1021/acs.jcim.5b00052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fei Qi
- Graduate School of Pharmaceutical
Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Satoshi Fudo
- Graduate School of Pharmaceutical
Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Saburo Neya
- Graduate School of Pharmaceutical
Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Tyuji Hoshino
- Graduate School of Pharmaceutical
Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
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69
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Maeki M, Pawate AS, Yamashita K, Kawamoto M, Tokeshi M, Kenis PJA, Miyazaki M. A Method of Cryoprotection for Protein Crystallography by Using a Microfluidic Chip and Its Application for in Situ X-ray Diffraction Measurements. Anal Chem 2015; 87:4194-200. [DOI: 10.1021/acs.analchem.5b00151] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Masatoshi Maeki
- Department
of Molecular and Material Sciences, Interdisciplinary Graduate School
of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
- Division
of Biotechnology and Macromolecular Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan
- Advanced
Manufacturing Research Institute, National Institute of Advanced Industrial Science and Technology, 807-1 Shuku, Tosu, Saga 841-0052, Japan
| | - Ashtamurthy S. Pawate
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Kenichi Yamashita
- Department
of Molecular and Material Sciences, Interdisciplinary Graduate School
of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
- Advanced
Manufacturing Research Institute, National Institute of Advanced Industrial Science and Technology, 807-1 Shuku, Tosu, Saga 841-0052, Japan
| | - Masahide Kawamoto
- Kyushu Synchrotron
Light Research Center, 8-7 Yayoigaoka, Tosu, Saga 841−0051, Japan
| | - Manabu Tokeshi
- Division
of Biotechnology and Macromolecular Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan
| | - Paul J. A. Kenis
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Masaya Miyazaki
- Department
of Molecular and Material Sciences, Interdisciplinary Graduate School
of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
- Advanced
Manufacturing Research Institute, National Institute of Advanced Industrial Science and Technology, 807-1 Shuku, Tosu, Saga 841-0052, Japan
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70
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Hekmat D. Large-scale crystallization of proteins for purification and formulation. Bioprocess Biosyst Eng 2015; 38:1209-31. [PMID: 25700885 DOI: 10.1007/s00449-015-1374-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 02/02/2015] [Indexed: 12/17/2022]
Abstract
Since about 170 years, salts were used to create supersaturated solutions and crystallize proteins. The dehydrating effect of salts as well as their kosmotropic or chaotropic character was revealed. Even the suitability of organic solvents for crystallization was already recognized. Interestingly, what was performed during the early times is still practiced today. A lot of effort was put into understanding the underlying physico-chemical interaction mechanisms leading to protein crystallization. However, it was understood that already the solvation of proteins is a highly complex process not to mention the intricate interrelation of electrostatic and hydrophobic interactions taking place. Although many basic questions are still unanswered, preparative protein crystallization was attempted as illustrated in the presented case studies. Due to the highly variable nature of crystallization, individual design of the crystallization process is needed in every single case. It was shown that preparative crystallization from impure protein solutions as a capture step is possible after applying adequate pre-treatment procedures like precipitation or extraction. Protein crystallization can replace one or more chromatography steps. It was further shown that crystallization can serve as an attractive alternative means for formulation of therapeutic proteins. Crystalline proteins can offer enhanced purity and enable highly concentrated doses of the active ingredient. Easy scalability of the proposed protein crystallization processes was shown using the maximum local energy dissipation as a suitable scale-up criterion. Molecular modeling and target-oriented protein engineering may allow protein crystallization to become part of a platform purification process in the near future.
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Affiliation(s)
- Dariusch Hekmat
- Institute of Biochemical Engineering, Technische Universität München, Boltzmannstr. 15, 85748, Garching, Germany,
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71
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Russo Krauss I, Merlino A, Pica A, Rullo R, Bertoni A, Capasso A, Amato M, Riccitiello F, De Vendittis E, Sica F. Fine tuning of metal-specific activity in the Mn-like group of cambialistic superoxide dismutases. RSC Adv 2015. [DOI: 10.1039/c5ra13559a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Metal-dependent activity and X-ray structures of superoxide dismutase (SOD) fromStreptococcus mutansandStreptococcus thermophilussuggest that they are members of the Mn-like group of cambialistic SODs.
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Affiliation(s)
- Irene Russo Krauss
- Dipartimento di Scienze Chimiche
- Università degli Studi di Napoli Federico II
- 80126 Napoli
- Italy
- Istituto di Biostrutture e Bioimmagini
| | - Antonello Merlino
- Dipartimento di Scienze Chimiche
- Università degli Studi di Napoli Federico II
- 80126 Napoli
- Italy
- Istituto di Biostrutture e Bioimmagini
| | - Andrea Pica
- Dipartimento di Scienze Chimiche
- Università degli Studi di Napoli Federico II
- 80126 Napoli
- Italy
- Istituto di Biostrutture e Bioimmagini
| | - Rosario Rullo
- Istituto per il Sistema Produzione Animale in Ambiente Mediterraneo
- CNR
- 80147 Napoli
- Italy
| | - Alessandra Bertoni
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche
- Università degli Studi di Napoli Federico II
- 80131 Napoli
- Italy
| | - Alessandra Capasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche
- Università degli Studi di Napoli Federico II
- 80131 Napoli
- Italy
| | - Massimo Amato
- Dipartimento di Medicina e Chirurgia
- Università di Salerno
- SA
- Italy
| | - Francesco Riccitiello
- Dipartimento di Neuroscienze
- Scienze Riproduttive e Odontostomatologiche
- Università degli Studi di Napoli Federico II
- 80131 Napoli
- Italy
| | - Emmanuele De Vendittis
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche
- Università degli Studi di Napoli Federico II
- 80131 Napoli
- Italy
| | - Filomena Sica
- Dipartimento di Scienze Chimiche
- Università degli Studi di Napoli Federico II
- 80126 Napoli
- Italy
- Istituto di Biostrutture e Bioimmagini
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72
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Hellmich J, Bommer M, Burkhardt A, Ibrahim M, Kern J, Meents A, Müh F, Dobbek H, Zouni A. Native-like Photosystem II Superstructure at 2.44 Å Resolution through Detergent Extraction from the Protein Crystal. Structure 2014; 22:1607-15. [DOI: 10.1016/j.str.2014.09.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/26/2014] [Accepted: 09/10/2014] [Indexed: 10/24/2022]
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73
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Merlino A, Russo Krauss I, Castellano I, Ruocco MR, Capasso A, De Vendittis E, Rossi B, Sica F. Structural and denaturation studies of two mutants of a cold adapted superoxide dismutase point to the importance of electrostatic interactions in protein stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:632-40. [DOI: 10.1016/j.bbapap.2014.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 01/07/2014] [Accepted: 01/10/2014] [Indexed: 10/25/2022]
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74
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Russo Krauss I, Parkinson GN, Merlino A, Mattia CA, Randazzo A, Novellino E, Mazzarella L, Sica F. A regular thymine tetrad and a peculiar supramolecular assembly in the first crystal structure of an all-LNA G-quadruplex. ACTA ACUST UNITED AC 2014; 70:362-70. [PMID: 24531470 DOI: 10.1107/s1399004713028095] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 10/13/2013] [Indexed: 01/19/2023]
Abstract
Locked nucleic acids (LNAs) are formed by bicyclic ribonucleotides where the O2' and C4' atoms are linked through a methylene bridge and the sugar is blocked in a 3'-endo conformation. They represent a promising tool for therapeutic and diagnostic applications and are characterized by higher thermal stability and nuclease resistance with respect to their natural counterparts. However, structural descriptions of LNA-containing quadruplexes are rather limited, since few NMR models have been reported in the literature. Here, the first crystallographically derived model of an all-LNA-substituted quadruplex-forming sequence 5'-TGGGT-3' is presented refined at 1.7 Å resolution. This high-resolution crystallographic analysis reveals a regular parallel G-quadruplex arrangement terminating in a well defined thymine tetrad at the 3'-end. The detailed picture of the hydration pattern reveals LNA-specific features in the solvent distribution. Interestingly, two closely packed quadruplexes are present in the asymmetric unit. They face one another with their 3'-ends giving rise to a compact higher-order structure. This new assembly suggests a possible way in which sequential quadruplexes can be disposed in the crowded cell environment. Furthermore, as the formation of ordered structures by molecular self-assembly is an effective strategy to obtain nanostructures, this study could open the way to the design of a new class of LNA-based building blocks for nanotechnology.
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Affiliation(s)
- Irene Russo Krauss
- Department of Chemical Sciences, University of Naples `Federico II', Complesso Universitario di Monte Sant'Angelo, Via Cinthia, I-80126 Napoli, Italy
| | - Gary Nigel Parkinson
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, England
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples `Federico II', Complesso Universitario di Monte Sant'Angelo, Via Cinthia, I-80126 Napoli, Italy
| | - Carlo Andrea Mattia
- Department of Pharmacy, University of Salerno, Via Ponte Don Melillo, I-84084 Fisciano, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples `Federico II', Via D. Montesano 49, I-80131 Napoli, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples `Federico II', Via D. Montesano 49, I-80131 Napoli, Italy
| | - Lelio Mazzarella
- Department of Chemical Sciences, University of Naples `Federico II', Complesso Universitario di Monte Sant'Angelo, Via Cinthia, I-80126 Napoli, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples `Federico II', Complesso Universitario di Monte Sant'Angelo, Via Cinthia, I-80126 Napoli, Italy
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75
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Yoshikawa HY, Murai R, Adachi H, Sugiyama S, Maruyama M, Takahashi Y, Takano K, Matsumura H, Inoue T, Murakami S, Masuhara H, Mori Y. Laser ablation for protein crystal nucleation and seeding. Chem Soc Rev 2014; 43:2147-58. [DOI: 10.1039/c3cs60226e] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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76
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Giegé R. A historical perspective on protein crystallization from 1840 to the present day. FEBS J 2013; 280:6456-97. [DOI: 10.1111/febs.12580] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 08/30/2013] [Accepted: 09/27/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Richard Giegé
- Institut de Biologie Moléculaire et Cellulaire; Université de Strasourg et CNRS; France
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77
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Russo Krauss I, Pica A, Merlino A, Mazzarella L, Sica F. Duplex-quadruplex motifs in a peculiar structural organization cooperatively contribute to thrombin binding of a DNA aptamer. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2403-11. [PMID: 24311581 DOI: 10.1107/s0907444913022269] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 08/08/2013] [Indexed: 11/10/2022]
Abstract
Potent second-generation thrombin aptamers adopt a duplex-quadruplex bimodular folding and recognize thrombin exosite II with very high affinity and specificity. A sound model of these oligonucleotides, either free or in complex with thrombin, is not yet available. Here, a structural study of one of these aptamers, HD22-27mer, is presented. The crystal structure of this aptamer in complex with thrombin displays a novel architecture in which the helical stem is enchained to a pseudo-G-quadruplex. The results also underline the role of the residues that join the duplex and quadruplex motifs and control their recruitment in thrombin binding.
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Affiliation(s)
- Irene Russo Krauss
- Department of Chemical Sciences, University of Naples `Federico II', Complesso Universitario di Monte Sant'Angelo, I-80126 Naples, Italy
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78
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Pica A, Russo Krauss I, Merlino A, Nagatoishi S, Sugimoto N, Sica F. Dissecting the contribution of thrombin exosite I in the recognition of thrombin binding aptamer. FEBS J 2013; 280:6581-8. [PMID: 24128303 DOI: 10.1111/febs.12561] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/30/2013] [Accepted: 10/03/2013] [Indexed: 11/29/2022]
Abstract
Thrombin plays a pivotal role in the coagulation cascade; therefore, it represents a primary target in the treatment of several blood diseases. The 15-mer DNA oligonucleotide 5'-GGTTGGTGTGGTTGG-3', known as thrombin binding aptamer (TBA), is a highly potent inhibitor of the enzyme. TBA folds as an antiparallel chair-like G-quadruplex structure, with two G-tetrads surrounded by two TT loops on one side and a TGT loop on the opposite side. Previous crystallographic studies have shown that TBA binds thrombin exosite I by its TT loops, T3T4 and T12T13. In order to get a better understanding of the thrombin-TBA interaction, we have undertaken a crystallographic characterization of the complexes between thrombin and two TBA mutants, TBAΔT3 and TBAΔT12, which lack the nucleobase of T3 and T12, respectively. The structural details of the two complexes show that exosite I is actually split into two regions, which contribute differently to TBA recognition. These results provide the basis for a more rational design of new aptamers with improved therapeutic action.
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Affiliation(s)
- Andrea Pica
- Department of Chemical Sciences, University of Naples Federico II, Italy
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