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Carrozzini B, Cascarano GL, Giacovazzo C. The Automatic Solution of Macromolecular Crystal Structures via Molecular Replacement Techniques: REMO22 and Its Pipeline. Int J Mol Sci 2023; 24:ijms24076070. [PMID: 37047043 PMCID: PMC10094557 DOI: 10.3390/ijms24076070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 04/14/2023] Open
Abstract
A description of REMO22, a new molecular replacement program for proteins and nucleic acids, is provided. This program, as with REMO09, can use various types of prior information through appropriate conditional distribution functions. Its efficacy in model searching has been validated through several test cases involving proteins and nucleic acids. Although REMO22 can be configured with different protocols according to user directives, it has been developed primarily as an automated tool for determining the crystal structures of macromolecules. To evaluate REMO22's utility in the current crystallographic environment, its experimental results must be compared favorably with those of the most widely used Molecular Replacement (MR) programs. To accomplish this, we chose two leading tools in the field, PHASER and MOLREP. REMO22, along with MOLREP and PHASER, were included in pipelines that contain two additional steps: phase refinement (SYNERGY) and automated model building (CAB). To evaluate the effectiveness of REMO22, SYNERGY and CAB, we conducted experimental tests on numerous macromolecular structures. The results indicate that REMO22, along with its pipeline REMO22 + SYNERGY + CAB, presents a viable alternative to currently used phasing tools.
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Affiliation(s)
- Benedetta Carrozzini
- Istituto di Cristallografia, The National Research Council (CNR), Via G. Amendola 122/o, I-70126 Bari, Italy
| | - Giovanni Luca Cascarano
- Istituto di Cristallografia, The National Research Council (CNR), Via G. Amendola 122/o, I-70126 Bari, Italy
| | - Carmelo Giacovazzo
- Istituto di Cristallografia, The National Research Council (CNR), Via G. Amendola 122/o, I-70126 Bari, Italy
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2
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Crystal Structure of the Human Copper Chaperone ATOX1 Bound to Zinc Ion. Biomolecules 2022; 12:biom12101494. [PMID: 36291703 PMCID: PMC9599288 DOI: 10.3390/biom12101494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/09/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022] Open
Abstract
The bioavailability of copper (Cu) in human cells may depend on a complex interplay with zinc (Zn) ions. We investigated the ability of the Zn ion to target the human Cu-chaperone Atox1, a small cytosolic protein capable of anchoring Cu(I), by a conserved surface-exposed Cys-X-X-Cys (CXXC) motif, and deliver it to Cu-transporting ATPases in the trans-Golgi network. The crystal structure of Atox1 loaded with Zn displays the metal ion bridging the CXXC motifs of two Atox1 molecules in a homodimer. The identity and location of the Zn ion were confirmed through the anomalous scattering of the metal by collecting X-ray diffraction data near the Zn K-edge. Furthermore, soaking experiments of the Zn-loaded Atox1 crystals with a strong chelating agent, such as EDTA, caused only limited removal of the metal ion from the tetrahedral coordination cage, suggesting a potential role of Atox1 in Zn metabolism and, more generally, that Cu and Zn transport mechanisms could be interlocked in human cells.
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Cascarano GL, Giacovazzo C. Towards the automatic crystal structure solution of nucleic acids: automated model building using the new CAB program. Acta Crystallogr D Struct Biol 2021; 77:1602-1613. [PMID: 34866615 DOI: 10.1107/s2059798321010937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/20/2021] [Indexed: 11/10/2022] Open
Abstract
CAB, a recently described automated model-building (AMB) program, has been modified to work effectively with nucleic acids. To this end, several new algorithms have been introduced and the libraries have been updated. To reduce the input average phase error, ligand heavy atoms are now located before starting the CAB interpretation of the electron-density maps. Furthermore, alternative approaches are used depending on whether the ligands belong to the target or to the model chain used in the molecular-replacement step. Robust criteria are then applied to decide whether the AMB model is acceptable or whether it must be modified to fit prior information on the target structure. In the latter case, the model chains are rearranged to fit prior information on the target chains. Here, the performance of the new AMB program CAB applied to various nucleic acid structures is discussed. Other well documented programs such as Nautilus, ARP/wARP and phenix.autobuild were also applied and the experimental results are described.
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Affiliation(s)
| | - Carmelo Giacovazzo
- Istituto di Cristallografia, CNR, Via G. Amendola 122/o, I-70126 Bari, Italy
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4
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Three-dimensional structure of human cyclooxygenase (hCOX)-1. Sci Rep 2021; 11:4312. [PMID: 33619313 PMCID: PMC7900114 DOI: 10.1038/s41598-021-83438-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 02/02/2021] [Indexed: 12/11/2022] Open
Abstract
The beneficial effects of Cyclooxygenases (COX) inhibitors on human health have been known for thousands of years. Nevertheless, COXs, particularly COX-1, have been linked to a plethora of human diseases such as cancer, heart failure, neurological and neurodegenerative diseases only recently. COXs catalyze the first step in the biosynthesis of prostaglandins (PGs) and are among the most important mediators of inflammation. All published structural work on COX-1 deals with the ovine isoenzyme, which is easier to produce in milligram-quantities than the human enzyme and crystallizes readily. Here, we report the long-sought structure of the human cyclooxygenase-1 (hCOX-1) that we refined to an R/Rfree of 20.82/26.37, at 3.36 Å resolution. hCOX-1 structure provides a detailed picture of the enzyme active site and the residues crucial for inhibitor/substrate binding and catalytic activity. We compared hCOX-1 crystal structure with the ovine COX-1 and human COX-2 structures by using metrics based on Cartesian coordinates, backbone dihedral angles, and solvent accessibility coupled with multivariate methods. Differences and similarities among structures are discussed, with emphasis on the motifs responsible for the diversification of the various enzymes (primary structure, stability, catalytic activity, and specificity). The structure of hCOX-1 represents an essential step towards the development of new and more selective COX-1 inhibitors of enhanced therapeutic potential.
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Abstract
Obtaining high-quality models for nucleic acid structures by automated model building programs (AMB) is still a challenge. The main reasons are the rather low resolution of the diffraction data and the large number of rotatable bonds in the main chains. The application of the most popular and documented AMB programs (e.g., PHENIX.AUTOBUILD, NAUTILUS and ARP/wARP) may provide a good assessment of the state of the art. Quite recently, a cyclic automated model building (CAB) package was described; it is a new AMB approach that makes the use of BUCCANEER for protein model building cyclic without modifying its basic algorithms. The applications showed that CAB improves the efficiency of BUCCANEER. The success suggested an extension of CAB to nucleic acids—in particular, to check if cyclically including NAUTILUS in CAB may improve its effectiveness. To accomplish this task, CAB algorithms designed for protein model building were modified to adapt them to the nucleic acid crystallochemistry. CAB was tested using 29 nucleic acids (DNA and RNA fragments). The phase estimates obtained via molecular replacement (MR) techniques were automatically submitted to phase refinement and then used as input for CAB. The experimental results from CAB were compared with those obtained by NAUTILUS, ARP/wARP and PHENIX.AUTOBUILD.
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Burla MC, Carrozzini B, Cascarano GL, Giacovazzo C, Polidori G. How far are we from automatic crystal structure solution via molecular-replacement techniques? ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:9-18. [PMID: 31909739 PMCID: PMC6939436 DOI: 10.1107/s2059798319015468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/15/2019] [Indexed: 11/10/2022]
Abstract
Although the success of molecular-replacement techniques requires the solution of a six-dimensional problem, this is often subdivided into two three-dimensional problems. REMO09 is one of the programs which have adopted this approach. It has been revisited in the light of a new probabilistic approach which is able to directly derive conditional distribution functions without passing through a previous calculation of the joint probability distributions. The conditional distributions take into account various types of prior information: in the rotation step the prior information may concern a non-oriented model molecule alone or together with one or more located model molecules. The formulae thus obtained are used to derive figures of merit for recognizing the correct orientation in the rotation step and the correct location in the translation step. The phases obtained by this new version of REMO09 are used as a starting point for a pipeline which in its first step extends and refines the molecular-replacement phases, and in its second step creates the final electron-density map which is automatically interpreted by CAB, an automatic model-building program for proteins and DNA/RNA structures.
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Affiliation(s)
- Maria Cristina Burla
- Dipartimento di Fisica e Geologia, Università di Perugia, Piazza Università, I-06123 Perugia, Italy
| | | | | | - Carmelo Giacovazzo
- Istituto di Cristallografia, CNR, Via Amendola 122/O, I-70126 Bari, Italy
| | - Giampiero Polidori
- Istituto di Cristallografia, CNR, Via Amendola 122/O, I-70126 Bari, Italy
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Nardella MI, Rosato A, Belviso BD, Caliandro R, Natile G, Arnesano F. Oxidation of Human Copper Chaperone Atox1 and Disulfide Bond Cleavage by Cisplatin and Glutathione. Int J Mol Sci 2019; 20:ijms20184390. [PMID: 31500118 PMCID: PMC6769983 DOI: 10.3390/ijms20184390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/03/2019] [Accepted: 09/03/2019] [Indexed: 01/11/2023] Open
Abstract
Cancer cells cope with high oxidative stress levels, characterized by a shift toward the oxidized form (GSSG) of glutathione (GSH) in the redox couple GSSG/2GSH. Under these conditions, the cytosolic copper chaperone Atox1, which delivers Cu(I) to the secretory pathway, gets oxidized, i.e., a disulfide bond is formed between the cysteine residues of the Cu(I)-binding CxxC motif. Switching to the covalently-linked form, sulfur atoms are not able to bind the Cu(I) ion and Atox1 cannot play an antioxidant role. Atox1 has also been implicated in the resistance to platinum chemotherapy. In the presence of excess GSH, the anticancer drug cisplatin binds to Cu(I)-Atox1 but not to the reduced apoprotein. With the aim to investigate the interaction of cisplatin with the disulfide form of the protein, we performed a structural characterization in solution and in the solid state of oxidized human Atox1 and explored its ability to bind cisplatin under conditions mimicking an oxidizing environment. Cisplatin targets a methionine residue of oxidized Atox1; however, in the presence of GSH as reducing agent, the drug binds irreversibly to the protein with ammine ligands trans to Cys12 and Cys15. The results are discussed with reference to the available literature data and a mechanism is proposed connecting platinum drug processing to redox and copper homeostasis.
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Affiliation(s)
- Maria I Nardella
- Department of Chemistry, University of Bari, via Orabona, 4, 70125 Bari, Italy
| | - Antonio Rosato
- Department of Chemistry, University of Bari, via Orabona, 4, 70125 Bari, Italy
| | - Benny D Belviso
- Institute of Crystallography, CNR, via Amendola, 122/o, 70126 Bari, Italy
| | - Rocco Caliandro
- Institute of Crystallography, CNR, via Amendola, 122/o, 70126 Bari, Italy
| | - Giovanni Natile
- Department of Chemistry, University of Bari, via Orabona, 4, 70125 Bari, Italy
| | - Fabio Arnesano
- Department of Chemistry, University of Bari, via Orabona, 4, 70125 Bari, Italy.
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Abstract
Protein crystallization is a powerful purification tool. It is the first step for crystallographic structural investigations, and can be preparatory for biotechnological applications. However, crystallizing proteins is challenging and methods to control the crystallization process are needed. Ionic-liquid hydrogel composite membranes (IL-HCMs) have been used here as material capable of supporting protein crystallization and hosting grown crystals. We found that IL-HCMs affect the selection mechanism of glucose isomerase (GI) polymorphs and make GI crystals grow completely immersed into the hydrogel layer. X-ray diffraction studies show that IL ions do not bind to the protein, likely because IL molecules are constrained in the polymeric framework. Our GI crystal structures have been compared with many existing GI crystal structures using multivariate analysis tools, allowing a comprehensive overview of factors determining structural similarities, i.e., temperature variations and external stresses exerted during or after crystal growth, such as dehydration or presence of hydrogel of a different nature. GI crystals grown on IL-HCM fit perfectly in this framework, showing typical features induced by external forces. Overall, protein crystallization by IL-HCMs show potential for biotechnological applications, as it could constitute a natural means for containing crystallized enzymes in working conditions.
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Shen Y, Mevius DE, Caliandro R, Carrozzini B, Roh Y, Kim J, Kim S, Ha SC, Morishita M, di Luccio E. Set7 Is a H3K37 Methyltransferase in Schizosaccharomyces pombe and Is Required for Proper Gametogenesis. Structure 2019; 27:631-638.e8. [DOI: 10.1016/j.str.2019.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 11/23/2018] [Accepted: 01/18/2019] [Indexed: 11/15/2022]
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Simpkin AJ, Simkovic F, Thomas JMH, Savko M, Lebedev A, Uski V, Ballard C, Wojdyr M, Wu R, Sanishvili R, Xu Y, Lisa MN, Buschiazzo A, Shepard W, Rigden DJ, Keegan RM. SIMBAD: a sequence-independent molecular-replacement pipeline. Acta Crystallogr D Struct Biol 2018; 74:595-605. [PMID: 29968670 PMCID: PMC6038384 DOI: 10.1107/s2059798318005752] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 04/12/2018] [Indexed: 12/13/2022] Open
Abstract
The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here, SIMBAD, a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two steps fail to yield a solution, a final step in SIMBAD can be invoked to perform a brute-force search of a nonredundant PDB database provided by the MoRDa MR software. Through early-access usage of SIMBAD, this approach has solved novel cases that have otherwise proved difficult to solve.
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Affiliation(s)
- Adam J. Simpkin
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Felix Simkovic
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Jens M. H. Thomas
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Martin Savko
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Andrey Lebedev
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Ville Uski
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Charles Ballard
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Marcin Wojdyr
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- Global Phasing Ltd, Cambridge CB3 0AX, England
| | - Rui Wu
- Feil Family Brain and Mind Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ruslan Sanishvili
- GM/CA@APS, The X-Ray Science Division, The Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Yibin Xu
- Division of Structural Biology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Royal Parade, Parkville, VIC 3050, Australia
| | - María-Natalia Lisa
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
| | - Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
| | - William Shepard
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Ronan M. Keegan
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
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Mirabelli V, Majidi Salehi S, Angiolillo L, Belviso BD, Conte A, Del Nobile MA, Di Profio G, Caliandro R. Enzyme Crystals and Hydrogel Composite Membranes as New Active Food Packaging Material. GLOBAL CHALLENGES (HOBOKEN, NJ) 2018; 2:1700089. [PMID: 31565305 PMCID: PMC6607345 DOI: 10.1002/gch2.201700089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/01/2017] [Indexed: 06/10/2023]
Abstract
The great antimicrobial and antioxidant potential of enzymes makes them prone to be used as active packaging materials to preserve food from contamination or degradation. Major drawbacks are connected to the use of enzymes freely dispersed in solution, due to reduced protein stability. The immobilization of enzymes on solid supports to create biocatalytic interfaces has instead been proven to increase their stability and efficiency. In this work, it is shown that enzymes crystallized on hydrogel composite membranes (HCMs) can exert an effective antimicrobial action, thus making the composite membrane and crystals biofilm a potential active substrate for food packaging applications. The antimicrobial hen egg white lysozyme is crystallized on the surface of the hydrogel layer of HCMs, and its activity is determined by measuring the decrease in absorbance of Micrococcus lysodeikticus culture incubated with the specimen. The overall catalytic efficiency of the antimicrobial HCMs increases by a factor of 2 compared to the pure enzyme dissolved in solution at the same quantity. Because the enzyme in crystalline form is present in higher concentration and purity than in the solution, both its overall catalytic efficiency and antimicrobial action increase. Moreover, the hydrogel environment allows a better protein stabilization and retention during crystals dissolution.
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Affiliation(s)
- Valentina Mirabelli
- Institute of Crystallography (IC)National Research Council of Italy (CNR)via G. Amendola 122/o70126BariItaly
- Department of EconomicsUniversity of FoggiaLargo Papa Giovanni Paolo II, 171121FoggiaItaly
| | - Shabnam Majidi Salehi
- National Research Council of Italy (CNR) – Institute on Membrane Technology (ITM)via P. Bucci Cubo 17/C87036Rende (CS)Italy
| | - Luisa Angiolillo
- Department of Agricultural SciencesUniversity of FoggiaFood and Environment – Via Napoli 2571121FoggiaItaly
| | - Benny Danilo Belviso
- Institute of Crystallography (IC)National Research Council of Italy (CNR)via G. Amendola 122/o70126BariItaly
| | - Amalia Conte
- Department of Agricultural SciencesUniversity of FoggiaFood and Environment – Via Napoli 2571121FoggiaItaly
| | | | - Gianluca Di Profio
- National Research Council of Italy (CNR) – Institute on Membrane Technology (ITM)via P. Bucci Cubo 17/C87036Rende (CS)Italy
| | - Rocco Caliandro
- Institute of Crystallography (IC)National Research Council of Italy (CNR)via G. Amendola 122/o70126BariItaly
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Burla MC, Cascarano GL, Giacovazzo C, Polidori G. Synergy among phase-refinement techniques in macromolecular crystallography. Acta Crystallogr D Struct Biol 2017; 73:877-888. [PMID: 29095160 DOI: 10.1107/s2059798317014590] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/10/2017] [Indexed: 11/10/2022] Open
Abstract
Ab initio and non-ab initio phasing methods are often unable to provide phases of sufficient quality to allow the molecular interpretation of the resulting electron-density maps. Phase extension and refinement is therefore a necessary step: its success or failure can make the difference between solution and nonsolution of the crystal structure. Today phase refinement is trusted to electron-density modification (EDM) techniques, and in practice to dual-space methods which try, via suitable constraints in direct and in reciprocal space, to generate higher quality electron-density maps. The most popular EDM approaches, denoted here as mainstream methods, are usually part of packages which assist crystallographers in all of the structure-solution steps from initial phasing to the point where the molecular model perfectly fits the known features of protein chemistry. Other phase-refinement approaches that are based on different sources of information, denoted here as out-of-mainstream methods, are not frequently employed. This paper aims to show that mainstream and out-of-mainstream methods may be combined and may lead to dramatic advances in the present state of the art. The statement is confirmed by experimental tests using molecular-replacement, SAD-MAD and ab initio techniques.
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Affiliation(s)
- Maria Cristina Burla
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | | | - Carmelo Giacovazzo
- Istituto di Cristallografia, CNR, Via G. Amendola 122/o, I-70126 Bari, Italy
| | - Giampiero Polidori
- Istituto di Cristallografia, CNR, Via G. Amendola 122/o, I-70126 Bari, Italy
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13
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Belviso BD, Galliani A, Lasorsa A, Mirabelli V, Caliandro R, Arnesano F, Natile G. Oxaliplatin Binding to Human Copper Chaperone Atox1 and Protein Dimerization. Inorg Chem 2016; 55:6563-73. [DOI: 10.1021/acs.inorgchem.6b00750] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Benny D. Belviso
- Institute of Crystallography, Consiglio Nazionale delle Ricerche, via Amendola 122/o, 70126 Bari, Italy
| | - Angela Galliani
- Department
of Chemistry, University of Bari “A. Moro”, via E.
Orabona 4, 70125 Bari, Italy
| | - Alessia Lasorsa
- Department
of Chemistry, University of Bari “A. Moro”, via E.
Orabona 4, 70125 Bari, Italy
| | - Valentina Mirabelli
- Institute of Crystallography, Consiglio Nazionale delle Ricerche, via Amendola 122/o, 70126 Bari, Italy
- Department of Economics, University of Foggia, Via A. Gramsci 89/91, 71122 Foggia, Italy
| | - Rocco Caliandro
- Institute of Crystallography, Consiglio Nazionale delle Ricerche, via Amendola 122/o, 70126 Bari, Italy
| | - Fabio Arnesano
- Department
of Chemistry, University of Bari “A. Moro”, via E.
Orabona 4, 70125 Bari, Italy
| | - Giovanni Natile
- Department
of Chemistry, University of Bari “A. Moro”, via E.
Orabona 4, 70125 Bari, Italy
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14
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Carrozzini B, Cascarano GL, Giacovazzo C, Mazzone A. Advances in molecular-replacement procedures: theREVANpipeline. ACTA ACUST UNITED AC 2015; 71:1856-63. [DOI: 10.1107/s1399004715012730] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/01/2015] [Indexed: 11/10/2022]
Abstract
TheREVANpipeline aiming at the solution of protein structuresviamolecular replacement (MR) has been assembled. It is the successor toREVA, a pipeline that is particularly efficient when the sequence identity (SI) between the target and the model is greater than 0.30. TheREVANandREVAprocedures coincide when the SI is >0.30, but differ substantially in worse conditions. To treat these cases,REVANcombines a variety of programs and algorithms (REMO09,REFMAC,DM,DSR,VLD,free lunch,Coot,Buccaneerandphenix.autobuild). The MR model, suitably rotated and positioned, is first refined by a standardREFMACrefinement procedure, and the corresponding electron density is then submitted to cycles ofDM–VLD–REFMAC. The nextREFMACapplications exploit the better electron densities obtained at the end of theVLD–EDM sections (a procedure called vector refinement). In order to make the model more similar to the target, the model is submitted to mutations, in whichCootplays a basic role, and it is then cyclically resubmitted toREFMAC–EDM–VLDcycles. The phases thus obtained are submitted tofree lunchand allow most of the test structures studied by DiMaioet al.[(2011),Nature (London),473, 540–543] to be solved without using energy-guided programs.
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15
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Burla MC, Caliandro R, Carrozzini B, Cascarano GL, Cuocci C, Giacovazzo C, Mallamo M, Mazzone A, Polidori G. Crystal structure determination and refinementviaSIR2014. J Appl Crystallogr 2015. [DOI: 10.1107/s1600576715001132] [Citation(s) in RCA: 596] [Impact Index Per Article: 66.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
SIR2014is the latest program of theSIRsuite for crystal structure solution of small, medium and large structures. A variety of phasing algorithms have been implemented, bothab initio(standard or modern direct methods, Patterson techniques,Vive la Différence) and non-ab initio(simulated annealing, molecular replacement). The program contains tools for crystal structure refinement and for the study of three-dimensional electron-density mapsviasuitable viewers.
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16
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Abstract
Crystallography is a major tool for structure-driven drug design, as it allows knowledge of the 3D structure of protein targets and protein-ligand complexes. However, the route for crystal structure determination involves many steps, some of which may hamper its high-throughput use. Recent efforts have produced significant advances in experimental and computational tools and protocols. They include automatic crystallization tools, faster data collection devices, more efficient phasing methods and improved ligand-fitting procedures. The timescales of drug-discovery processes have been also reduced by using a fragment-based screening approach. Herein, the achievements in protein crystallography over the last 5 years are reviewed, and advantages and disadvantages of the fragment-based approaches to drug discovery that make use of x-ray crystallography as a primary screening method are examined. In particular, in some detail, five recent case studies pertaining to the development of new hits or leads in relevant therapeutic areas, such as cancer, immune response, inflammation, metabolic syndrome and neurology are described.
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Carrozzini B, Cascarano GL, Comunale G, Giacovazzo C, Mazzone A. The use ofVLD(vive la difference) in the molecular-replacement approach: a pipeline. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1038-44. [DOI: 10.1107/s0907444913004435] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 02/14/2013] [Indexed: 11/10/2022]
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Phasing in crystallography: a modern perspective. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2012. [DOI: 10.1007/s12210-012-0209-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Burla MC, Caliandro R, Camalli M, Carrozzini B, Cascarano GL, Giacovazzo C, Mallamo M, Mazzone A, Polidori G, Spagna R. SIR2011: a new package for crystal structure determination and refinement. J Appl Crystallogr 2012. [DOI: 10.1107/s0021889812001124] [Citation(s) in RCA: 474] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
SIR2011, the successor ofSIR2004, is the latest program of theSIRsuite. It can solveab initiocrystal structures of small- and medium-size molecules, as well as protein structures, using X-ray or electron diffraction data. With respect to the predecessor the program has several new abilities:e.g.a new phasing method (VLD) has been implemented, it is able to exploit prior knowledge of the molecular geometryviasimulated annealing techniques, it can use molecular replacement methods for solving proteins, it includes new tools like free lunch and new approaches for electron diffraction data, and it visualizes three-dimensional electron density maps. The graphical interface has been further improved and allows the straightforward use of the program even in difficult cases.
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Chirikjian GS. Mathematical aspects of molecular replacement. I. Algebraic properties of motion spaces. Acta Crystallogr A 2011; 67:435-46. [PMID: 21844648 PMCID: PMC3171898 DOI: 10.1107/s0108767311021003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Accepted: 06/09/2011] [Indexed: 11/10/2022] Open
Abstract
Molecular replacement (MR) is a well established method for phasing of X-ray diffraction patterns for crystals composed of biological macromolecules of known chemical structure but unknown conformation. In MR, the starting point is known structural domains that are presumed to be similar in shape to those in the macromolecular structure which is to be determined. A search is then performed over positions and orientations of the known domains within a model of the crystallographic asymmetric unit so as to best match a computed diffraction pattern with experimental data. Unlike continuous rigid-body motions in Euclidean space and the discrete crystallographic space groups, the set of motions over which molecular replacement searches are performed does not form a group under the operation of composition, which is shown here to lack the associative property. However, the set of rigid-body motions in the asymmetric unit forms another mathematical structure called a quasigroup, which can be identified with right-coset spaces of the full group of rigid-body motions with respect to the chiral space group of the macromolecular crystal. The algebraic properties of this space of motions are articulated here.
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Affiliation(s)
- Gregory S Chirikjian
- Department of Mechanical Engineering, Johns Hopkins University, 223 Latrobe Hall, 3400 N. Charles Street, Baltimore, Maryland, MD 21218, USA.
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Burla MC, Carrozzini B, Cascarano GL, Giacovazzo C, Polidori G. About the hybrid Fourier syntheses: a probabilistic approach. Acta Crystallogr A 2011; 67:447-55. [PMID: 21844649 DOI: 10.1107/s0108767311017843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 05/11/2011] [Indexed: 11/10/2022] Open
Abstract
The difference electron density has recently been revisited via the method of joint probability distribution functions [Burla et al. (2010). Acta Cryst. A 66, 347-361]. New Fourier coefficients were devised which were the basis of a new ab initio method for the solution of the phase problem (i.e. VLD, vive la difference). In this paper we study the joint probability distribution functions P(F, F(p), F(Q)), where F(Q) is the structure factor corresponding to the ideal hybrid Fourier synthesis ρ(Q) = τρ - ωρ(p) and τ and ω are any pair of real numbers. New Fourier coefficients for the calculations of any hybrid synthesis are obtained, and the properties of the corresponding electron-density maps are discussed. The first applications show the correctness of our theoretical approach and suggest possible applications in phasing procedures.
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Burla MC, Caliandro R, Giacovazzo C, Polidori G. The difference electron density: a probabilistic reformulation. Acta Crystallogr A 2010; 66:347-61. [DOI: 10.1107/s010876731000365x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 01/29/2010] [Indexed: 11/10/2022] Open
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