51
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De N, Navarro MVAS, Wang Q, Krasteva PV, Sondermann H. Biophysical assays for protein interactions in the Wsp sensory system and biofilm formation. Methods Enzymol 2010; 471:161-84. [PMID: 20946848 DOI: 10.1016/s0076-6879(10)71010-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Many signal transduction and regulatory events are mediated by a change in oligomeric state upon posttranslational modification or ligand binding. Hence, the characterization of proteins and protein complexes with respect to their size and shape is crucial for elucidating the molecular mechanisms that control their activities. Commonly used methods for the determination of molecular weights of biological polymers such as standard size-exclusion chromatography or analytical ultracentrifugation have been applied successfully but have some limitations. Static multiangle light scattering presents an attractive alternative approach for absolute molecular weight measurements in solution. We review the biophysical principles, advantages, and pitfalls of some popular methods for determining the quaternary structure of proteins, using the response regulator diguanylate cyclase WspR from Pseudomonas and FimX, a protein involved in Pseudomonas aeruginosa twitching motility, as examples.
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Affiliation(s)
- Nabanita De
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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52
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Yadav S, Liu J, Shire SJ, Kalonia DS. Specific interactions in high concentration antibody solutions resulting in high viscosity. J Pharm Sci 2010; 99:1152-68. [DOI: 10.1002/jps.21898] [Citation(s) in RCA: 196] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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53
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Li W, Jaffe JS. Sizing homogeneous spherical particles from intensity-only angular scatter. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2010; 27:151-158. [PMID: 20126224 DOI: 10.1364/josaa.27.000151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A set of algorithms is proposed to retrieve the size of spherically symmetric particles from the measured intensity of angular scatter data. Of special interest are low-contrast particles whose real part of the index of refraction is between 1.03 and 1.09 and whose size ka is constrained so that pi < or = ka < or = 16pi, where k=2pi/lambda and a is particle radius. Several algorithms are evaluated and compared that are based on either simple matching to the Mie theory predictions or inverse tomography methods. In the tomography methods, a previously proposed algorithm [Opt. Express. 15, 12217 (2007)] was used after estimating the phase of the scattered data or adapted to use intensity-only data. In order to ensure stability, all algorithms' performance was evaluated in the presence of moderate noise. The performance varied as a function of particle size, refractive index, and algorithm. Results suggest that a scattering device that collects only the angular scatter that is perpendicular to the polarization of incident light, usually denoted as S(1), can be used to accurately estimate the size of homogeneous, low-contrast, spherical particles whose diameters are close to the wavelength of the incident light.
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Affiliation(s)
- Wei Li
- Wuhan National Laboratory for Optoelectronics, College of Optoelectronic Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
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54
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55
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Kami K, Rajesh S, Overduin M. Phospholipid-interacting proteins by solution-state NMR spectroscopy. Methods Mol Biol 2009; 462:291-306. [PMID: 19160678 DOI: 10.1007/978-1-60327-115-8_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Signaling lipids are found in specific subcellular membranes, where they recruit and regulate cytosolic proteins and contribute to bilayer structure and dynamics. These interactions are vital for signaling and membrane trafficking pathways and contribute to the organization, growth, and differentiation of the cell. However, the analysis of the physical and chemical mechanisms of membrane interaction and lipid recognition is technically challenging, motivating the development of new NMR methods to study lipid and bilayer binding by peripheral membrane proteins in solution. We describe methods that have been optimized for the FYVE and phox (PX) domains of the EEA1 and Vam7p proteins, respectively, both of which specifically recognize phosphatidylinositol 3-phosphate (PtdIns3P) within endocytic membranes. Solution-state NMR methods were used to characterize the phosphoinositide and membrane interaction sites and affinities and can be used to illustrate protein:micelle structures and phospholipid specificities. The methods are generally applicable and can be used to discover and characterize the phospholipid interactions of other membrane-interacting protein domains.
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Affiliation(s)
- Keiichiro Kami
- CR-UK Institute for Cancer Studies, School of Medicine, University of Birmingham, Birmingham, UK
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56
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Snell EH, Lauricella AM, Potter SA, Luft JR, Gulde SM, Collins RJ, Franks G, Malkowski MG, Cumbaa C, Jurisica I, DeTitta GT. Establishing a training set through the visual analysis of crystallization trials. Part II: crystal examples. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2008; 64:1131-7. [PMID: 19020351 PMCID: PMC2631118 DOI: 10.1107/s0907444908028059] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Accepted: 09/02/2008] [Indexed: 11/17/2022]
Abstract
As part of a training set for automated image analysis, crystallization screening experiments for 269 different macromolecules were visually analyzed and a set of crystal images extracted. Outcomes and trends are analyzed. In the automated image analysis of crystallization experiments, representative examples of outcomes can be obtained rapidly. However, while the outcomes appear to be diverse, the number of crystalline outcomes can be small. To complement a training set from the visual observation of 147 456 crystallization outcomes, a set of crystal images was produced from 106 and 163 macromolecules under study for the North East Structural Genomics Consortium (NESG) and Structural Genomics of Pathogenic Protozoa (SGPP) groups, respectively. These crystal images have been combined with the initial training set. A description of the crystal-enriched data set and a preliminary analysis of outcomes from the data are described.
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Affiliation(s)
- Edward H Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.
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57
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Busso D, Thierry JC, Moras D. The structural biology and genomics platform in strasbourg: an overview. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2008; 426:523-36. [PMID: 18542888 DOI: 10.1007/978-1-60327-058-8_35] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
This chapter describes the modules and facilities of the Structural Biology and Genomics Platform (SBGP), Strasbourg, France. The platform consists of three modules (cloning, mini-expression screening; optimization-large scale protein production; characterization, crystallization) with dedicated scientists, and other facilities for purifying recombinant proteins and solving three-dimensional (3D) structures. Strong collaborations have been established with the Integrative Bioinformatics and Genomics group, located in the same institition, for target selection and domains definition. To handle large numbers of samples, classical and new protocols were adapted to automation, increasing reproducibility and reducing error risks as well. Using the platform and its facilities, over 2,000 expression vectors have been constructed and more than 40 novel structures, of mostly human proteins, have been solved.
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Affiliation(s)
- Didier Busso
- Structural Biology and Genomics Platform, IGBMC, CNRS/INSERM/Université Louis Pasteur, Illkirch, France
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58
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An approach to quality management in structural biology: Biophysical selection of proteins for successful crystallization. J Struct Biol 2008; 162:451-9. [DOI: 10.1016/j.jsb.2008.03.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2007] [Revised: 03/05/2008] [Accepted: 03/06/2008] [Indexed: 11/23/2022]
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59
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Klupsch T, Walter A, Mühlig P, Hilgenfeld R. Combined kinetic osmometry and pyrometric microcalorimetry: Direct measurement of the protein–precipitant (salt) interaction. Colloids Surf A Physicochem Eng Asp 2008. [DOI: 10.1016/j.colsurfa.2007.11.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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60
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Lu P, Liu J, Melikishvili M, Fried MG, Chi YI. Crystallization of hepatocyte nuclear factor 4 alpha (HNF4 alpha) in complex with the HNF1 alpha promoter element. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:313-7. [PMID: 18391435 PMCID: PMC2374247 DOI: 10.1107/s1744309108007136] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Accepted: 03/14/2008] [Indexed: 12/31/2022]
Abstract
Sample preparation, characterization, crystallization and preliminary X-ray analysis are reported for the HNF4α–DNA binary complex. Hepatocyte nuclear factor 4α (HNF4α) is a member of the nuclear receptor superfamily that plays a central role in organ development and metabolic functions. Mutations on HNF4α cause maturity-onset diabetes of the young (MODY), a dominant monogenic cause of diabetes. In order to understand the molecular mechanism of promoter recognition and the molecular basis of disease-causing mutations, the recombinant HNF4α DNA-binding domain was prepared and used in a study of its binding properties and in crystallization with a 21-mer DNA fragment that contains the promoter element of another MODY gene, HNF1α. The HNF4α protein displays a cooperative and specific DNA-binding activity towards its target gene-recognition elements. Crystals of the complex diffract to 2.0 Å using a synchrotron-radiation source under cryogenic (100 K) conditions and belong to space group C2, with unit-cell parameters a = 121.63, b = 35.43, c = 70.99 Å, β = 119.36°. A molecular-replacement solution has been obtained and structure refinement is in progress. This structure and the binding studies will provide the groundwork for detailed functional and biochemical studies of the MODY mutants.
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Affiliation(s)
- Peng Lu
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536, USA
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61
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Protein-protein interaction on lysozyme crystallization revealed by rotational diffusion analysis. Biophys J 2008; 94:4484-92. [PMID: 18310245 DOI: 10.1529/biophysj.107.111872] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Intermolecular interactions between protein molecules diffusing in various environments underlie many biological processes as well as control protein crystallization, which is a crucial step in x-ray protein structure determinations. Protein interactions were investigated through protein rotational diffusion analysis. First, it was confirmed that tetragonal lysozyme crystals containing fluorescein-tagged lysozyme were successfully formed with the same morphology as that of native protein. Using this nondisruptive fluorescent tracer system, we characterized the effects of sodium chloride and ammonium sulfate concentrations on lysozyme-lysozyme interactions by steady-state and time-resolved fluorescence anisotropy measurements and the introduction of a novel interaction parameter, k(rot). The results suggested that the specific attractive interaction, which was reflected in the retardation of the protein rotational diffusion, was induced depending on the salt type and its concentration. The change in the attractive interactions also correlated with the crystallization/precipitation behavior of lysozyme. Moreover, we discuss the validity of our rotational diffusion analysis through comparison with the osmotic second virial coefficient, B(22), previously reported for lysozyme and those estimated from k(rot).
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62
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Chayen NE, Saridakis E. Protein crystallization: from purified protein to diffraction-quality crystal. Nat Methods 2008; 5:147-53. [DOI: 10.1038/nmeth.f.203] [Citation(s) in RCA: 262] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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63
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McKenna SA, Lindhout DA, Shimoike T, Puglisi JD. Biophysical and biochemical investigations of dsRNA-activated kinase PKR. Methods Enzymol 2008; 430:373-96. [PMID: 17913645 DOI: 10.1016/s0076-6879(07)30014-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Protein kinase RNA-activated (PKR) is a serine/threonine kinase that contains an N-terminal RNA-binding domain (dsRNA) and a C-terminal kinase domain. On binding viral dsRNA molecules, PKR can become activated and phosphorylate cellular targets, such as eukaryotic translation initiation factor 2alpha (eIF-2alpha). Phosphorylation of eIF-2alpha results in attenuation of protein translation initiation. Therefore, PKR plays an integral role in the antiviral response to cellular infection. Here we provide a methodological framework for probing PKR function by use of assays for phosphorylation, RNA-protein stability, PKR dimerization, and in vitro translation. These methods are complemented by nuclear magnetic resonance approaches for probing structural features of PKR activation. Considerations required for both PKR and dsRNA sample preparation are also discussed.
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Affiliation(s)
- Sean A McKenna
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA
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64
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Dumetz AC, Chockla AM, Kaler EW, Lenhoff AM. Protein phase behavior in aqueous solutions: crystallization, liquid-liquid phase separation, gels, and aggregates. Biophys J 2008; 94:570-83. [PMID: 18160663 PMCID: PMC2157236 DOI: 10.1529/biophysj.107.116152] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2007] [Accepted: 08/09/2007] [Indexed: 12/21/2022] Open
Abstract
The aggregates and gels commonly observed during protein crystallization have generally been considered disordered phases without further characterization. Here their physical nature is addressed by investigating protein salting-out in ammonium sulfate and sodium chloride for six proteins (ovalbumin, ribonuclease A, soybean trypsin inhibitor, lysozyme, and beta-lactoglobulin A and B) at 4 degrees C, 23 degrees C, and 37 degrees C. When interpreted within the framework of a theoretical phase diagram obtained for colloidal particles displaying short-range attractive interactions, the results show that the formation of aggregates can be interpreted theoretically in terms of a gas-liquid phase separation for aggregates that are amorphous or gel-like. A notable additional feature is the existence of a second aggregation line observed for both ovalbumin and ribonuclease A in ammonium sulfate, interpreted theoretically as the spinodal. Further investigation of ovalbumin and lysozyme reveals that the formation of aggregates can be interpreted, in light of theoretical results from mode-coupling theory, as a kinetically trapped state or a gel phase that occurs through the intermediate of a gas-liquid phase separation. Despite the limitations of simple theoretical models of short-range attractive interactions, such as their inability to reproduce the effect of temperature, they provide a framework useful to describe the main features of protein phase behavior.
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Affiliation(s)
- André C Dumetz
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716, USA
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65
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Derewenda ZS. Protein crystallization in drug design: towards a rational approach. Expert Opin Drug Discov 2007; 2:1329-40. [PMID: 23484529 DOI: 10.1517/17460441.2.10.1329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
X-ray crystallography is the method of choice for the detailed characterization of stereochemistry of interactions of drug leads and potential chemotherapeutics with their protein targets. The resulting atomic models allow for rational enhancement of the lead properties and consequently for the design of high-affinity inhibitors. However, a major bottleneck of the technique is the requirement for the protein and its complexes to yield high quality single crystals. Furthermore, it is highly desirable that such crystals diffract to high resolution, preferably ≥ 1.2 Å, revealing the structures in atomic detail. Unfortunately, only a small portion of proteins readily crystallize in that fashion. New approaches are being developed to circumvent this problem. One proposed option includes rational protein surface engineering to systematically improve the crystallizability of the protein. This is accomplished by creating surface patches readily mediating weak, but specific, intermolecular interactions that take on the role of crystal contacts during nucleation and crystal growth phase.
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Affiliation(s)
- Zygmunt S Derewenda
- University of Virginia, Integrated Center for Structure and Function Innovation (PSI2), Departments of Molecular Physiology and Biological Physics, PO Box 800736, Jordan Hall, Charlottesville, VA 22908-0736, USA +1 434 243 6842 ; +1 434 982 1616 ;
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66
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Benvenuti M, Mangani S. Crystallization of soluble proteins in vapor diffusion for x-ray crystallography. Nat Protoc 2007; 2:1633-51. [PMID: 17641629 DOI: 10.1038/nprot.2007.198] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The preparation of protein single crystals represents one of the major obstacles in obtaining the detailed 3D structure of a biological macromolecule. The complete automation of the crystallization procedures requires large investments in terms of money and labor, which are available only to large dedicated infrastructures and is mostly suited for genomic-scale projects. On the other hand, many research projects from departmental laboratories are devoted to the study of few specific proteins. Here, we try to provide a series of protocols for the crystallization of soluble proteins, especially the difficult ones, tailored for small-scale research groups. An estimate of the time needed to complete each of the steps described can be found at the end of each section.
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Affiliation(s)
- Manuela Benvenuti
- Dipartimento di Chimica, Università di Siena, Via Aldo Moro 2, Siena 53100, Italy
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67
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Suvarna S, Espinasse B, Qi R, Lubica R, Poncz M, Cines DB, Wiesner MR, Arepally GM. Determinants of PF4/heparin immunogenicity. Blood 2007; 110:4253-60. [PMID: 17848616 PMCID: PMC2234783 DOI: 10.1182/blood-2007-08-105098] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Heparin-induced thrombocytopenia (HIT) is an antibody-mediated disorder that occurs with variable frequency in patients exposed to heparin. HIT antibodies preferentially recognize large macromolecular complexes formed between PF4 and heparin over a narrow range of molar ratios, but the biophysical properties of complexes that initiate antibody production are unknown. To identify structural determinants underlying PF4/heparin immunogenicity, we characterized the in vitro interactions of murine PF4 (mPF4) and heparin with respect to light absorption, size, and surface charge (zeta potential). We show that PF4/heparin macromolecular assembly occurs through colloidal interactions, wherein heparin facilitates the growth of complexes through charge neutralization. The size of PF4/heparin macromolecules is governed by the molar ratios of the reactants. Maximal complex size occurs at molar ratios of PF4/heparin at which surface charge is neutral. When mice are immunized with complexes that differ in size and/or zeta potential, antibody formation varies inversely with heparin concentration and is most robust in animals immunized with complexes displaying a net positive zeta-potential. These studies suggest that the clinical heterogeneity in the HIT immune response may be due in part to requirements for specific biophysical parameters of the PF4/heparin complexes that occur in settings of intense platelet activation and PF4 release.
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Affiliation(s)
- Shayela Suvarna
- Division of Hematology, Duke University Medical Center, Durham, NC 27710, USA
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68
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Minor DL. The neurobiologist's guide to structural biology: a primer on why macromolecular structure matters and how to evaluate structural data. Neuron 2007; 54:511-33. [PMID: 17521566 PMCID: PMC3011226 DOI: 10.1016/j.neuron.2007.04.026] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Structural biology now plays a prominent role in addressing questions central to understanding how excitable cells function. Although interest in the insights gained from the definition and dissection of macromolecular anatomy is high, many neurobiologists remain unfamiliar with the methods employed. This primer aims to help neurobiologists understand approaches for probing macromolecular structure and where the limits and challenges remain. Using examples of macromolecules with neurobiological importance, the review covers X-ray crystallography, electron microscopy (EM), small-angle X-ray scattering (SAXS), and nuclear magnetic resonance (NMR) and biophysical methods with which these approaches are often paired: isothermal titration calorimetry (ITC), equilibrium analytical ultracentifugation, and molecular dynamics (MD).
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Affiliation(s)
- Daniel L Minor
- Cardiovascular Research Institute, Department of Biochemistry and Biophysics, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158-2330, USA.
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69
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Gutmann DAP, Mizohata E, Newstead S, Ferrandon S, Postis V, Xia X, Henderson PJF, van Veen HW, Byrne B. A high-throughput method for membrane protein solubility screening: the ultracentrifugation dispersity sedimentation assay. Protein Sci 2007; 16:1422-8. [PMID: 17567744 PMCID: PMC2206705 DOI: 10.1110/ps.072759907] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
One key to successful crystallization of membrane proteins is the identification of detergents that maintain the protein in a soluble, monodispersed state. Because of their hydrophobic nature, membrane proteins are particularly prone to forming insoluble aggregates over time. This nonspecific aggregation of the molecules reduces the likelihood of the regular association of the protein molecules essential for crystal lattice formation. Critical buffer components affecting the aggregation of membrane proteins include detergent choice, salt concentration, and presence of glycerol. The optimization of these parameters is often a time- and protein-consuming process. Here we describe a novel ultracentrifugation dispersity sedimentation (UDS) assay in which ultracentrifugation of very small (5 microL) volumes of purified, soluble membrane protein is combined with SDS-PAGE analysis to rapidly assess the degree of protein aggregation. The results from the UDS method correlate very well with established methods like size-exclusion chromatography (SEC), while consuming considerably less protein. In addition, the UDS method allows rapid screening of detergents for membrane protein crystallization in a fraction of the time required by SEC. Here we use the UDS method in the identification of suitable detergents and buffer compositions for the crystallization of three recombinant prokaryotic membrane proteins. The implications of our results for membrane protein crystallization prescreening are discussed.
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Affiliation(s)
- Daniel A P Gutmann
- Membrane Protein Crystallography Group, Division of Molecular Biosciences, Imperial College London, UK
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70
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Malawski GA, Hillig RC, Monteclaro F, Eberspaecher U, Schmitz AAP, Crusius K, Huber M, Egner U, Donner P, Müller-Tiemann B. Identifying protein construct variants with increased crystallization propensity--a case study. Protein Sci 2007; 15:2718-28. [PMID: 17132859 PMCID: PMC2242438 DOI: 10.1110/ps.062491906] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
This study describes an efficient multiparallel automated workflow of cloning, expression, purification, and crystallization of a large set of construct variants for isolated protein domains aimed at structure determination by X-ray crystallography. This methodology is applied to MAPKAP kinase 2, a key enzyme in the inflammation pathway and thus an attractive drug target. The study reveals a distinct subset of truncation variants with improved crystallization properties. These constructs distinguish themselves by increased solubility and stability during a parallel automated multistep purification process including removal of the recombinant tag. High-throughput protein melting point analysis characterizes this subset of constructs as particularly thermostable. Both parallel purification screening and melting point determination clearly identify residue 364 as the optimal C terminus for the kinase domain. Moreover, all three constructs that ultimately crystallized feature this C terminus. At the N terminus, only three amino acids differentiate a noncrystallizing from a crystallizing construct. This study addresses the very common issues associated with difficult to crystallize proteins, those of solubility and stability, and the crucial importance of particular residues in the formation of crystal contacts. A methodology is suggested that includes biophysical measurements to efficiently identify and produce construct variants of isolated protein domains which exhibit higher crystallization propensity.
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71
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Borgstahl GEO. How to use dynamic light scattering to improve the likelihood of growing macromolecular crystals. Methods Mol Biol 2007; 363:109-29. [PMID: 17272839 DOI: 10.1007/978-1-59745-209-0_6] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dynamic light scattering (DLS) has become one of the most useful diagnostic tools for crystallization. The main purpose of using DLS in crystal screening is to help the investigator understand the size distribution, stability, and aggregation state of macromolecules in solution. It can also be used to understand how experimental variables influence aggregation. With commercially available instruments, DLS is easy to perform, and most of the sample is recoverable. Most usefully, the homogeneity or monodispersity of a sample, as measured by DLS, can be predictive of crystallizability.
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Affiliation(s)
- Gloria E O Borgstahl
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
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72
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Dafforn TR. So how do you know you have a macromolecular complex? ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2006; 63:17-25. [PMID: 17164522 PMCID: PMC2483502 DOI: 10.1107/s0907444906047044] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Accepted: 11/07/2006] [Indexed: 11/16/2022]
Abstract
Structures of protein complexes offer some of the most interesting insights into biological processes. In this article, the methods required to show that the complex observed is the physiological one are investigated. Protein in crystal form is at an extremely high concentration and yet retains the complex secondary structure that defines an active protein. The protein crystal itself is made up of a repeating lattice of protein–protein and protein–solvent interactions. The problem that confronts any crystallographer is to identify those interactions that represent physiological interactions and those that do not. This review explores the tools that are available to provide such information using the original crystal liquor as a sample. The review is aimed at postgraduate and postdoctoral researchers who may well be coming up against this problem for the first time. Techniques are discussed that will provide information on the stoichiometry of complexes as well as low-resolution information on complex structure. Together, these data will help to identify the physiological complex.
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Affiliation(s)
- Timothy R Dafforn
- Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, England.
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73
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Puri M, Robin G, Cowieson N, Forwood JK, Listwan P, Hu SH, Guncar G, Huber T, Kellie S, Hume DA, Kobe B, Martin JL. Focusing in on structural genomics: The University of Queensland structural biology pipeline. ACTA ACUST UNITED AC 2006; 23:281-9. [PMID: 17097918 DOI: 10.1016/j.bioeng.2006.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Revised: 09/22/2006] [Accepted: 09/25/2006] [Indexed: 10/24/2022]
Abstract
The flood of new genomic sequence information together with technological innovations in protein structure determination have led to worldwide structural genomics (SG) initiatives. The goals of SG initiatives are to accelerate the process of protein structure determination, to fill in protein fold space and to provide information about the function of uncharacterized proteins. In the long-term, these outcomes are likely to impact on medical biotechnology and drug discovery, leading to a better understanding of disease as well as the development of new therapeutics. Here we describe the high throughput pipeline established at the University of Queensland in Australia. In this focused pipeline, the targets for structure determination are proteins that are expressed in mouse macrophage cells and that are inferred to have a role in innate immunity. The aim is to characterize the molecular structure and the biochemical and cellular function of these targets by using a parallel processing pipeline. The pipeline is designed to work with tens to hundreds of target gene products and comprises target selection, cloning, expression, purification, crystallization and structure determination. The structures from this pipeline will provide insights into the function of previously uncharacterized macrophage proteins and could lead to the validation of new drug targets for chronic obstructive pulmonary disease and arthritis.
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Affiliation(s)
- Munish Puri
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
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74
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Berger BW, Gendron CM, Lenhoff AM, Kaler EW. Effects of additives on surfactant phase behavior relevant to bacteriorhodopsin crystallization. Protein Sci 2006; 15:2682-96. [PMID: 17088325 PMCID: PMC2242436 DOI: 10.1110/ps.062370506] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The interactions leading to crystallization of the integral membrane protein bacteriorhodopsin solubilized in n-octyl-beta-D-glucoside were investigated. Osmotic second virial coefficients (B(22)) were measured by self-interaction chromatography using a wide range of additives and precipitants, including polyethylene glycol (PEG) and heptane-1,2,3-triol (HT). In all cases, attractive protein-detergent complex (PDC) interactions were observed near the surfactant cloud point temperature, and there is a correlation between the surfactant cloud point temperatures and PDC B(22) values. Light scattering, isothermal titration calorimetry, and tensiometry reveal that although the underlying reasons for the patterns of interaction may be different for various combinations of precipitants and additives, surfactant phase behavior plays an important role in promoting crystallization. In most cases, solution conditions that led to crystallization fell within a similar range of slightly negative B(22) values, suggesting that weakly attractive interactions are important as they are for soluble proteins. However, the sensitivity of the cloud point temperatures and resultant coexistence curves varied significantly as a function of precipitant type, which suggests that different types of forces are involved in driving phase separation depending on the precipitant used.
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Affiliation(s)
- Bryan W Berger
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716, USA.
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75
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Capelle MAH, Gurny R, Arvinte T. High throughput screening of protein formulation stability: practical considerations. Eur J Pharm Biopharm 2006; 65:131-48. [PMID: 17107777 DOI: 10.1016/j.ejpb.2006.09.009] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Revised: 09/01/2006] [Accepted: 09/18/2006] [Indexed: 11/28/2022]
Abstract
The formulation of protein drugs is a difficult and time-consuming process, mainly due to the complexity of protein structure and the very specific physical and chemical properties involved. Understanding protein degradation pathways is essential for the success of a biopharmaceutical drug. The present review concerns the application of high throughput screening techniques in protein formulation development. A protein high throughput formulation (HTF) platform is based on the use of microplates. Basically, the HTF platform consists of two parts: (i) sample preparation and (ii) sample analysis. Sample preparation involves automated systems for dispensing the drug and the formulation ingredients in both liquid and powder form. The sample analysis involves specific methods developed for each protein to investigate physical and chemical properties of the formulations in microplates. Examples are presented of the use of protein intrinsic fluorescence for the analysis of protein aqueous properties (e.g., conformation and aggregation). Different techniques suitable for HTF analysis are discussed and some of the issues concerning implementation are presented with reference to the use of microplates.
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Affiliation(s)
- Martinus A H Capelle
- Department of Pharmaceutics and Biopharmaceutics, University of Geneva, University of Lausanne, CH-1211 Geneva 4, Switzerland
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76
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Busso D, Poussin-Courmontagne P, Rosé D, Ripp R, Litt A, Thierry JC, Moras D. Structural genomics of eukaryotic targets at a laboratory scale. ACTA ACUST UNITED AC 2006; 6:81-8. [PMID: 16211503 DOI: 10.1007/s10969-005-1909-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2004] [Accepted: 01/16/2005] [Indexed: 11/29/2022]
Abstract
Structural genomics programs are distributed worldwide and funded by large institutions such as the NIH in United-States, the RIKEN in Japan or the European Commission through the SPINE network in Europe. Such initiatives, essentially managed by large consortia, led to technology and method developments at the different steps required to produce biological samples compatible with structural studies. Besides specific applications, method developments resulted mainly upon miniaturization and parallelization. The challenge that academic laboratories faces to pursue structural genomics programs is to produce, at a higher rate, protein samples. The Structural Biology and Genomics Department (IGBMC - Illkirch - France) is implicated in a structural genomics program of high eukaryotes whose goal is solving crystal structures of proteins and their complexes (including large complexes) related to human health and biotechnology. To achieve such a challenging goal, the Department has established a medium-throughput pipeline for producing protein samples suitable for structural biology studies. Here, we describe the setting up of our initiative from cloning to crystallization and we demonstrate that structural genomics may be manageable by academic laboratories by strategic investments in robotic and by adapting classical bench protocols and new developments, in particular in the field of protein expression, to parallelization.
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Affiliation(s)
- Didier Busso
- Département de Biologie et de Génomique Structurales, IGBMC, CNRS/INSERM/Université Louis Pasteur, Parc d'Innovation, 1 rue Laurent Fries, BP10142, 67404, Illkirch, cedex, France.
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77
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Lu P, Li Y, Gorman A, Chi YI. Crystallization of hepatocyte nuclear factor 1beta in complex with DNA. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:525-9. [PMID: 16754972 PMCID: PMC1581457 DOI: 10.1107/s1744309106015168] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Accepted: 04/25/2006] [Indexed: 01/02/2023]
Abstract
Hepatocyte nuclear factor 1beta (HNF1beta) is a member of the POU transcription-factor family and binds the target DNA as a dimer with nanomolar affinity. The HNF1beta-DNA complex has been prepared and crystallized by hanging-drop vapor diffusion in 6%(v/v) PEG 300, 5%(w/v) PEG 8000, 8%(v/v) glycerol and 0.1 M Tris pH 8.0. The crystals diffracted to 3.2 A (93.9% completeness) using a synchrotron-radiation source under cryogenic (100 K) conditions and belong to space group R3, with unit-cell parameters a = b = 172.69, c = 72.43 A. A molecular-replacement solution has been obtained and structure refinement is in progress. This structure will shed light on the molecular mechanism of promoter recognition by HNF1beta and the molecular basis of the disease-causing mutations found in it.
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Affiliation(s)
- Peng Lu
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Yun Li
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Amanda Gorman
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Young-In Chi
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536, USA
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78
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Wanka J, Peukert W. Die Bedeutung des zweiten osmotischen Virialkoeffizienten für die Proteinkristallisation. CHEM-ING-TECH 2006. [DOI: 10.1002/cite.200500125] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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79
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Renzi F, Panetta G, Vallone B, Brunori M, Arceci M, Bozzoni I, Laneve P, Caffarelli E. Large-scale purification and crystallization of the endoribonuclease XendoU: troubleshooting with His-tagged proteins. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:298-301. [PMID: 16511328 PMCID: PMC2197201 DOI: 10.1107/s1744309106006373] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Accepted: 02/20/2006] [Indexed: 11/11/2022]
Abstract
XendoU is the first endoribonuclease described in higher eukaryotes as being involved in the endonucleolytic processing of intron-encoded small nucleolar RNAs. It is conserved among eukaryotes and its viral homologue is essential in SARS replication and transcription. The large-scale purification and crystallization of recombinant XendoU are reported. The tendency of the recombinant enzyme to aggregate could be reversed upon the addition of chelating agents (EDTA, imidazole): aggregation is a potential drawback when purifying and crystallizing His-tagged proteins, which are widely used, especially in high-throughput structural studies. Purified monodisperse XendoU crystallized in two different space groups: trigonal P3(1)21, diffracting to low resolution, and monoclinic C2, diffracting to higher resolution.
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Affiliation(s)
- Fabiana Renzi
- Dipartimento di Scienze Biochimiche, University of Rome ‘La Sapienza’, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Gianna Panetta
- Dipartimento di Scienze Biochimiche, University of Rome ‘La Sapienza’, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Beatrice Vallone
- Dipartimento di Scienze Biochimiche, University of Rome ‘La Sapienza’, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Maurizio Brunori
- Dipartimento di Scienze Biochimiche, University of Rome ‘La Sapienza’, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Massimo Arceci
- Istituto di Biologia e Patologia Molecolari CNR, University of Rome ‘La Sapienza’, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Irene Bozzoni
- Istituto Pasteur–Fondazione Cenci Bolognetti, University of Rome ‘La Sapienza’, Piazzale Aldo Moro 5, 00185 Roma, Italy
- Istituto di Biologia e Patologia Molecolari CNR, University of Rome ‘La Sapienza’, Piazzale Aldo Moro 5, 00185 Roma, Italy
- Dipartimento di Genetica e Biologia Molecolare, University of Rome ‘La Sapienza’, Piazalle Aldo Moro 5, 00185 Roma, Italy
| | - Pietro Laneve
- Istituto di Biologia e Patologia Molecolari CNR, University of Rome ‘La Sapienza’, Piazzale Aldo Moro 5, 00185 Roma, Italy
- Dipartimento di Genetica e Biologia Molecolare, University of Rome ‘La Sapienza’, Piazalle Aldo Moro 5, 00185 Roma, Italy
| | - Elisa Caffarelli
- Istituto di Biologia e Patologia Molecolari CNR, University of Rome ‘La Sapienza’, Piazzale Aldo Moro 5, 00185 Roma, Italy
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80
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Banachowicz E. Light scattering studies of proteins under compression. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:405-13. [PMID: 16510323 DOI: 10.1016/j.bbapap.2006.01.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Revised: 12/23/2005] [Accepted: 01/17/2006] [Indexed: 11/21/2022]
Abstract
The scattering techniques are very convenient and effective in investigation of the shape, size and interactions of biological molecules close to their natural states in solution. However, it seems that from among a wide spectrum of scattering techniques, the light scattering ones have been relatively rarely used for the study of proteins under elevated hydrostatic pressure. This paper gives a brief description of the well developed possibilities of this technique for potential applications in the study of dissociation, aggregation and structural changes in proteins under compression. A short review of the already known applications is also given. Finally, the high-pressure dynamic light scattering results obtained by author on the lysozyme solution are shown and discussed.
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Affiliation(s)
- Ewa Banachowicz
- Faculty of Physics, Adam Mickiewicz University, Umultowska 85, PL-61-614 Poznañ, Poland.
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81
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Collins B, Stevens RC, Page R. Crystallization Optimum Solubility Screening: using crystallization results to identify the optimal buffer for protein crystal formation. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:1035-8. [PMID: 16511228 PMCID: PMC1978149 DOI: 10.1107/s1744309105035244] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2005] [Accepted: 10/27/2005] [Indexed: 11/10/2022]
Abstract
An optimal solubility screen is described that uses the results of crystallization trials to identify buffers that improve protein solubility and, in turn, crystallization success. This screen is useful not only for standard crystallization experiments, but also can easily be implemented into any high-throughput structure-determination pipeline. As a proof of principle, the predicted novel-fold protein AF2059 from Archaeoglobus fulgidus, which was known to precipitate in most buffers and particularly during concentration experiments, was selected. Using the crystallization results of 192 independent crystallization trials, it was possible to identify a buffer containing 100 mM CHES pH 9.25 that significantly improves its solubility. After transferring AF2059 into this ;optimum-solubility' buffer, the protein was rescreened for crystal formation against these same 192 conditions. Instead of extensive precipitation, as observed initially, it was found that 24 separate conditions produced crystals and the exchange of AF2059 into CHES buffer significantly improved crystallization success. Fine-screen optimization of these conditions led to the production of a crystal suitable for high-resolution (2.2 A) structure determination.
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Affiliation(s)
- Bernard Collins
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Raymond C. Stevens
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Rebecca Page
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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82
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Ahamed T, Ottens M, van Dedem GWK, van der Wielen LAM. Design of self-interaction chromatography as an analytical tool for predicting protein phase behavior. J Chromatogr A 2005; 1089:111-24. [PMID: 16130779 DOI: 10.1016/j.chroma.2005.06.065] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solution conditions under which proteins have a tendency to crystallize correspond to a slightly negative osmotic second virial coefficient (B22). A positive B22 value guarantees no crystallization to occur. On the other hand, a B22 value within the so called "crystallization slot" thermodynamically supports the crystallization processes but does not guarantee successful crystal growth. It is, however, a prerequisite for protein crystallization that the B22 value must be in the slightly negative regime. Self-interaction chromatography (SIC) is designed in this work as an analytical tool for determining B22 in a precise and reproducible way. The methodology was demonstrated in detail in terms of its theoretical basis, experimental methodology, troubleshooting and data analysis for different protein samples and solution conditions. The inherent error limit of SIC is found to be comparatively less than other B22 measurement techniques. The designed experimental approach was applied for mapping crystallization conditions of a model protein, i.e. lysozyme. Good agreement between the obtained lysozyme B22 values and literature values confirms the accuracy of the approach.
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Affiliation(s)
- Tangir Ahamed
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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83
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Chayen NE. Methods for separating nucleation and growth in protein crystallisation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2005; 88:329-37. [PMID: 15652248 DOI: 10.1016/j.pbiomolbio.2004.07.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The availability of high-quality crystals is crucial to the structure determination of proteins by X-ray diffraction. With the advent of structural genomics the pressure to produce crystals is greater than ever before. Finding favourable conditions for crystallisation is usually achieved by screening of the protein solution with numerous crystallising agents. Optimisation of the crystallisation conditions involves the manipulation of the crystallisation phase diagram with the aim of leading crystal growth in the direction that will produce the desired results. This article highlights recent advances in experimental methods for improving crystal size and quality by separating the nucleation and growth phases of crystallisation using the vapour diffusion and microbatch techniques.
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Affiliation(s)
- Naomi E Chayen
- Biological Structure and Function Section, Division of Biomedical Sciences, Sir Alexander Fleming Building, Imperial College London, Exhibition Road, London SW7 2AZ, UK.
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84
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Goldsmith-Fischman S, Kuzin A, Edstrom WC, Benach J, Shastry R, Xiao R, Acton TB, Honig B, Montelione GT, Hunt JF. The SufE sulfur-acceptor protein contains a conserved core structure that mediates interdomain interactions in a variety of redox protein complexes. J Mol Biol 2004; 344:549-65. [PMID: 15522304 DOI: 10.1016/j.jmb.2004.08.074] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2004] [Revised: 08/09/2004] [Accepted: 08/10/2004] [Indexed: 12/21/2022]
Abstract
The isc and suf operons in Escherichia coli represent alternative genetic systems optimized to mediate the essential metabolic process of iron-sulfur cluster (Fe-S) assembly under basal or oxidative-stress conditions, respectively. Some of the proteins in these two operons share strong sequence homology, e.g. the cysteine desulfurases IscS and SufS, and presumably play the same role in the oxygen-sensitive assembly process. However, other proteins in these operons share no significant homology and occur in a mutually exclusive manner in Fe-S assembly operons in other organisms (e.g. IscU and SufE). These latter proteins presumably play distinct roles adapted to the different assembly mechanisms used by the two systems. IscU has three invariant cysteine residues that function as a template for Fe-S assembly while accepting a sulfur atom from IscS. SufE, in contrast, does not function as an Fe-S assembly template but has been suggested to function as a shuttle protein that uses a persulfide linkage to a single invariant cysteine residue to transfer a sulfur atom from SufS to an alternative Fe-S assembly template. Here, we present and analyze the 2.0A crystal structure of E.coli SufE. The structure shows that the persulfide-forming cysteine occurs at the tip of a loop with elevated B-factors, where its side-chain is buried from solvent exposure in a hydrophobic cavity located beneath a highly conserved surface. Despite the lack of sequence homology, the core of SufE shows strong structural similarity to IscU, and the sulfur-acceptor site in SufE coincides with the location of the cysteine residues mediating Fe-S cluster assembly in IscU. Thus, a conserved core structure is implicated in mediating the interactions of both SufE and IscU with the mutually homologous cysteine desulfurase enzymes present in their respective operons. A similar core structure is observed in a domain found in a variety of Fe-S cluster containing flavoenzymes including xanthine dehydrogenase, where it also mediates interdomain interactions. Therefore, the core fold of SufE/IscU has been adapted to mediate interdomain interactions in diverse redox protein systems in the course of evolution.
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Affiliation(s)
- Sharon Goldsmith-Fischman
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
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85
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Spiegel PC, Murphy P, Stoddard BL. Surface-exposed hemophilic mutations across the factor VIII C2 domain have variable effects on stability and binding activities. J Biol Chem 2004; 279:53691-8. [PMID: 15471879 DOI: 10.1074/jbc.m409389200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Factor VIII (fVIII) is a plasma glycoprotein that functions as an essential cofactor in blood coagulation. Its carboxyl-terminal "C2" domain is responsible for binding to both activated platelet surfaces and von Willebrand factor. We characterized the effect of 20 hemophilia-associated missense mutations across this domain (that all occur in patients in vivo) on its stability and its binding activities. At least six of these mutations were severely destabilizing, and another four caused moderate destabilization and corresponding reductions in both binding functions. One mutant (A2201P) displayed a significant reduction in its membrane binding activity but normal von Willebrand factor binding, while two others (P2300S and R2304H) caused the opposite effect. Several mutations (including L2210P, V2223M, M2238V, and R2304C) displayed near wild-type stabilities and binding activities and may instead affect mRNA splicing or alternative properties or functions of the protein. This study demonstrated that von Willebrand factor and membrane binding activities can be uncoupled and uniquely disrupted by different mutations and that either effect can lead to similar reductions in clotting activity. It also illustrated how a heterogeneous genetic disorder causes diverse molecular phenotypes that result in similar disease states.
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Affiliation(s)
- P Clint Spiegel
- Graduate Program in Biomolecular Structure and Design, University of Washington, Seattle, WA 98195, USA
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86
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Abstract
Protein crystallisation has gained a new strategic and commercial relevance in the post-genomic era because of its pivotal role in structural genomics. Producing high-quality crystals has always been a bottleneck to structure determination and, with the advent of proteomics, this problem is becoming increasingly acute. The task of producing suitable crystals may be tackled using two approaches. The first relies on empirical techniques that are based mainly on trial and error, and what is perceived to be the 'art' of crystallisation. The second approach is aimed at gaining an understanding of the fundamental principles that govern crystallisation; this knowledge may be applied to design experimental methodology for producing high-quality crystals of medical and industrial interest.
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Affiliation(s)
- Naomi E Chayen
- Biological Structure and Function Section, Division of Biomedical Sciences, Faculty of Medicine, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, UK.
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