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Li L, Nan J, Li D, Brostromer E, Wang Z, Liu C, Hou Q, Fan X, Ye Z, Su XD. Structural genomics studies of human caries pathogen Streptococcus mutans. ACTA ACUST UNITED AC 2014; 15:91-9. [PMID: 24474570 DOI: 10.1007/s10969-014-9172-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 01/17/2014] [Indexed: 10/25/2022]
Abstract
Gram-positive bacterium Streptococcus mutans is the primary causative agent of human dental caries. To better understand this pathogen at the atomic structure level and to establish potential drug and vaccine targets, we have carried out structural genomics research since 2005. To achieve the goal, we have developed various in-house automation systems including novel high-throughput crystallization equipment and methods, based on which a large-scale, high-efficiency and low-cost platform has been establish in our laboratory. From a total of 1,963 annotated open reading frames, 1,391 non-membrane targets were selected prioritized by protein sequence similarities to unknown structures, and clustered by restriction sites to allow for cost-effective high-throughput conventional cloning. Selected proteins were over-expressed in different strains of Escherichia coli. Clones expressed soluble proteins were selected, expanded, and expressed proteins were purified and subjected to crystallization trials. Finally, protein crystals were subjected to X-ray analysis and structures were determined by crystallographic methods. Using the previously established procedures, we have so far obtained more than 200 kinds of protein crystals and 100 kinds of crystal structures involved in different biological pathways. In this paper we demonstrate and review a possibility of performing structural genomics studies at moderate laboratory scale. Furthermore, the techniques and methods developed in our study can be widely applied to conventional structural biology research practice.
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Affiliation(s)
- Lanfen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China,
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Gräslund S, Nordlund P, Weigelt J, Hallberg BM, Bray J, Gileadi O, Knapp S, Oppermann U, Arrowsmith C, Hui R, Ming J, dhe-Paganon S, Park HW, Savchenko A, Yee A, Edwards A, Vincentelli R, Cambillau C, Kim R, Kim SH, Rao Z, Shi Y, Terwilliger TC, Kim CY, Hung LW, Waldo GS, Peleg Y, Albeck S, Unger T, Dym O, Prilusky J, Sussman JL, Stevens RC, Lesley SA, Wilson IA, Joachimiak A, Collart F, Dementieva I, Donnelly MI, Eschenfeldt WH, Kim Y, Stols L, Wu R, Zhou M, Burley SK, Emtage JS, Sauder JM, Thompson D, Bain K, Luz J, Gheyi T, Zhang F, Atwell S, Almo SC, Bonanno JB, Fiser A, Swaminathan S, Studier FW, Chance MR, Sali A, Acton TB, Xiao R, Zhao L, Ma LC, Hunt JF, Tong L, Cunningham K, Inouye M, Anderson S, Janjua H, Shastry R, Ho CK, Wang D, Wang H, Jiang M, Montelione GT, Stuart DI, Owens RJ, Daenke S, Schütz A, Heinemann U, Yokoyama S, Büssow K, Gunsalus KC. Protein production and purification. Nat Methods 2008; 5:135-46. [PMID: 18235434 PMCID: PMC3178102 DOI: 10.1038/nmeth.f.202] [Citation(s) in RCA: 614] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In selecting a method to produce a recombinant protein, a researcher is faced with a bewildering array of choices as to where to start. To facilitate decision-making, we describe a consensus 'what to try first' strategy based on our collective analysis of the expression and purification of over 10,000 different proteins. This review presents methods that could be applied at the outset of any project, a prioritized list of alternate strategies and a list of pitfalls that trip many new investigators.
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Cornvik T, Dahlroth SL, Magnusdottir A, Flodin S, Engvall B, Lieu V, Ekberg M, Nordlund P. An efficient and generic strategy for producing soluble human proteins and domains in E. coli by screening construct libraries. Proteins 2006; 65:266-73. [PMID: 16948159 DOI: 10.1002/prot.21090] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The implementation of generic and efficient technologies for the production of recombinant eukaryotic proteins remains an outstanding challenge in structural genomics programs. We have recently developed a new method for rapid identification of soluble protein expression in E. coli, the colony filtration blot (CoFi blot). In this study, the CoFi blot was used to screen libraries where the N-terminal translation start point was randomized. To investigate the efficiency of this strategy, we have attributed a large number of proteins to this process. In a set of 32 mammalian proteins, we were able to double the success rate (from 34 to 68%) of producing soluble and readily purifiable proteins in E. coli. Most of the selected constructs had their N-termini close to predicted domain borders and the method therefore provides a mean for experimental "domain foot printing." Surprisingly, for most of the targets, we also observed expressing constructs that were close to full-length. In summary this strategy constitutes a generic and efficient method for producing mammalian proteins for structural and functional studies.
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Affiliation(s)
- Tobias Cornvik
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
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Zhou CZ, Meyer P, Quevillon-Cheruel S, Li De La Sierra-Gallay I, Collinet B, Graille M, Blondeau K, François JM, Leulliot N, Sorel I, Poupon A, Janin J, Van Tilbeurgh H. Crystal structure of the YML079w protein from Saccharomyces cerevisiae reveals a new sequence family of the jelly-roll fold. Protein Sci 2005; 14:209-15. [PMID: 15608122 PMCID: PMC2253319 DOI: 10.1110/ps.041121305] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We determined the three-dimensional crystal structure of the protein YML079wp, encoded by a hypothetical open reading frame from Saccharomyces cerevisiae to a resolution of 1.75 A. The protein has no close homologs and its molecular and cellular functions are unknown. The structure of the protein is a jelly-roll fold consisting of ten beta-strands organized in two parallel packed beta-sheets. The protein has strong structural resemblance to the plant storage and ligand binding proteins (canavalin, glycinin, auxin binding protein) but also to some plant and bacterial enzymes (epimerase, germin). The protein forms homodimers in the crystal, confirming measurements of its molecular mass in solution. Two monomers have their beta-sheet packed together to form the dimer. The presence of a hydrophobic ligand in a well conserved pocket inside the barrel and local sequence similarity with bacterial epimerases may suggest a biochemical function for this protein.
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Affiliation(s)
- Cong-Zhao Zhou
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Centre National de la Recherche Scientifique-Unité Mixte de Recherche 8619, Université Paris-Sud, 91405 Orsay, France
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Huang YJ, Moseley HNB, Baran MC, Arrowsmith C, Powers R, Tejero R, Szyperski T, Montelione GT. An integrated platform for automated analysis of protein NMR structures. Methods Enzymol 2005; 394:111-41. [PMID: 15808219 DOI: 10.1016/s0076-6879(05)94005-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Recent developments provide automated analysis of NMR assignments and three-dimensional (3D) structures of proteins. These approaches are generally applicable to proteins ranging from about 50 to 150 amino acids. In this chapter, we summarize progress by the Northeast Structural Genomics Consortium in standardizing the NMR data collection process for protein structure determination and in building an integrated platform for automated protein NMR structure analysis. Our integrated platform includes the following principal steps: (1) standardized NMR data collection, (2) standardized data processing (including spectral referencing and Fourier transformation), (3) automated peak picking and peak list editing, (4) automated analysis of resonance assignments, (5) automated analysis of NOESY data together with 3D structure determination, and (6) methods for protein structure validation. In particular, the software AutoStructure for automated NOESY data analysis is described in this chapter, together with a discussion of practical considerations for its use in high-throughput structure production efforts. The critical area of data quality assessment has evolved significantly over the past few years and involves evaluation of both intermediate and final peak lists, resonance assignments, and structural information derived from the NMR data. Methods for quality control of each of the major automated analysis steps in our platform are also discussed. Despite significant remaining challenges, when good quality data are available, automated analysis of protein NMR assignments and structures with this platform is both fast and reliable.
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Affiliation(s)
- Yuanpeng Janet Huang
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
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Liu JF, Wang XQ, Wang ZX, Chen JR, Jiang T, An XM, Chang WR, Liang DC. Crystal structure of KD93, a novel protein expressed in human hematopoietic stem/progenitor cells. J Struct Biol 2004; 148:370-4. [PMID: 15522784 DOI: 10.1016/j.jsb.2004.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2004] [Revised: 06/11/2004] [Indexed: 11/19/2022]
Abstract
The crystal structure of a novel hypothetical protein, KD93, expressed in human hematopoietic stem/progenitor cells, was determined at 1.9A resolution using the multiple-wavelength anomalous dispersion (MAD) method. The protein KD93, which is encoded by the open reading frame HSPC031, is a NIP7 homologue and belongs to the UPF0113 family. The structural and functional information for the group of homologues has not yet been determined. Crystallographic analysis revealed that the overall fold of KD93 consists of two interlinked alpha/beta domains. Structure-based homology analysis with DALI revealed that the C domain of KD93 matches the PUA domain of some RNA modification enzymes, especially that of archaeosine tRNA-ribosyltransferase (ArcTGT), which suggests that its possible molecular function is related to RNA binding. The difference between the RNA binding regions of KD93 and ArcTGT in amino acid constitution and surface electrostatic potential indicate that they may have different RNA binding modes. The N domain of KD93 is a unique structure with no obvious similarity to other proteins with known three-dimensional structures. The high-resolution structure of KD93 provides a first view of a member of the family of hypothetical proteins. And the structure provides a framework to deduce and assay the molecular function of other proteins of the UPF0113 family.
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Affiliation(s)
- Jun-Feng Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Academia Sinica, Beijing 100101, People's Republic of China
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Baran MC, Huang YJ, Moseley HNB, Montelione GT. Automated analysis of protein NMR assignments and structures. Chem Rev 2004; 104:3541-56. [PMID: 15303826 DOI: 10.1021/cr030408p] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael C Baran
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers University, 679 Hoes Lane, Piscataway, NJ 08854, USA
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Wunderlich Z, Acton TB, Liu J, Kornhaber G, Everett J, Carter P, Lan N, Echols N, Gerstein M, Rost B, Montelione GT. The protein target list of the Northeast Structural Genomics Consortium. Proteins 2004; 56:181-7. [PMID: 15211503 DOI: 10.1002/prot.20091] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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