Structure of apo acyl carrier protein and a proposal to engineer protein crystallization through metal ions.

A topic of current interest is engineering surface mutations in order to improve the success rate of protein crystallization. This report explores the possibility of using metal-ion-mediated crystal-packing interactions to facilitate rational design. Escherichia coli apo acyl carrier protein was chosen as a test case because of its high content of negatively charged carboxylates suitable for metal binding with moderate affinity. The protein was successfully crystallized in the presence of zinc ions. The crystal structure was determined to 1.1 A resolution with MAD phasing using anomalous signals from the co-crystallized Zn(2+) ions. The case study suggested an integrated strategy for crystallization and structure solution of proteins via engineering surface Asp and Glu mutants, crystallizing them in the presence of metal ions such as Zn(2+) and solving the structures using anomalous signals.

[1]  F. Neidhart Escherichia coli and Salmonella. , 1996 .

[2]  D. Auld Zinc coordination sphere in biochemical zinc sites , 2001, Biometals.

[3]  Richard J Morris,et al.  ARP/wARP and automatic interpretation of protein electron density maps. , 2003, Methods in enzymology.

[4]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[5]  W G Hol,et al.  High-resolution structure of the diphtheria toxin repressor complexed with cobalt and manganese reveals an SH3-like third domain and suggests a possible role of phosphate as co-corepressor. , 1996, Biochemistry.

[6]  D. McRee Practical Protein Crystallography , 1993 .

[7]  C. Walsh,et al.  Holo-[acyl-carrier-protein] synthase of Escherichia coli. , 1997, Methods in enzymology.

[8]  K. Nagayama,et al.  Stabilization of protein crystals by electrostatic interactions as revealed by a numerical approach. , 1993, Journal of molecular biology.

[9]  J. Sodroski,et al.  Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody , 1998, Nature.

[10]  S L Mowbray,et al.  Strange bedfellows: interactions between acidic side-chains in proteins. , 1995, Journal of molecular biology.

[11]  J. E. Villafranca,et al.  Studies on engineering crystallizability by mutation of surface residues of human thymidylate synthase , 1992 .

[12]  J. Richardson,et al.  Preliminary X-ray diffraction studies of acyl carrier protein from Escherichia coli. , 1985, Journal of molecular biology.

[13]  D. Rice,et al.  X-ray crystallographic studies on butyryl-ACP reveal flexibility of the structure around a putative acyl chain binding site. , 2002, Structure.

[14]  Ivan Rayment,et al.  [12] Reductive alkylation of lysine residues to alter crystallization properties of proteins. , 1997, Methods in enzymology.

[15]  F. Arnold,et al.  A Metal-Chelating Lipid for 2D Protein Crystallization via Coordination of Surface Histidines , 1997 .

[16]  Martyn D Winn,et al.  Macromolecular TLS refinement in REFMAC at moderate resolutions. , 2003, Methods in enzymology.

[17]  B. Segelke,et al.  Efficiency analysis of sampling protocols used in protein crystallization screening , 2001 .

[18]  Thomas C Terwilliger,et al.  SOLVE and RESOLVE: automated structure solution and density modification. , 2003, Methods in enzymology.

[19]  W. L. Mock,et al.  Synergistic inhibition of carboxypeptidase A by zinc ion and imidazole. , 1999, Biochemical and biophysical research communications.

[20]  Zygmunt S Derewenda,et al.  Rational protein crystallization by mutational surface engineering. , 2004, Structure.

[21]  H. L. Carrell,et al.  Structural aspects of metal ion carboxylate interactions , 1988 .

[22]  E. Cedergren-Zeppezauer Crystal-structure determination of reduced nicotinamide adenine dinucleotide complex with horse liver alcohol dehydrogenase maintained in its apo conformation by zinc-bound imidazole. , 1983, Biochemistry.

[23]  A. Edmundson,et al.  Designing proteins to crystallize through beta-strand pairing. , 2003, Protein engineering.

[24]  D C Rees,et al.  Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive ion channel. , 1998, Science.

[25]  F. Arnold,et al.  Engineered metal-binding proteins: purification to protein folding. , 1991, Science.

[26]  Tetsuya Hayashi,et al.  Escherichia coli , 1983, CABI Compendium.

[27]  W G Hol,et al.  A model for the mechanism of human topoisomerase I. , 1998, Science.

[28]  C. Strader,et al.  Interaction of the unique competitive inhibitor imidazole with human carbonic anhydrase B. , 1977, Biochemistry.

[29]  A. Engelman,et al.  Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. , 1994, Science.

[30]  S H Bryant,et al.  Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers , 1997, Proteins.

[31]  P. Kraulis A program to produce both detailed and schematic plots of protein structures , 1991 .

[32]  Francis Rodier,et al.  Protein–protein interaction at crystal contacts , 1995, Proteins.

[33]  W. V. Shaw,et al.  Solving the structure of human H ferritin by genetically engineering intermolecular crystal contacts , 1991, Nature.