Abstract
Genetic selection provides an effective way to obtain active catalysts from a diverse population of protein variants. We have used this tool to investigate the role of loop sequences in determining the quaternary structure of a domain-swapped enzyme. By inserting random loops of four to seven residues into a dimeric chorismate mutase and selecting for functional variants by genetic complementation, we have obtained and characterized both monomeric and hexameric enzymes that retain considerable catalytic activity. The low percentage of active proteins recovered from these selection experiments indicates that relatively few loop sequences permit a change in quaternary structure without affecting active site structure. The results of our experiments suggest further that protein stability can be an important driving force in the evolution of oligomeric proteins.
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- Albright R. A., Mossing M. C., Matthews B. W. High-resolution structure of an engineered Cro monomer shows changes in conformation relative to the native dimer. Biochemistry. 1996 Jan 23;35(3):735–742. doi: 10.1021/bi951958n. [DOI] [PubMed] [Google Scholar]
- Bennett M. J., Choe S., Eisenberg D. Domain swapping: entangling alliances between proteins. Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):3127–3131. doi: 10.1073/pnas.91.8.3127. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bennett M. J., Schlunegger M. P., Eisenberg D. 3D domain swapping: a mechanism for oligomer assembly. Protein Sci. 1995 Dec;4(12):2455–2468. doi: 10.1002/pro.5560041202. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Brunet A. P., Huang E. S., Huffine M. E., Loeb J. E., Weltman R. J., Hecht M. H. The role of turns in the structure of an alpha-helical protein. Nature. 1993 Jul 22;364(6435):355–358. doi: 10.1038/364355a0. [DOI] [PubMed] [Google Scholar]
- Castagnoli L., Vetriani C., Cesareni G. Linking an easily detectable phenotype to the folding of a common structural motif. Selection of rare turn mutations that prevent the folding of Rop. J Mol Biol. 1994 Apr 8;237(4):378–387. doi: 10.1006/jmbi.1994.1241. [DOI] [PubMed] [Google Scholar]
- Chen Y. H., Yang J. T., Chau K. H. Determination of the helix and beta form of proteins in aqueous solution by circular dichroism. Biochemistry. 1974 Jul 30;13(16):3350–3359. doi: 10.1021/bi00713a027. [DOI] [PubMed] [Google Scholar]
- Di Donato A., Cafaro V., D'Alessio G. Ribonuclease A can be transformed into a dimeric ribonuclease with antitumor activity. J Biol Chem. 1994 Jul 1;269(26):17394–17396. [PubMed] [Google Scholar]
- Dickason R. R., Huston D. P. Creation of a biologically active interleukin-5 monomer. Nature. 1996 Feb 15;379(6566):652–655. doi: 10.1038/379652a0. [DOI] [PubMed] [Google Scholar]
- Green S. M., Gittis A. G., Meeker A. K., Lattman E. E. One-step evolution of a dimer from a monomeric protein. Nat Struct Biol. 1995 Sep;2(9):746–751. doi: 10.1038/nsb0995-746. [DOI] [PubMed] [Google Scholar]
- Greenfield N., Fasman G. D. Computed circular dichroism spectra for the evaluation of protein conformation. Biochemistry. 1969 Oct;8(10):4108–4116. doi: 10.1021/bi00838a031. [DOI] [PubMed] [Google Scholar]
- Görisch H. On the mechanism of the chorismate mutase reaction. Biochemistry. 1978 Sep 5;17(18):3700–3705. doi: 10.1021/bi00611a004. [DOI] [PubMed] [Google Scholar]
- Janin J., Miller S., Chothia C. Surface, subunit interfaces and interior of oligomeric proteins. J Mol Biol. 1988 Nov 5;204(1):155–164. doi: 10.1016/0022-2836(88)90606-7. [DOI] [PubMed] [Google Scholar]
- Ku J., Schultz P. G. Alternate protein frameworks for molecular recognition. Proc Natl Acad Sci U S A. 1995 Jul 3;92(14):6552–6556. doi: 10.1073/pnas.92.14.6552. [DOI] [PMC free article] [PubMed] [Google Scholar]
- MacBeath G., Kast P., Hilvert D. A small, thermostable, and monofunctional chorismate mutase from the archaeon Methanococcus jannaschii. Biochemistry. 1998 Jul 14;37(28):10062–10073. doi: 10.1021/bi980449t. [DOI] [PubMed] [Google Scholar]
- MacBeath G., Kast P., Hilvert D. Exploring sequence constraints on an interhelical turn using in vivo selection for catalytic activity. Protein Sci. 1998 Feb;7(2):325–335. doi: 10.1002/pro.5560070212. [DOI] [PMC free article] [PubMed] [Google Scholar]
- MacBeath G., Kast P., Hilvert D. Redesigning enzyme topology by directed evolution. Science. 1998 Mar 20;279(5358):1958–1961. doi: 10.1126/science.279.5358.1958. [DOI] [PubMed] [Google Scholar]
- MacBeath G., Kast P. UGA read-through artifacts--when popular gene expression systems need a pATCH. Biotechniques. 1998 May;24(5):789–794. doi: 10.2144/98245st02. [DOI] [PubMed] [Google Scholar]
- Mossing M. C., Sauer R. T. Stable, monomeric variants of lambda Cro obtained by insertion of a designed beta-hairpin sequence. Science. 1990 Dec 21;250(4988):1712–1715. doi: 10.1126/science.2148648. [DOI] [PubMed] [Google Scholar]
- Nagi A. D., Regan L. An inverse correlation between loop length and stability in a four-helix-bundle protein. Fold Des. 1997;2(1):67–75. doi: 10.1016/S1359-0278(97)00007-2. [DOI] [PubMed] [Google Scholar]
- Neet K. E., Timm D. E. Conformational stability of dimeric proteins: quantitative studies by equilibrium denaturation. Protein Sci. 1994 Dec;3(12):2167–2174. doi: 10.1002/pro.5560031202. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Predki P. F., Regan L. Redesigning the topology of a four-helix-bundle protein: monomeric Rop. Biochemistry. 1995 Aug 8;34(31):9834–9839. doi: 10.1021/bi00031a003. [DOI] [PubMed] [Google Scholar]
- Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Studier F. W., Moffatt B. A. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol. 1986 May 5;189(1):113–130. doi: 10.1016/0022-2836(86)90385-2. [DOI] [PubMed] [Google Scholar]
- Studier F. W., Rosenberg A. H., Dunn J. J., Dubendorff J. W. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 1990;185:60–89. doi: 10.1016/0076-6879(90)85008-c. [DOI] [PubMed] [Google Scholar]
- Trinkl S., Glockshuber R., Jaenicke R. Dimerization of beta B2-crystallin: the role of the linker peptide and the N- and C-terminal extensions. Protein Sci. 1994 Sep;3(9):1392–1400. doi: 10.1002/pro.5560030905. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Van Dyke M. W., Sirito M., Sawadogo M. Single-step purification of bacterially expressed polypeptides containing an oligo-histidine domain. Gene. 1992 Feb 1;111(1):99–104. doi: 10.1016/0378-1119(92)90608-r. [DOI] [PubMed] [Google Scholar]
- Vlassi M., Steif C., Weber P., Tsernoglou D., Wilson K. S., Hinz H. J., Kokkinidis M. Restored heptad pattern continuity does not alter the folding of a four-alpha-helix bundle. Nat Struct Biol. 1994 Oct;1(10):706–716. doi: 10.1038/nsb1094-706. [DOI] [PubMed] [Google Scholar]
- Zhang S., Kongsaeree P., Clardy J., Wilson D. B., Ganem B. Site-directed mutagenesis of monofunctional chorismate mutase engineered from the E. coli P-protein. Bioorg Med Chem. 1996 Jul;4(7):1015–1020. doi: 10.1016/0968-0896(96)00099-5. [DOI] [PubMed] [Google Scholar]