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Tsai MY, Chang WH, Liang JY, Lin LL, Chang GG, Chang HP. Essential covalent linkage between the chymotrypsin-like domain and the extra domain of the SARS-CoV main protease. J Biochem 2010; 148:349-58. [PMID: 20587646 PMCID: PMC7110190 DOI: 10.1093/jb/mvq071] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The main protease of the coronavirus causing severe acute respiratory syndrome performs proteolytic processing of the viral polyproteins. The active form of the enzyme is a homodimer with each subunit consisting of three structural domains. Domains I and II, hosting the complete catalytic machinery, constitute the N-terminal chymotrypsin-like folding scaffold and connect to the extra C-terminal domain III by a long loop. Previously, the domain III-truncated enzyme was demonstrated to fold independently into an intact chymotrypsin-like fold, but it showed no enzyme activity. To further delineate the structure-function relationships of the domain III and the long loop, we generated some truncated and mutated M(pro) forms bearing various combinations of the loop with other structural parts of the enzyme. Their conformational and association properties were investigated in detail. Far-ultraviolet circular dichroism (CD) measurements revealed that these fragments could fold independently. The secondary, tertiary and quaternary structures of these mixtures were monitored by CD, fluorescence spectroscopy and analytical ultracentrifugation. However, no enzyme activity was observed for any mutant or mixtures. These observations indicate that the covalent linkage between the chymotrypsin like and the extra domain is essential for enzymatic activity of the main coronavirus protease and for the integrity of its quaternary structure.
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Affiliation(s)
- Meng-Ying Tsai
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, 155 Li-Nong St., Section 2, Taipei 112, Taiwan
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2
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Fluorescence complementation via EF-hand interactions. J Biotechnol 2009; 142:205-13. [PMID: 19500621 DOI: 10.1016/j.jbiotec.2009.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Revised: 05/06/2009] [Accepted: 05/12/2009] [Indexed: 11/20/2022]
Abstract
Fluorescence complementation technology with fluorescent proteins is a powerful approach to investigate molecular recognition by monitoring fluorescence enhancement when non-fluorescent fragments of fluorescent proteins are fused with target proteins, resulting in a new fluorescent complex. Extension of the technology to calcium-dependent protein-protein interactions has, however, rarely been reported. Here, a linker containing trypsin cleavage sites was grafted onto enhanced green fluorescent protein (EGFP). Under physiological conditions, a modified fluorescent protein, EGFP-T1, was cleaved into two major fragments which continue to interact with each other, exhibiting strong optical and fluorescence signals. The larger fragment, comprised of amino acids 1-172, including the chromophore, retains only weak fluorescence. Strong green fluorescence was observed when plasmid DNA encoding complementary EGFP fragments fused to the EF-hand motifs of calbindin D9k (EF1 and EF2) were co-transfected into HeLa cells, suggesting that chromophore maturation and fluorescence complementation from EGFP fragments can be accomplished intracellularly by reassembly of EF-hand motifs, which have a strong tendency for dimerization. Moreover, an intracellular calcium increase upon addition of a calcium ionophore, ionomycin in living cells, results in an increase of fluorescence signal. This novel application of calcium-dependent fluorescence complementation has the potential to monitor protein-protein interactions triggered by calcium signalling pathways in living cells.
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3
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Protein GB1 folding and assembly from structural elements. Int J Mol Sci 2009; 10:1552-1566. [PMID: 19468325 PMCID: PMC2680633 DOI: 10.3390/ijms10041552] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Revised: 03/20/2009] [Accepted: 03/31/2009] [Indexed: 11/17/2022] Open
Abstract
Folding of the Protein G B1 domain (PGB1) shifts with increasing salt concentration from a cooperative assembly of inherently unstructured subdomains to an assembly of partly pre-folded structures. The salt-dependence of pre-folding contributes to the stability minimum observed at physiological salt conditions. Our conclusions are based on a study in which the reconstitution of PGB1 from two fragments was studied as a function of salt concentrations and temperature using circular dichroism spectroscopy. Salt was found to induce an increase in β-hairpin structure for the C-terminal fragment (residues 41 – 56), whereas no major salt effect on structure was observed for the isolated N-terminal fragment (residues 1 – 41). In line with the increasing evidence on the interrelation between fragment complementation and stability of the corresponding intact protein, we also find that salt effects on reconstitution can be predicted from salt dependence of the stability of the intact protein. Our data show that our variant (which has the mutations T2Q, N8D, N37D and reconstitutes in a manner similar to the wild type) displays the lowest equilibrium association constant around physiological salt concentration, with higher affinity observed both at lower and higher salt concentration. This corroborates the salt effects on the stability towards denaturation of the intact protein, for which the stability at physiological salt is lower compared to both lower and higher salt concentrations. Hence we conclude that reconstitution reports on molecular factors that govern the native states of proteins.
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Haspel N, Tsai CJ, Wolfson H, Nussinov R. Reducing the computational complexity of protein folding via fragment folding and assembly. Protein Sci 2003; 12:1177-87. [PMID: 12761388 PMCID: PMC2323902 DOI: 10.1110/ps.0232903] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2002] [Revised: 12/23/2002] [Accepted: 02/23/2003] [Indexed: 10/27/2022]
Abstract
Understanding, and ultimately predicting, how a 1-D protein chain reaches its native 3-D fold has been one of the most challenging problems during the last few decades. Data increasingly indicate that protein folding is a hierarchical process. Hence, the question arises as to whether we can use the hierarchical concept to reduce the practically intractable computational times. For such a scheme to work, the first step is to cut the protein sequence into fragments that form local minima on the polypeptide chain. The conformations of such fragments in solution are likely to be similar to those when the fragments are embedded in the native fold, although alternate conformations may be favored during the mutual stabilization in the combinatorial assembly process. Two elements are needed for such cutting: (1) a library of (clustered) fragments derived from known protein structures and (2) an assignment algorithm that selects optimal combinations to "cover" the protein sequence. The next two steps in hierarchical folding schemes, not addressed here, are the combinatorial assembly of the fragments and finally, optimization of the obtained conformations. Here, we address the first step in a hierarchical protein-folding scheme. The input is a target protein sequence and a library of fragments created by clustering building blocks that were generated by cutting all protein structures. The output is a set of cutout fragments. We briefly outline a graph theoretic algorithm that automatically assigns building blocks to the target sequence, and we describe a sample of the results we have obtained.
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Affiliation(s)
- Nurit Haspel
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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6
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Tsai CJ, Polverino de Laureto P, Fontana A, Nussinov R. Comparison of protein fragments identified by limited proteolysis and by computational cutting of proteins. Protein Sci 2002; 11:1753-70. [PMID: 12070328 PMCID: PMC2373665 DOI: 10.1110/ps.4100102] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2001] [Revised: 04/17/2002] [Accepted: 04/17/2002] [Indexed: 10/14/2022]
Abstract
Here we present a comparison between protein fragments produced by limited proteolysis and those identified by computational cutting based on the building block folding model. The principles upon which the two methods are based are different. Limited proteolysis of natively folded proteins occurs at flexible sites and never at the level of chain segments of regular secondary structure such as alpha-helices. Therefore, the targets for limited proteolysis are locally unfolded regions. In contrast, the computational cutting algorithm considers the compactness of the fragments, their nonpolar buried surface area, and their isolatedness, that is, the surface area which was buried prior to the cutting and becomes exposed subsequently. Despite the different criteria, there is an overall correspondence between sites or regions of limited proteolysis with those identified by computational cutting. The computational cutting method has been applied to several model proteins for which detailed limited proteolysis data are available, namely apomyoglobin, cytochrome c, ribonuclease A, alpha-lactalbumin, and thermolysin. As expected, more cuts are obtained computationally than experimentally and the agreement is better when a number of proteolytic enzymes are used. For example, cytochrome c is cleaved by thermolysin at 56-57, 45-46, and at 80-81, and by proteinase K at 48-49 and 50-51. Incubation of the noncovalent and native-like complex of cytochrome c fragments 1-56 and 57-104 with proteinase K yielded the gapped protein species 1-48/57-104 and finally 1-40/57-104. Computational cutting of cytochrome c reproduced the major experimental observations, with cuts at 47, 64-65 or 65-66 and 80-81 and an unstable 32-47 region not assigned to any building block. The next step, not addressed in this work, is to probe the ability of the generated fragments to fold independently. Since both the computational algorithm and limited proteolysis attempt to dissect the protein folding problem, the general agreement between the two procedures is gratifying. This consistency allows us to propose the use of limited proteolysis to produce protein fragments that can adopt an independent folding and, therefore, to study folding intermediates. The results of the present study appear to validate the building block folding model and are in line with the proposal that protein folding is a hierarchical process, where parts constituting local minima of energy fold first, with their subsequent association and mutual stabilization to finally yield the global fold.
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Affiliation(s)
- Chung-Jung Tsai
- Laboratory of Experimental and Computational Biology, National Cancer Institute, Frederick, MD 21702, USA
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7
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Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins 2002; 47:409-43. [PMID: 12001221 DOI: 10.1002/prot.10115] [Citation(s) in RCA: 771] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The docking field has come of age. The time is ripe to present the principles of docking, reviewing the current state of the field. Two reasons are largely responsible for the maturity of the computational docking area. First, the early optimism that the very presence of the "correct" native conformation within the list of predicted docked conformations signals a near solution to the docking problem, has been replaced by the stark realization of the extreme difficulty of the next scoring/ranking step. Second, in the last couple of years more realistic approaches to handling molecular flexibility in docking schemes have emerged. As in folding, these derive from concepts abstracted from statistical mechanics, namely, populations. Docking and folding are interrelated. From the purely physical standpoint, binding and folding are analogous processes, with similar underlying principles. Computationally, the tools developed for docking will be tremendously useful for folding. For large, multidomain proteins, domain docking is probably the only rational way, mimicking the hierarchical nature of protein folding. The complexity of the problem is huge. Here we divide the computational docking problem into its two separate components. As in folding, solving the docking problem involves efficient search (and matching) algorithms, which cover the relevant conformational space, and selective scoring functions, which are both efficient and effectively discriminate between native and non-native solutions. It is universally recognized that docking of drugs is immensely important. However, protein-protein docking is equally so, relating to recognition, cellular pathways, and macromolecular assemblies. Proteins function when they are bound to other molecules. Consequently, we present the review from both the computational and the biological points of view. Although large, it covers only partially the extensive body of literature, relating to small (drug) and to large protein-protein molecule docking, to rigid and to flexible. Unfortunately, when reviewing these, a major difficulty in assessing the results is the non-uniformity in the formats in which they are presented in the literature. Consequently, we further propose a way to rectify it here.
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Affiliation(s)
- Inbal Halperin
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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Michnick SW, Remy I, Campbell-Valois FX, Vallée-Bélisle A, Pelletier JN. Detection of protein-protein interactions by protein fragment complementation strategies. Methods Enzymol 2001; 328:208-30. [PMID: 11075347 DOI: 10.1016/s0076-6879(00)28399-7] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- S W Michnick
- Département de Biochimie, Université de Montréal, Québec, Canada
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9
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Ni X, Schachman HK. In vivo assembly of aspartate transcarbamoylase from fragmented and circularly permuted catalytic polypeptide chains. Protein Sci 2001; 10:519-27. [PMID: 11344320 PMCID: PMC2374128 DOI: 10.1110/ps.38901] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Previous studies on Escherichia coli aspartate transcarbamoylase (ATCase) demonstrated that active, stable enzyme was formed in vivo from complementing polypeptides of the catalytic (c) chain encoded by gene fragments derived from the pyrBI operon. However, the enzyme lacked the allosteric properties characteristic of wild-type ATCase. In order to determine whether the loss of homotropic and heterotropic properties was attributable to the location of the interruption in the polypeptide chain rather than to the lack of continuity, we constructed a series of fragmented genes so that the breaks in the polypeptide chains would be dispersed in different domains and diverse regions of the structure. Also, analogous molecules containing circularly permuted c chains with altered termini were constructed for comparison with the ATCase molecules containing fragmented c chains. Studies were performed on four sets of ATCase molecules containing cleaved c chains at positions between residues 98 and 99, 121 and 122, 180 and 181, and 221 and 222; the corresponding circularly permuted chains had N termini at positions 99, 122, 181, and 222. All of the ATCase molecules containing fragmented or circularly permuted c chains exhibited the homotropic and heterotropic properties characteristic of the wild-type enzyme. Hill coefficients (n(H:)) and changes in them upon the addition of ATP and CTP were similar to those observed with wild-type ATCase. In addition, the conformational changes revealed by the decrease in sedimentation coefficient upon the addition of a bisubstrate analog were virtually identical to that for the wild-type enzyme. Differential scanning calorimetry showed that neither the breakage of the polypeptide chains nor the newly formed covalent bond between the termini in the wild-type enzyme had a significant impact on the thermal stability of the assembled dodecamers. The studies demonstrate that continuity of the polypeptide chain within structural domains is not essential for the assembly, activity, and allosteric properties of ATCase.
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Affiliation(s)
- X Ni
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
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10
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Abstract
This review focuses on a very important but little understood type of molecular recognition--the recognition between highly flexible molecular structures. The formation of a specific complex in this case is a dynamic process that can occur through sequential steps of mutual conformational adaptation. This allows modulation of specificity and affinity of interaction in extremely broad ranges. The interacting partners can interact together to form a complex with entirely new properties and produce conformational signal transduction at substantial distance. We show that this type of recognition is frequent in formation of different protein-protein and protein-nucleic acid complexes. It is also characteristic for self-assembly of protein molecules from their unfolded fragments as well as for interaction of molecular chaperones with their substrates and it can be the origin of 'protein misfolding' diseases. Thermodynamic and kinetic features of this type of dynamic recognition and the principles underlying their modeling and analysis are discussed.
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Affiliation(s)
- A P Demchenko
- The Palladin Institute of Biochemistry of the Academy of Sciences of Ukraine, Kiev 252030, Ukraine.
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11
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Abstract
Calbindin D28k is a highly conserved Ca2+-binding protein abundant in brain and sensory neurons. The 261-residue protein contains six EF-hands packed into one globular domain. In this study, we have reconstituted calbindin D28k from two fragments containing three EF-hands each (residues 1-132 and 133-261, respectively), and from other combinations of small and large fragments. Complex formation is studied by ion-exchange and size-exclusion chromatography, electrophoresis, surface plasmon resonance, as well as circular dichroism (CD), fluorescence, and NMR spectroscopy. Similar chromatographic behavior to the native protein is observed for reconstituted complexes formed by mixing different sets of complementary fragments, produced by introducing a cut between EF-hands 1, 2, 3, or 4. The C-terminal half (residues 133-261) appears to have a lower intrinsic stability compared to the N-terminal half (residues 1-132). In the presence of Ca2+, NMR spectroscopy reveals a high degree of structural similarity between the intact protein and the protein reconstituted from the 1-132 and 133-261 fragments. The affinity between these two fragments is 2 x 10(7) M(-1), with association and dissociation rate constants of 2.7 x 10(4) M(-1) s(-1) and 1.4 x 10(-3) s(-1), respectively. The complex formed in the presence of Ca2+ is remarkably stable towards unfolding by urea and heat. Both the complex and intact protein display cold and heat denaturation, although residual alpha-helical structure is seen in the urea denatured state at high temperature. In the absence of Ca2+, the fragments do not recombine to yield a complex resembling the intact apo protein. Thus, calbindin D28k is an example of a protein that can only be reconstituted in the presence of bound ligand. The alpha-helical CD signal is increased by 26% after addition of Ca2+ to each half of the protein. This suggests that Ca2+-induced folding of the fragments is important for successful reconstitution of calbindin D28k.
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Affiliation(s)
- T Berggård
- Physical Chemistry 2, Chemical Center, University of Lund, Sweden
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12
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Otzen DE, Kristensen O, Oliveberg M. Designed protein tetramer zipped together with a hydrophobic Alzheimer homology: a structural clue to amyloid assembly. Proc Natl Acad Sci U S A 2000; 97:9907-12. [PMID: 10944185 PMCID: PMC27622 DOI: 10.1073/pnas.160086297] [Citation(s) in RCA: 155] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2000] [Indexed: 11/18/2022] Open
Abstract
Limited solubility and precipitation of amyloidogenic sequences such as the Alzheimer peptide (beta-AP) are major obstacles to a molecular understanding of protein fibrillation and deposition processes. Here we have circumvented the solubility problem by stepwise engineering a beta-AP homology into a soluble scaffold, the monomeric protein S6. The S6 construct with the highest beta-AP homology crystallizes as a tetramer that is linked by the beta-AP residues forming intermolecular antiparallel beta-sheets. This construct also shows increased coil aggregation during refolding, and a 14-mer peptide encompassing the engineered sequence forms fibrils. Mutational analysis shows that intermolecular association is linked to the overall hydrophobicity of the sticky sequence and implies the existence of "structural gatekeepers" in the wild-type protein, that is, charged side chains that prevent aggregation by interrupting contiguous stretches of hydrophobic residues in the primary sequence.
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Affiliation(s)
- D E Otzen
- Department of Biochemistry, Umeâ University, S-901 87 Umeâ, Sweden
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Affiliation(s)
- K D Ridge
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, Rockville, Maryland, USA
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14
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Fedorov AN, Baldwin TO. Process of biosynthetic protein folding determines the rapid formation of native structure. J Mol Biol 1999; 294:579-86. [PMID: 10610781 DOI: 10.1006/jmbi.1999.3281] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Biosynthetic folding, beginning with the growing nascent chain and leading to the biologically active structure within its proper cellular context, is one function shared by all proteins. We show that the bacterial luciferase beta subunit reaches its final native form in the alphabeta heterodimer much more rapidly during biosynthetic folding than during refolding from urea. The rate of formation of active enzyme is determined by a short-lived folding intermediate, which is able to associate with the alpha subunit very rapidly following release from the ribosome. This intermediate appears to involve a transient interaction of the C-terminal region of the beta subunit, a region distant from the subunit interface, but intimately involved in heterodimerization. Refolding of the beta subunit under similar conditions proceeds much more slowly. We have characterized both pathways and show that the basic difference between biosynthetic folding and refolding from urea is that the newly synthesized beta subunit enters the folding pathway at a point beyond the slow, rate-determining step that limits the rate of the renaturation process and constitutes a kinetic trap. This mechanism embodies a major strategy, the avoidance of slow-folding intermediates and kinetic traps, that may be employed by many proteins to achieve fast and efficient biosynthetic folding.
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Affiliation(s)
- A N Fedorov
- College Station, Texas A&M University, TX 77843-2128, USA.
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15
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Wallqvist A, Lavoie TA, Chanatry JA, Covell DG, Carey J. Cooperative folding units of escherichia coli tryptophan repressor. Biophys J 1999; 77:1619-26. [PMID: 10465773 PMCID: PMC1300450 DOI: 10.1016/s0006-3495(99)77010-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
A previously published computational procedure was used to identify cooperative folding units within tryptophan repressor. The theoretical results predict the existence of distinct stable substructures in the protein chain for the monomer and the dimer. The predictions were compared with experimental data on structure and folding of the repressor and its proteolytic fragments and show excellent agreement for the dimeric form of the protein. The results suggest that the monomer, the structure of which is currently unknown, is likely to have a structure different from the one it has within the context of the highly intertwined dimer. Application of this method to the repressor monomer represents an extension of the computations into the realm of evaluating hypothetical structures such as those produced by threading.
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Affiliation(s)
- A Wallqvist
- Frederick Cancer Research and Development Center, National Cancer Institute, Science Applications International Corporation, Frederick, Maryland 21702 USA
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Ray SS, Balaram H, Balaram P. Unusual stability of a multiply nicked form of Plasmodium falciparum triosephosphate isomerase. CHEMISTRY & BIOLOGY 1999; 6:625-37. [PMID: 10467131 DOI: 10.1016/s1074-5521(99)80114-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND The limited proteolytic cleavage of proteins can result in distinct polypeptides that remain noncovalently associated so that the structural and biochemical properties of the 'nicked' protein are virtually indistinguishable from those of the native protein. The remarkable observation that rabbit muscle triosephosphate isomerase (TIM) can be multiply nicked by subtilisin and efficiently religated in the presence of an organic solvent formed the stimulus for our study on a homologous system, Plasmodium falciparum triosephosphate isomerase (PfTIM). RESULTS The subtilisin nicked form of PfTIM was prepared by limited proteolysis using subtilisin and the major fragments identified using electrospray ionization mass spectrometry. The order of susceptibility of the peptide bonds in the protein was also determined. The structure of the nicked form of TIM was investigated using circular dichroism, fluorescence and gel filtration. The nicked enzyme exhibited remarkable stability to denaturants, although significant differences were observed with the wild-type enzyme. Efficient religation could be achieved by addition of an organic cosolvent, such as acetonitrile, in the presence of subtilisin. Religation was also demonstrated after dissociation of the proteolytic fragments in guanidinium chloride, followed by reassembly after removal of the denaturant. CONCLUSIONS The eight-stranded beta8/alpha8 barrel is a robust, widely used protein structural motif. This study demonstrates that the TIM barrel can withstand several nicks in the polypeptide backbone with a limited effect on its structure and stability.
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Affiliation(s)
- S S Ray
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
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18
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Chakshusmathi G, Ratnaparkhi GS, Madhu PK, Varadarajan R. Native-state hydrogen-exchange studies of a fragment complex can provide structural information about the isolated fragments. Proc Natl Acad Sci U S A 1999; 96:7899-904. [PMID: 10393919 PMCID: PMC22159 DOI: 10.1073/pnas.96.14.7899] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ordered protein complexes are often formed from partially ordered fragments that are difficult to structurally characterize by conventional NMR and crystallographic techniques. We show that concentration-dependent hydrogen exchange studies of a fragment complex can provide structural information about the solution structures of the isolated fragments. This general methodology can be applied to any bimolecular or multimeric system. The experimental system used here consists of Ribonuclease S, a complex of two fragments of Ribonuclease A. Ribonuclease S and Ribonuclease A have identical three-dimensional structures but exhibit significant differences in their dynamics and stability. We show that the apparent large dynamic differences between Ribonuclease A and Ribonuclease S are caused by small amounts of free fragments in equilibrium with the folded complex, and that amide exchange rates in Ribonuclease S can be used to determine corresponding rates in the isolated fragments. The studies suggest that folded RNase A and the RNase S complex exhibit very similar dynamic behavior. Thus cleavage of a protein chain at a single site need not be accompanied by a large increase in flexibility of the complex relative to that of the uncleaved protein.
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Affiliation(s)
- G Chakshusmathi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India
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19
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Yoshikawa F, Iwasaki H, Michikawa T, Furuichi T, Mikoshiba K. Trypsinized cerebellar inositol 1,4,5-trisphosphate receptor. Structural and functional coupling of cleaved ligand binding and channel domains. J Biol Chem 1999; 274:316-27. [PMID: 9867846 DOI: 10.1074/jbc.274.1.316] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The type 1 inositol 1,4,5-trisphosphate receptor (IP3R1) is a tetrameric intracellular inositol 1,4,5-trisphosphate (IP3)-gated Ca2+ release channel (calculated molecular mass = approximately 313 kDa/subunit). We studied structural and functional coupling in this protein complex by limited (controlled) trypsinization of membrane fractions from mouse cerebellum, the predominant site for IP3R1. Mouse IP3R1 (mIP3R1) was trypsinized into five major fragments (I-V) that were positioned on the entire mIP3R1 sequence by immuno-probing with 11 site-specific antibodies and by micro-sequencing of the N termini. Four fragments I-IV were derived from the N-terminal cytoplasmic region where the IP3-binding region extended over two fragments I (40/37 kDa) and II (64 kDa). The C-terminal fragment V (91 kDa) included the membrane-spanning channel region. All five fragments were pelleted by centrifugation as were membrane proteins. Furthermore, after solubilizing with 1% Triton X-100, all were co-immunoprecipitated with the C terminus-specific monoclonal antibody that recognized only the fragment V. These data suggested that the native mIP3R1-channel is an assembly of four subunits, each of which is constituted by non-covalent interactions of five major, well folded structural components I-V that are not susceptible to attack by mild trypsinolysis. Ca2+ release experiments further revealed that even the completely fragmented mIP3R1 retained significant IP3-induced Ca2+ release activity. These data suggest that structural coupling among five split components conducts functional coupling for IP3-induced Ca2+ release, despite the loss of peptide linkages. We propose structural-functional coupling in the mIP3R1, that is neighboring coupling between components I and II for IP3 binding and long-distant coupling between the IP3 binding region and the channel region (component V) beyond trypsinized gaps for ligand gating.
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Affiliation(s)
- F Yoshikawa
- Department of Molecular Neurobiology, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
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20
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Gianazza E, Eberini I, Santi O, Vignati M. Denaturant-gradient gel electrophoresis: technical aspects and practical applications. Anal Chim Acta 1998. [DOI: 10.1016/s0003-2670(98)00333-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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21
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de los Santos T, Wang J, Reich E. Structure and function of microplasminogen: reconstitution of microplasminogen and microplasmin from isolated fragments. CIBA FOUNDATION SYMPOSIUM 1998; 212:66-76; discussion 76-83. [PMID: 9524764 DOI: 10.1002/9780470515457.ch5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We describe limited chemical proteolysis of microplasminogen/microplasmin (mPlg/mPlm) and their reconstitution from isolated fragments. A V141-->M141 substitution in methionineless human mPlg/mPlm allowed the protein(s) to be cleaved in CNBr/formic acid. The resulting two fragments (141 and 118 residues, respectively), each internally disulfide bonded, were separated by preparative non-reducing gradient SDS-PAGE, and could then be mixed to reconstitute the characteristic mPlg/mPlm, including their activation by urokinase (uPA) and streptokinase (SK), and inhibition by macromolecular inhibitors. The isolated larger, N-terminal fragment, which contains the mPlg activation site in a normal disulfide configuration, was not cleaved by uPA in the absence of its smaller C-terminal companion, showing that the linear amino acid sequence is not by itself sufficient to confer substrate character, even when its conformation is constrained by the disulfide structure.
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Affiliation(s)
- T de los Santos
- Department of Pharmacological Sciences, State University of New York at Stony Brook 11794-8651, USA
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22
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Ladurner AG, Itzhaki LS, de Prat Gay G, Fersht AR. Complementation of peptide fragments of the single domain protein chymotrypsin inhibitor 2. J Mol Biol 1997; 273:317-29. [PMID: 9367764 DOI: 10.1006/jmbi.1997.1303] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Chymotrypsin inhibitor 2 (CI2) folds kinetically as a single domain protein. It has been shown that elements of native secondary structure do not significantly form in fragments as the 64 residue protein is progressively increased in length from its N terminus, until at least 60 residues are present. Here, we analyse peptides of increasing length from the C terminus and find that native-like structure is not present even in the largest, fragment (7-64). We have examined sets of peptides of the form (1 - x) and ((x + 1)-64) to detect complementation. The only pair that readily complements and gives native-like structure is (1-40) and (41-64), where cleavage occurs in the protease-binding loop of CI2. But, all the pairs of peptides (1 - x) + (41-64) complement for x > 40, as do all pairs of (1-40) + (x-64), where x < 40. The resultant complexes appear to be equivalent to (1-40). (41-64) with the overlapping sequence being unstructured. Thus, the folding of CI2 is extremely co-operative, and interactions have to be made between subdomains (1-40) and (41-64). This is consistent with the mechanism proposed for the folding pathway of intact CI2 in which a diffuse nucleus is formed in the transition state between the alpha-helix in the N-terminal region of the protein and conserved hydrophobic contacts in the C-terminal region of the polypeptide. It is with these protein design features that CI2 can be an effective protease inhibitor.
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Affiliation(s)
- A G Ladurner
- MRC Cambridge Centre for Protein Engineering, MRC Centre, UK
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23
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Affiliation(s)
- J R Beasley
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544-1009, USA
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24
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Nadig G, Ratnaparkhi GS, Varadarajan R, Vishveshwara S. Dynamics of ribonuclease A and ribonuclease S: computational and experimental studies. Protein Sci 1996; 5:2104-14. [PMID: 8897611 PMCID: PMC2143277 DOI: 10.1002/pro.5560051017] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
RNase S is a complex consisting of two proteolytic fragments of RNase A: the S peptide (residues 1-20) and S protein (residues 21-124). RNase S and RNase A have very similar X-ray structures and enzymatic activities. Previous experiments have shown increased rates of hydrogen exchange and greater sensitivity to tryptic cleavage for RNase S relative to RNase A. It has therefore been asserted that the RNase S complex is considerably more dynamically flexible than RNase A. In the present study we examine the differences in the dynamics of RNase S and RNase A computationally, by MD simulations, and experimentally, using trypsin cleavage as a probe of dynamics. The fluctuations around the average solution structure during the simulation were analyzed by measuring the RMS deviation in coordinates. No significant differences between RNase S and RNase A dynamics were observed in the simulations. We were able to account for the apparent discrepancy between simulation and experiment by a simple model. According to this model, the experimentally observed differences in dynamics can be quantitatively explained by the small amounts of free S peptide and S protein that are present in equilibrium with the RNase S complex. Thus, folded RNase A and the RNase S complex have identical dynamic behavior, despite the presence of a break in polypeptide chain between residues 20 and 21 in the latter molecule. This is in contrast to what has been widely believed for over 30 years about this important fragment complementation system.
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Affiliation(s)
- G Nadig
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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25
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Schonberger O, Knox C, Bibi E, Pines O. Split invertase polypeptides form functional complexes in the yeast periplasm in vivo. Proc Natl Acad Sci U S A 1996; 93:9612-7. [PMID: 8790378 PMCID: PMC38476 DOI: 10.1073/pnas.93.18.9612] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The assembly of functional proteins from fragments in vivo has been recently described for several proteins, including the secreted maltose binding protein in Escherichia coli. Here we demonstrate for the first time that split gene products can function within the eukaryotic secretory system. Saccharomyces cerevisiae strains able to use sucrose produce the enzyme invertase, which is targeted by a signal peptide to the central secretory pathway and the periplasmic space. Using this enzyme as a model we find the following: (i) Polypeptide fragments of invertase, each containing a signal peptide, are independently translocated into the endoplasmic reticulum (ER) are modified by glycosylation, and travel the entire secretory pathway reaching the yeast periplasm. (ii) Simultaneous expression of independently translated and translocated overlapping fragments of invertase leads to the formation of an enzymatically active complex, whereas individually expressed fragments exhibit no activity. (iii) An active invertase complex is assembled in the ER, is targeted to the yeast periplasm, and is biologically functional, as judged by its ability to facilitate growth on sucrose as a single carbon source. These observation are discussed in relation to protein folding and assembly in the ER and to the trafficking of proteins through the secretory pathway.
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Affiliation(s)
- O Schonberger
- Department of Molecular Biology, Hebrew University-Hadassah Medical School, Jerusalem, Israel
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26
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Abstract
Frameshift mutations in a restricted portion of the arabinose operon regulatory gene araC from Escherichia coli give rise to active AraC protein, likely from the in vivo synthesis of two incomplete fragments that are active together. Synthesis of corresponding fragments, each separately inactive, from two plasmids within cells also resulted in complementation.
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Affiliation(s)
- R J Eustance
- Biology Department, Johns Hopkins University, Baltimore, Maryland 21218, USA
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27
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Eustance RJ, Schleif RF. In vivo association of protein fragments giving active AraC. Proteins 1996. [DOI: 10.1002/(sici)1097-0134(199608)25:4<501::aid-prot9>3.0.co;2-f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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28
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Abstract
Semisynthesis is used to create defined analogues of proteins by the chemical manipulation of peptide fragments largely derived from the natural protein and the subsequent reassembly of those fragments into a near-native conformation. In common with the total synthesis of proteins, it requires efficient and non-destructive methods for peptide religation. Recently, a wide range of chemoselective ligation schemes have been elaborated that now permit the assembly of minimally protected peptides from either synthetic or natural sources.
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29
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Tasayco ML, Chao K. NMR study of the reconstitution of the beta-sheet of thioredoxin by fragment complementation. Proteins 1995; 22:41-4. [PMID: 7675785 DOI: 10.1002/prot.340220106] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The study of complementary protein fragments is thought to be generally useful to identify early folding intermediates. A prerequisite for these studies is the reconstitution of the native-like structure by fragment complementation. Structural analysis of the complementation of the domain-sized proteolytic fragments of E. coli thioredoxin, using a combination of H-exchange and 2D NMR experiments as a fingerprint technique, provide evidence for the extensive reconstitution of a native beta-sheet, with local conformational adjustments near the cleavage site. Remarkably, the antiparallel beta-strand between the fragments shows a native-like protection of the amide protons to solvent exchange. Our results indicate that these fragments can be useful to study the early events in the still little understood formation of beta-sheets.
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Affiliation(s)
- M L Tasayco
- Department of Chemistry, City College, City University of New York, New York 10031, USA
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30
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Ridge KD, Lee SS, Yao LL. In vivo assembly of rhodopsin from expressed polypeptide fragments. Proc Natl Acad Sci U S A 1995; 92:3204-8. [PMID: 7724540 PMCID: PMC42134 DOI: 10.1073/pnas.92.8.3204] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Rhodopsin folding and assembly were investigated by expression of five bovine opsin gene fragments separated at points corresponding to proteolytic cleavage sites in the second or third cytoplasmic regions. The CH(1-146) and CH(147-348) gene fragments encode amino acids 1-146 and 147-348 of opsin, while the TH(1-240) and TH(241-348) gene fragments encode amino acids 1-240 and 241-348, respectively. Another gene fragment, CT(147-240), encodes amino acids 147-240. All five opsin polypeptide fragments were stably produced upon expression of the corresponding gene fragments in COS-1 cells. The singly expressed polypeptide fragments failed to form a chromophore with 11-cis-retinal, whereas coexpression of two or three complementary fragments [CH(1-146) + CH(147-348), TH(1-240) + TH(241-348), or CH(1-146) + CT(147-240) + TH(241-348)] formed pigments with spectral properties similar to wild-type rhodopsin. The NH2-terminal polypeptide in these rhodopsins showed a glycosylation pattern characteristic of wild-type COS-1 cell rhodopsin and was noncovalently associated with its complementary fragment(s). Further, the CH(1-146) + CH(147-348) rhodopsin showed substantial light-dependent activation of transducin. We conclude that the functional assembly of rhodopsin is mediated by the association of at least three protein-folding domains.
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Affiliation(s)
- K D Ridge
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, Rockville, MD, USA
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31
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Abstract
Proteolytic dissection of native trp repressor and horse heart cytochrome c has been used to infer some of the steps in the folding pathways of the intact proteins. For both proteins, small fragments are capable of undergoing spontaneous noncovalent association to form subdomains with native-like secondary and/or tertiary structural features, suggesting that dissection/reassembly may be a general method to gain insight into the structures of folding intermediates. The importance of this approach is its simplicity and potential applicability to studying the folding pathways of a wide range of proteins. The proteases report on the structure and dynamics of the native state, circumventing the need for prior knowledge of the structures of folding intermediates. The observation that small fragments of proteins can associated noncovalently suggests that protein folding can be viewed as an intramolecular "recognition" process. The results imply that substantial information about protein structure and folding is encoded at the level of subdomains, and that chain connectivity has only a minor role in determining the fold.
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Affiliation(s)
- L C Wu
- Chemistry Department, Princeton University, New Jersey 08544-1009
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32
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Munier H, Bouhss A, Gilles AM, Krin E, Glaser P, Danchin A, Bârzu O. Structural flexibility of the calmodulin-binding locus in Bordetella pertussis adenylate cyclase. Reconstitution of catalytically active species from fragments or inactive forms of the enzyme. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 217:581-6. [PMID: 8223601 DOI: 10.1111/j.1432-1033.1993.tb18280.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The catalytic domain of Bordetella pertussis adenylate cyclase, a calmodulin-activated enzyme with toxic properties, is a modular construct cleaved by trypsin into two subdomains of 224 (T25) and 175 (T18) amino acids. The calmodulin-binding locus of the bacterial enzyme consists of approximately 70 amino acids and overlaps the C-terminus of T25 and the N-terminus of T18. This region, exposed to the solvent or proteases, also exhibits an unusual high flexibility and allows, as demonstrated in this study, reconstitution in the presence of calmodulin of active species of adenylate cyclase from overlapping inactive fragments of the enzyme. Moreover, several combinations of inactive variants of the bacterial enzyme obtained by site-directed mutagenesis can yield active species. Heterodimers, resulting from a few selected combinations of inactive species of adenylate cyclase, exhibit specific activity similar to that of the native enzyme. Productive complementation from inactive fragments is a unique phenomenon among calmodulin-activated enzymes and represents a new and helpful tool in the understanding of the molecular mechanism of activation of B. pertussis adenylate cyclase upon binding of calmodulin.
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Affiliation(s)
- H Munier
- Unité de Biochimie des Régulations Cellulaires, Institut Pasteur, Paris, France
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33
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Yang YR, Schachman HK. In vivo formation of active aspartate transcarbamoylase from complementing fragments of the catalytic polypeptide chains. Protein Sci 1993; 2:1013-23. [PMID: 8318886 PMCID: PMC2142402 DOI: 10.1002/pro.5560020614] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Despite the complexity of Escherichia coli aspartate transcarbamoylase (ATCase), composed of 12 polypeptide chains organized as two catalytic (C) trimers and three regulatory (R) dimers, it is possible to form active stable enzyme in vivo even with fragmented catalytic (c) chains. Based on the observation that chymotryptic digestion of the C trimers yields an active protein that can be dissociated into fragmented chains and then reconstituted in high yield, genetically engineered plasmids carrying the genes encoding each of the fragments were constructed. When the N-terminal peptide (residues 1-242) and the C-terminal peptide (residues 235-310) were expressed separately, each incomplete polypeptide chain was found in the insoluble fraction of the individual cell extracts. Mixing the two insoluble pellets in 6.5 M urea, followed by a 10-fold dilution in buffer, led to the formation of active C trimers composed of incomplete polypeptide chains with an 8-amino acid redundancy. When the two partial genes were linked into a single transcriptional unit separated by a 15-nucleotide untranslated region containing a sequence for ribosome binding, the cells produced high yields of active C trimers composed of the incomplete, partially overlapping chains. The resulting protein, purified as C trimers or as holoenzyme formed by the addition of R subunits, has a specific activity (Vmax) only slightly less than that of the wild-type C trimer and ATCase. However, Km for aspartate exhibited by the C trimer composed of fragmented chains is more than 10-fold larger than that of the wild-type trimer. The holoenzyme formed from the C trimer containing the coexpressed peptides is devoid of cooperativity with a Hill coefficient of 1.0, as contrasted to wild-type ATCase for which the Hill coefficient is 1.7. Km for aspartate as well as Kd for the binding of the bisubstrate analog N-(phosphonacetyl)-L-aspartate are significantly higher than the analogous values for wild-type ATCase. Sedimentation velocity experiments indicate that the holoenzyme containing the incomplete chains has a conformation analogous to that of the R state of wild-type ATCase.
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Affiliation(s)
- Y R Yang
- Department of Molecular and Cell Biology, University of California, Berkeley 94720
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34
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Powers VM, Yang YR, Fogli MJ, Schachman HK. Reconstitution of active catalytic trimer of aspartate transcarbamoylase from proteolytically cleaved polypeptide chains. Protein Sci 1993; 2:1001-12. [PMID: 8318885 PMCID: PMC2142411 DOI: 10.1002/pro.5560020613] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Treatment of the catalytic (C) trimer of Escherichia coli aspartate transcarbamoylase (ATCase) with alpha-chymotrypsin by a procedure similar to that used by Chan and Enns (1978, Can. J. Biochem. 56, 654-658) has been shown to yield an intact, active, proteolytically cleaved trimer containing polypeptide fragments of 26,000 and 8,000 MW. Vmax of the proteolytically cleaved trimer (CPC) is 75% that of the wild-type C trimer, whereas Km for aspartate and Kd for the bisubstrate analog, N-(phosphonacetyl)-L-aspartate, are increased about 7- and 15-fold, respectively. CPC trimer is very stable to heat denaturation as shown by differential scanning microcalorimetry. Amino-terminal sequence analyses as well as results from electrospray ionization mass spectrometry indicate that the limited chymotryptic digestion involves the rupture of only a single peptide bond leading to the production of two fragments corresponding to residues 1-240 and 241-310. This cleavage site involving the bond between Tyr 240 and Ala 241 is in a surface loop known to be involved in intersubunit contacts between the upper and lower C trimers in ATCase when it is in the T conformation. Reconstituted holoenzyme comprising two CPC trimers and three wild-type regulatory (R) dimers was shown by enzyme assays to be devoid of the homotropic and heterotropic allosteric properties characteristic of wild-type ATCase. Moreover, sedimentation velocity experiments demonstrate that the holoenzyme reconstituted from CPC trimers is in the R conformation. These results indicate that the intact flexible loop containing Tyr 240 is essential for stabilizing the T conformation of ATCase. Following denaturation of the CPC trimer in 4.7 M urea and dilution of the solution, the separate proteolytic fragments re-associate to form active trimers in about 60% yield. How this refolding of the fragments, docking, and association to form trimers are achieved is not known.
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Affiliation(s)
- V M Powers
- Department of Molecular and Cell Biology, University of California, Berkeley 94720
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35
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Vita C, Gozzini L, Di Bello C. Total synthesis of horse heart apocytochrome c by conformation-assisted condensation of two chemically synthesized fragments. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 204:631-40. [PMID: 1311676 DOI: 10.1111/j.1432-1033.1992.tb16676.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A fully synthetic peptide, corresponding to the entire 104-residue sequence of horse heart apocytochrome c with Met65 replaced by homoserine, has been obtained by an original conformation-assisted three-fragment condensation procedure. The method involves the selective joining of two synthetic fragments, namely residues 1-65 of the apopeptide with Met65 replaced by homoserine lactone and residues 66-104 of the protein in the presence of fragment 1-25 of the native heme-containing peptide. The joining conditions have been optimized with regard to solvent, pH and possible influence of additives. The presence of radical scavengers and the complete exclusion of oxygen were found essential in order to prevent oxidative side reactions. A sensitive method based on reverse-phase HPLC has been used to monitor the course of the reaction. Condensation yields up to 80% were obtained. The data obtained by this new three-fragment rejoining approach are discussed and compared to those of a similar two-fragment condensation procedure. Our data demonstrate how the folding properties of large synthetic peptide fragments, organized in a complex, can be utilized to extend the presently improved solid-phase peptide methods to the synthesis of a functioning protein with more than 100 residues.
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Affiliation(s)
- C Vita
- Institute of Industrial Chemistry, University of Padua, Italy
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36
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Buchwalder A, Szadkowski H, Kirschner K. A fully active variant of dihydrofolate reductase with a circularly permuted sequence. Biochemistry 1992; 31:1621-30. [PMID: 1737018 DOI: 10.1021/bi00121a006] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The amino acid sequence of mouse dihydrofolate reductase was permuted circularly at the level of the gene. By transposing the 3'-terminal half of the coding sequence to its 5' terminus, the naturally adjacent amino and carboxyl termini of the native protein were fused, and one of the flexible peptide loops at the protein surface was cleaved. The steady-state kinetic constants, the dissociation constants of folate analogues, and the degree of activation by both mercurials and salt as well as the resistance toward digestion by trypsin were almost indistinguishable from those of a recombinant wild-type protein. Judged by these criteria, the circularly permuted variant has the same active site and overall structure as the wild-type enzyme. The only significant difference was the lower stability toward guanidinium chloride and the lower solubility of the circularly permuted variant. This behavior may be due to moving a mononucleotide binding fold from the interior of the sequence to the carboxyl terminus. Thus, dihydrofolate reductase requires neither the natural termini nor the cleaved loop for stability, for the conformational changes that accompany catalysis as well as the binding of inhibitors, and for the folding process.
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Affiliation(s)
- A Buchwalder
- Abteilung Biophysikalische Chemie, Biozentrum der Universität, Basel, Switzerland
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37
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Tasayco ML, Carey J. Ordered self-assembly of polypeptide fragments to form nativelike dimeric trp repressor. Science 1992; 255:594-7. [PMID: 1736361 DOI: 10.1126/science.1736361] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Subdomain-size proteolytic fragments of Escherichia coli trp repressor have been produced that assemble in defined order to regenerate fully native dimers. By characterization of the secondary and tertiary structures of isolated and recombined fragments, the structure of assembly intermediates can be correlated with the kinetic folding pathway of the intact repressor deduced from spectroscopic measurement of folding rates. The nativelike structure of these intermediates provides further evidence that protein folding pathways reflect the stabilities of secondary structural units and assemblies found in the native state. The proteolytic method should be generally useful in adding structural detail to spectroscopically determined folding mechanisms.
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Affiliation(s)
- M L Tasayco
- Chemistry Department, Princeton University, NJ 08544
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38
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Urfer R, Kirschner K. The importance of surface loops for stabilizing an eightfold beta alpha barrel protein. Protein Sci 1992; 1:31-45. [PMID: 1304881 PMCID: PMC2142075 DOI: 10.1002/pro.5560010105] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
An important step in understanding how a protein folds is to determine those regions of the sequence that are critical to both its stability and its folding pathway. We chose phosphoribosyl anthranilate isomerase from Escherichia coli, which is a monomeric representative of the (beta alpha)8 barrel family of proteins, to construct a variant that carries an internal tandem duplication of the fifth beta alpha module. This (beta alpha)9 variant was enzymically active and therefore must have a wild-type (beta alpha)8 core. It had a choice a priori to fold to three different folding frames, which are distinguished by carrying the duplicated segment as an insert into one out of three different loops. Steady-state kinetic constants, the fluorescence properties of a crucial tryptophan residue, and limited proteolysis showed that the stable (beta alpha)9 variant carries the insertion between beta-strand 5 and alpha-helix 5. This preference can be explained by the important role of loops between alpha helices and beta strands in stabilizing the structure of the enzyme.
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Affiliation(s)
- R Urfer
- Abteilung Biophysikalische Chemie, Universität Basel, Switzerland
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39
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Pósfai G, Kim SC, Szilák L, Kovács A, Venetianer P. Complementation by detached parts of GGCC-specific DNA methyltransferases. Nucleic Acids Res 1991; 19:4843-7. [PMID: 1923753 PMCID: PMC328777 DOI: 10.1093/nar/19.18.4843] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Individually inactive N- and C-terminal fragments of the m5C-methyltransferase M.BspRI can complement each other resulting in specific, in vivo methylation of the DNA. This was shown by cloning the coding regions for N- and C-terminal parts of the enzyme in compatible plasmids and co-transforming them into E.coli cells. The enzyme could be detached at several different sites, producing either non-overlapping or partially overlapping fragments capable of complementation. Reconstitution of the active methyltransferase from inactive fragments was demonstrated in vitro, as well. Another GGCC-specific methyltransferase, M.BsuRI, showed a similar complementation phenomenon. Moreover, interspecies complementation was observed between appropriate fragments of the two closely related enzymes M.BspRI and M.BsuRI. Fragments of structurally and functionally more different methyltransferases were unable to complement each other.
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Affiliation(s)
- G Pósfai
- Institute of Biochemistry, Hungarian Academy of Sciences, Szeged
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40
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di Bello C, Tonellato M, Lucchiari A, Buso O, Gozzini L, Vita C. Solid-phase synthesis of the native sequence of horse heart cytochrome c-(66-104)-nonatriacontapeptide and of a C-terminal carboxyamide analog selectively modified at Met-80. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1990; 35:336-45. [PMID: 2160918 DOI: 10.1111/j.1399-3011.1990.tb00058.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The peptide corresponding to the (66-104) sequence of horse heart cytochrome c and its carboxyamide analog, selectively modified at the critical Met80 residue, have been synthesized by stepwise solid-phase methods on PAM and BHA resins respectively. The correctness of the growing peptide chain as well as the homogeneity of the final products have been monitored by several analytical methods including quantitative Edman degradation. After HF cleavage both peptides were purified by semipreparative HPLC. The overall yields were 24% for the native (66-104) and 10% for the carboxyamide analog. The homogeneity of the purified synthetic peptides have been determined by different criteria including HPLC, amino acid composition, Edman degradation, electrophoresis, and tryptic peptide mapping. The synthetic fragments have been utilized for preliminary semisynthesis experiments with the native [Hse greater than 65] (1-65)H heme-sequence.
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Affiliation(s)
- C di Bello
- Institute of Industrial Chemistry, University of Padua, Italy
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41
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Garvey EP, Matthews CR. Site-directed mutagenesis and its application to protein folding. BIOTECHNOLOGY (READING, MASS.) 1990; 14:37-63. [PMID: 2183900 DOI: 10.1016/b978-0-409-90116-0.50011-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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42
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Abstract
Our previous work has shown that the amino-terminal residue of a short-lived protein is a distinct component of the protein's degradation signal. To define the complete signal, otherwise identical dihydrofolate reductase test proteins bearing different extensions and either a "stabilizing" or a "destabilizing" amino-terminal residue were expressed in the yeast S. cerevisiae and their in vivo half-lives compared. The amino-terminal degradation signal is shown to comprise two distinct determinants. One, discovered previously, is the protein's amino-terminal residue. The second determinant, identified in the present work, is a specific lysine residue whose function in the degradation signal is not dependent on the unique amino acid sequences in the vicinity of the residue. The mechanistic significance of the second determinant is illuminated by the finding that in a targeted, short-lived protein, a chain of branched ubiquitin-ubiquitin conjugates is confined to a lysine residue that has been identified in the present work as the second determinant of the degradation signal.
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Affiliation(s)
- A Bachmair
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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