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Luo Y, Raso SW, Gallant J, Steinmeyer C, Mabuchi Y, Lu Z, Entrican C, Rouse JC. Evidence for intermolecular domain exchange in the Fab domains of dimer and oligomers of an IgG1 monoclonal antibody. MAbs 2017; 9:916-926. [PMID: 28590212 DOI: 10.1080/19420862.2017.1331803] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Recombinant protein therapeutics have become increasingly useful in combating human diseases, such as cancer and those of genetic origin. One quality concern for protein therapeutics is the content and the structure of the aggregated proteins in the product, due to the potential immunogenicity of these aggregates. Collective efforts have led to a better understanding of some types of protein aggregates, and have revealed the diversity in the structure and cause of protein aggregation. In this work we used a broad range of analytical techniques to characterize the quinary structure (complexes in which each composing unit maintains native quaternary structure) of the stable non-covalent dimer and oligomers of a monoclonal IgG1λ antibody. The results supported a mechanism of intermolecular domain exchange involving the Fab domains of 2 or more IgG molecules. This mechanism can account for the native-like higher order (secondary, tertiary and disulfide bonding) structure, the stability of the non-covalent multimers, and the previously observed partial loss of the antigen-binding sites without changing the antigen-binding affinity and kinetics of the remaining sites (Luo et al., 2009, mAbs 1:491). Furthermore, the previously observed increase in the apparent affinity to various Fcγ receptors (ibid), which may potentially promote immunogenicity, was also explained by the quinary structure proposed here. Several lines of evidence indicated that the formation of multimers by the mechanism of intermolecular domain exchange took place mostly during expression, not in the purified materials. The findings in this work will advance our knowledge of the mechanisms for aggregation in therapeutic monoclonal antibodies.
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Affiliation(s)
- Yin Luo
- a Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences , Pfizer Inc. , Andover , USA
| | - Stephen W Raso
- a Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences , Pfizer Inc. , Andover , USA
| | - Judith Gallant
- a Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences , Pfizer Inc. , Andover , USA
| | - Colleen Steinmeyer
- a Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences , Pfizer Inc. , Andover , USA
| | - Yasuko Mabuchi
- a Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences , Pfizer Inc. , Andover , USA
| | - Zhaojiang Lu
- a Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences , Pfizer Inc. , Andover , USA
| | - Clifford Entrican
- a Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences , Pfizer Inc. , Andover , USA
| | - Jason C Rouse
- a Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences , Pfizer Inc. , Andover , USA
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2
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Khattar V, Thottassery JV. Cks1: Structure, Emerging Roles and Implications in Multiple Cancers. ACTA ACUST UNITED AC 2013; 4:1341-1354. [PMID: 24563807 PMCID: PMC3930463 DOI: 10.4236/jct.2013.48159] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Deregulation of the cell cycle results in loss of normal control mechanisms that prevent aberrant cell proliferation and cancer progression. Regulation of the cell cycle is a highly complex process with many layers of control. One of these mechanisms involves timely degradation of CDK inhibitors (CKIs) like p27Kip1 by the ubiquitin proteasomal system (UPS). Cks1 is a 9 kDa protein which is frequently overexpressed in different tumor subtypes, and has pleiotropic roles in cell cycle progression, many of which remain to be fully characterized. One well characterized molecular role of Cks1 is that of an essential adaptor that regulates p27Kip1 abundance by facilitating its interaction with the SCF-Skp2 E3 ligase which appends ubiquitin to p27Kip1 and targets it for degradation through the UPS. In addition, emerging research has uncovered p27Kip1-independent roles of Cks1 which have provided crucial insights into how it may be involved in cancer progression. We review here the structural features of Cks1 and their functional implications, and also some recently identified Cks1 roles and their involvement in breast and other cancers.
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Affiliation(s)
| | - Jaideep V Thottassery
- Southern Research Institute, Birmingham, USA ; University of Alabama Comprehensive Cancer Center, Birmingham, USA
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3
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Galzitskaya OV. Regions which are Responsible for Swapping are also Responsible for Folding and Misfolding. Open Biochem J 2011; 5:27-36. [PMID: 21769300 PMCID: PMC3134983 DOI: 10.2174/1874091x01105010027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 05/17/2011] [Accepted: 05/28/2011] [Indexed: 12/01/2022] Open
Abstract
Domain swapping is a term used to describe a process when two or more protein chains exchange identical structural elements. Some cases of amyloid formation can be explained through a domain swapping mechanism therefore this deserves theoretical consideration and studying. It has been demonstrated that diverse proteins in sequence and structure are able to oligomerize via domain swapping. This allows us to suggest that the exchangeable regions are important in folding and misfolding processes of proteins, i.e. the residues from the swapping regions are typically incorporated into the native structure early during its formation. The modeling of folding of the proteins with swapped domains demonstrates that the regions exchanged in the oligomeric form in most cases are also responsible for folding and misfolding. For 11 out of 17 proteins, swapping regions intersect with the predicted amyloidogenic regions. Moreover, for 10 out of 17 proteins, high Φ-values (>0.5) belong to residues from the swapping regions. Our data confirm that the exchangeable regions are important in folding, misfolding, and domain swapping processes of the proteins, therefore the suggestion that domain swapping can serve as a mechanism for functional interconversion between monomers and oligomers is likely to be correct.
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Affiliation(s)
- Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya str. 4, Pushchino, Moscow Region, 142290, Russia
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4
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Bader R, Seeliger MA, Kelly SE, Ilag LL, Meersman F, Limones A, Luisi BF, Dobson CM, Itzhaki LS. Folding and fibril formation of the cell cycle protein Cks1. J Biol Chem 2006; 281:18816-24. [PMID: 16675442 DOI: 10.1074/jbc.m603628200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Saccharomyces cerevisiae Cks protein Cks1 has a COOH-terminal glutamine-rich sequence not present in other homologues. Cks proteins domain swap to form dimers but unique to Cks1 is the anti-parallel arrangement of protomers within the dimer. Despite the differences in Cks1 compared with other Cks proteins, we find the domain swapping properties are very similar. However, aggregation of Cks1 occurs by a route distinct from the other Cks proteins studied to date. Cks1 formed fibrillar aggregates at room temperature and neutral pH. During this process, Cks1 underwent proteolytic cleavage at a trypsin-like site into two fragments, the globular Cks domain and the glutamine-rich COOH terminus. At high protein concentrations, the rate of fibril formation was the same as the rate of proteolysis. The dominant species present within the fibrils was the glutamine-rich sequence. Consistent with this result, fibril formation was enhanced by addition of trypsin. Moreover, a truncated variant lacking the glutamine-rich sequence did not form fibrils under the same conditions. A lag phase at low protein concentrations indicates that fibril formation occurs through a nucleation and growth mechanism. The aggregates appear to resemble amyloid fibrils, in that they show the typical cross-beta x-ray diffraction pattern. Moreover, infrared spectroscopy data indicate that the glutamine side chains are hydrogen-bonded along the axis of the fibril. Our results indicate that the proteolytic reaction is the crucial step initiating aggregation and demonstrate that Cks1 is a simple, tunable model system for exploring aggregation mechanisms associated with polyglutamine deposition diseases.
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Affiliation(s)
- Reto Bader
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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5
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Yang S, Levine H, Onuchic JN. Protein oligomerization through domain swapping: role of inter-molecular interactions and protein concentration. J Mol Biol 2005; 352:202-11. [PMID: 16061250 DOI: 10.1016/j.jmb.2005.06.062] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Revised: 06/22/2005] [Accepted: 06/27/2005] [Indexed: 11/19/2022]
Abstract
Domain swapping has been shown to be an important mechanism controlling multiprotein assembly and has been suggested recently as a possible mechanism underlying protein aggregation. Understanding oligomerization via domain swapping is therefore of theoretical and practical importance. By using a symmetrized structure-based (Gō) model, we demonstrate that in the free-energy landscape of domain swapping, a large free-energy barrier separates monomeric and domain-swapped dimeric configurations. We investigate the effect of finite monomer concentration, by implementing a new semi-analytical method, which involves computing the second virial coefficient, a thermodynamic indicator of inter-molecular interactions. This method, together with the symmetrized structure-based (Gō) model, minimizes the need for expensive many-protein simulations, providing a convenient framework to investigate concentration effect. Finally, we perform direct simulations of domain-swapped trimer formation, showing that this modeling approach can be used for higher-order oligomers.
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Affiliation(s)
- Sichun Yang
- Center for Theoretical Biological Physics and Department of Physics, University of California San Diego, La Jolla, CA 92093-0374, USA
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6
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Kelly JA, Williams EA, Wilce MCJ. Preliminary crystallographic analysis of the Cks protein p13(suc1P90AP92A) from Schizosacharromyces pombe. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2005; 34:430-3. [PMID: 15843986 DOI: 10.1007/s00249-005-0474-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 02/08/2005] [Accepted: 02/12/2005] [Indexed: 11/25/2022]
Abstract
The p13(suc1) is the fission yeast member of the Cks (Cdc28-dependant kinase subunit) family of proteins. The Cks proteins bind to and are required for the function of cyclin-dependant kinase (Cdk) proteins during cell cycle progression in eukaryotic cells. Two conformations of Cks have been detected crystallographically; a compact monomer with the C-terminal fourth beta-strand inserted into the core of the molecule between strands 2 and 3, and a strand-exchanged dimer where the fourth beta-strand is inserted into the core of the dimer partner in an equivalent position. There is a highly conserved "hinge" region consisting of the motif PEP, N-terminal to the fourth beta-strand. In the monomer this motif constitutes a beta-turn, while in the dimeric structure it is extended, allowing strand exchange. The mutant protein p13(suc1P90AP92A), in which alanine residues replace both prolines of the turn, provides an opportunity to examine the role of the prolines in this hinge region and how they may allow for the formation of strand-exchanged dimers by Cks proteins. We have expressed and purified this mutant protein. Two millimolar p13(suc1P90AP92A) crystallised in 50 mM tris(hydroxymethyl)aminomethane pH 7.5, 30% poly(ethylene glycol) 1500. Diffraction data were collected at room temperature on an MAR345 image plate using Cu Kalpha radiation from a Rigaku RU200 rotating-anode generator source to 2.70A. The crystal has unit cell parameters a=b=75.1 A, c=34.9 A, alpha=beta=90 degrees , gamma=120 degrees. Diffraction data were indexed to the space group P6 and systematic absences 00l indicate a screw axis consistent with P6(3).
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Affiliation(s)
- Joyanne A Kelly
- Pharmacology Unit, School of Pharmacology and Medicine, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
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7
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Luo X, Tang Z, Xia G, Wassmann K, Matsumoto T, Rizo J, Yu H. The Mad2 spindle checkpoint protein has two distinct natively folded states. Nat Struct Mol Biol 2004; 11:338-45. [PMID: 15024386 DOI: 10.1038/nsmb748] [Citation(s) in RCA: 234] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2003] [Accepted: 02/23/2004] [Indexed: 12/20/2022]
Abstract
The spindle checkpoint delays chromosome segregation in response to misaligned sister chromatids during mitosis, thus ensuring the fidelity of chromosome inheritance. Through binding to Cdc20, the Mad2 spindle checkpoint protein inhibits the target of this checkpoint, the ubiquitin protein ligase APC/C(Cdc20). We now show that without cofactor binding or covalent modification Mad2 adopts two distinct folded conformations at equilibrium (termed N1-Mad2 and N2-Mad2). The structure of N2-Mad2 has been determined by NMR spectroscopy. N2-Mad2 is much more potent in APC/C inhibition. Overexpression of a Mad2 mutant that specifically sequesters N2-Mad2 partially blocks checkpoint signaling in living cells. The two Mad2 conformers interconvert slowly in vitro, but interconversion is accelerated by a fragment of Mad1, an upstream regulator of Mad2. Our results suggest that the unusual two-state behavior of Mad2 is critical for spindle checkpoint signaling.
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Affiliation(s)
- Xuelian Luo
- Department of Pharmacology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
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8
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Rousseau F, Schymkowitz JWH, Wilkinson HR, Itzhaki LS. Intermediates Control Domain Swapping during Folding of p13. J Biol Chem 2004; 279:8368-77. [PMID: 14662764 DOI: 10.1074/jbc.m310640200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 13-kDa protein p13(suc1) has two folded states, a monomer and a structurally similar domain-swapped dimer formed by exchange of a beta-strand. The refolding reaction of p13(suc1) is multiphasic, and in this paper we analyze the kinetics as a function of denaturant and protein concentration and compare the behavior of wild type and a set of mutants previously designed with dimerization propensities that span 9 orders of magnitude. We show that the folding reactions of wild type and all mutants produce the monomer predominantly despite their very different equilibrium behavior. However, the addition of low concentrations of denaturant in the refolding buffer leads to thermodynamic control of the folding reaction with products that correspond to the wild type and mutant equilibrium dimerization propensities. We present evidence that the kinetic control in the absence of urea arises because of the population of the folding intermediates. Intermediates are usually considered to be detrimental to folding because they slow down the reaction; however, our work shows that intermediates buffer the monomeric folding pathway against the effect of mutations that favor the nonfunctional, dimeric state at equilibrium.
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Affiliation(s)
- Frederic Rousseau
- Medical Research Council Centre for Protein Engineering, Cambridge University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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9
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Abstract
Three-dimensional domain swapping is the event by which a monomer exchanges part of its structure with identical monomers to form an oligomer where each subunit has a similar structure to the monomer. The accumulating number of observations of this phenomenon in crystal structures has prompted speculation as to its biological relevance. Domain swapping was originally proposed to be a mechanism for the emergence of oligomeric proteins and as a means for functional regulation, but also to be a potentially harmful process leading to misfolding and aggregation. We highlight experimental studies carried out within the last few years that have led to a much greater understanding of the mechanism of domain swapping and of the residue- and structure-specific features that facilitate the process. We discuss the potential biological implications of domain swapping in light of these findings.
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Affiliation(s)
- Frederic Rousseau
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
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10
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Abstract
Three-dimensional (3D) domain swapping creates a bond between two or more protein molecules as they exchange their identical domains. Since the term '3D domain swapping' was first used to describe the dimeric structure of diphtheria toxin, the database of domain-swapped proteins has greatly expanded. Analyses of the now about 40 structurally characterized cases of domain-swapped proteins reveal that most swapped domains are at either the N or C terminus and that the swapped domains are diverse in their primary and secondary structures. In addition to tabulating domain-swapped proteins, we describe in detail several examples of 3D domain swapping which show the swapping of more than one domain in a protein, the structural evidence for 3D domain swapping in amyloid proteins, and the flexibility of hinge loops. We also discuss the physiological relevance of 3D domain swapping and a possible mechanism for 3D domain swapping. The present state of knowledge leads us to suggest that 3D domain swapping can occur under appropriate conditions in any protein with an unconstrained terminus. As domains continue to swap, this review attempts not only a summary of the known domain-swapped proteins, but also a framework for understanding future findings of 3D domain swapping.
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Affiliation(s)
- Yanshun Liu
- Howard Hughes Medical Institute, UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, Department of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, California 90095, USA
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11
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Rousseau F, Schymkowitz JWH, Wilkinson HR, Itzhaki LS. The structure of the transition state for folding of domain-swapped dimeric p13suc1. Structure 2002; 10:649-57. [PMID: 12015148 DOI: 10.1016/s0969-2126(02)00762-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
suc1 has two native states, a monomer and a domain-swapped dimer, in which one molecule exchanges a beta strand with an identical partner. Thus, monomer and dimer have the same structures but are topologically distinct. Importantly, residues that exchange are part of the folding nucleus of the monomer and therefore forming these interactions in the dimer would be expected to incur a large entropic cost. Here we present the transition state for folding/unfolding of domain-swapped dimeric suc1 and compare it with its monomeric counterpart. The same overall structure is observed in the two transition states but the phi values are consistently higher for the domain-swapped dimer. Thus, a greater entropic penalty for bringing together the key interactions in the dimer is overcome by mobilizing more contacts in the transition state, thereby achieving a greater enthalpic gain.
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Affiliation(s)
- Frederic Rousseau
- MRC Centre for Protein Engineering, University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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12
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Odaert B, Landrieu I, Dijkstra K, Schuurman-Wolters G, Casteels P, Wieruszeski JM, Inze D, Scheek R, Lippens G. Solution NMR study of the monomeric form of p13suc1 protein sheds light on the hinge region determining the affinity for a phosphorylated substrate. J Biol Chem 2002; 277:12375-81. [PMID: 11812792 DOI: 10.1074/jbc.m111741200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyclin-dependent kinase subunit (CKS) proteins bind to cyclin-dependent kinases and target various proteins to phosphorylation and proteolysis during cell division. Crystal structures showed that CKS can exist both in a closed monomeric conformation when bound to the kinase and in an inactive C-terminal beta-strand-exchanged conformation. With the exception of the hinge loop, however, both crystal structures are identical, and no new protein interface is formed in the dimer. Protein engineering studies have pinpointed the crucial role of the proline 90 residue of the p13(suc1) CKS protein from Schizosaccharomyces pombe in the monomer-dimer equilibrium and have led to the concept of a loaded molecular spring of the beta-hinge motif. Mutation of this hinge proline into an alanine stabilizes the protein and prevents the occurrence of swapping. However, other mutations further away from the hinge as well as ligand binding can equally shift the equilibrium between monomer and dimer. To address the question of differential affinity through relief of the strain, here we compare the ligand binding of the monomeric form of wild-type S. pombe p13(suc1) and its hinge mutant P90A in solution by NMR spectroscopy. We indeed observed a 5-fold difference in affinity with the wild-type protein being the most strongly binding. Our structural study further indicates that both wild-type and the P90A mutant proteins adopt in solution the closed conformation but display different dynamic properties in the C-terminal beta-sheet involved in domain swapping and protein interactions.
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Affiliation(s)
- Benoît Odaert
- CNRS-Université de Lille 2 UMR 8525, Institut Pasteur de Lille-Institut de Biologie de Lille, 59019 Lille Cedex, France
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13
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Vogel L, Baratte B, Détivaud L, Azzi L, Leopold P, Meijer L. Molecular cloning and characterisation of p15(CDK-BP), a novel CDK-binding protein. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1589:219-31. [PMID: 12007796 DOI: 10.1016/s0167-4889(02)00175-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
The suc1/Cks proteins are well-conserved regulatory components of cyclin-dependent kinases 1 and 2 (CDK1/2). These small molecular mass proteins form a stable complex with CDK1/2 and are essential for normal regulation of CDKs during the cell division cycle and for degradation of p27(kip1). Despite the high degree of homology between the nine known CDKs, only CDK1, CDK2 and, to a lesser extent, CDK3 are able to bind to the suc1/Cks proteins. No additional suc1/Cks-related proteins interacting with other CDKs have been reported. We have purified, from starfish oocytes, a 15 kDa protein, p15(CDK-BP), which cross-reacts with anti-Cks antibodies (L. Azzi, L. Meijer, A.C. Ostvold, J. Lew, J.H. Wang, J. Biol. Chem. 269 (1994)). Following microsequencing of internal peptides and generation of corresponding oligonucleotides we cloned two cDNAs encoding two closely related proteins, p15A and p15B. The predicted protein sequences display distant but distinct homology with the Suc1/Cks proteins, including the genuine starfish Cks homologue protein, p9(CksMg). P15 transcripts are essentially expressed in oocytes. Recombinant p15B or native p15(CDK-BP) bind a 34 kDa protein cross-reacting with anti-PSTAIRE antibodies, a feature characteristic of CDK-related proteins. In addition p15B interacts tightly with CDK4, CDK6, CDK8 and the yeast CDC28-related kinase Pho85, but not with CDK1, CDK2 or CDK7. P15 does not appear to alter the catalytic activity of the bound kinases.
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Affiliation(s)
- Lee Vogel
- CNRS, Station Biologique, Roscoff, Bretagne, France
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14
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Abstract
Many proteins function as multimeric assemblies into which the folded individual promoters organize as higher order structures. An oligomerization mechanism that appears to impose the coordination of events during folding and oligomer assembly is three-dimensional domain swapping. Recent studies have focused on revealing the structural basis of domain swapping and a possible role for domain swapping in the regulation of protein aggregation and activity.
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Affiliation(s)
- Marcia E Newcomer
- Departments of Biological Sciences and Chemistry, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA.
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15
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O'Neill JW, Kim DE, Johnsen K, Baker D, Zhang KY. Single-site mutations induce 3D domain swapping in the B1 domain of protein L from Peptostreptococcus magnus. Structure 2001; 9:1017-27. [PMID: 11709166 DOI: 10.1016/s0969-2126(01)00667-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Thermodynamic and kinetic studies of the Protein L B1 domain (Ppl) suggest a folding pathway in which, during the folding transition, the first beta hairpin is formed while the second beta hairpin and the alpha helix are largely unstructured. The same mutations in the two beta turns have opposite effects on the folding and unfolding rates. Three of the four residues composing the second beta turn in Ppl have consecutive positive phi angles, indicating strain in the second beta turn. RESULTS We have determined the crystal structures of the beta turn mutants G55A, K54G, and G15A, as well as a core mutant, V49A, in order to investigate how backbone strain affects the overall structure of Ppl. Perturbation of the hydrophobic interactions at the closed interface by the V49A mutation triggered the domain swapping of the C-terminal beta strand that relieved the strain in the second beta turn. Interestingly, the asymmetric unit of V49A contains two monomers and one domain-swapped dimer. The G55A mutation escalated the strain in the second beta turn, and this increased strain shifted the equilibrium toward the domain-swapped dimer. The K54G structure revealed that the increased stability is due to the reduction of strain in the second beta turn, while the G15A structure showed that increased strain alone is insufficient to trigger domain swapping. CONCLUSIONS Domain swapping in Ppl is determined by the balance of two opposing components of the free energy. One is the strain in the second beta turn that favors the dimer, and the other is the entropic cost of dimer formation that favors the monomer. A single-site mutation can disrupt this balance and trigger domain swapping.
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Affiliation(s)
- J W O'Neill
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
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16
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Endicott JA, Noble ME, Tucker JA. Cyclin-dependent kinases: inhibition and substrate recognition. Curr Opin Struct Biol 1999; 9:738-44. [PMID: 10607671 DOI: 10.1016/s0959-440x(99)00038-x] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Four unresolved issues of cyclin-dependent kinase (CDK) regulation have been addressed by structural studies this year - the mechanism of CDK inhibition by members of the INK4 family of CDK inhibitors, consensus substrate sequence recognition by CDKs, the role of the cyclin subunit in substrate recognition and the structural mechanism underlying CDK inhibition by phosphorylation.
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Affiliation(s)
- J A Endicott
- Laboratory of Molecular Biophysics, Department of Biochemistry, Oxford Centre for Molecular Sciences, Oxford, OX1 3QU, UK.
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17
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Affiliation(s)
- J Pines
- Wellcome/CRC Institute, Cambridge, UK.
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18
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Norledge BV, Trinkl S, Jaenicke R, Slingsby C. The X-ray structure of a mutant eye lens beta B2-crystallin with truncated sequence extensions. Protein Sci 1997; 6:1612-20. [PMID: 9260274 PMCID: PMC2143762 DOI: 10.1002/pro.5560060802] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
beta-Crystallins are oligomeric eye lens proteins that are related to monomeric gamma-crystallins by domain swapping: like gamma-crystallins, they are comprised of two similar domains but they differ in having long sequence extensions. beta B2, a major component of beta-crystallin oligomers, self-associates to a homodimer in solution. In two crystal structures of native beta B2, the protein is a 222-symmetric tetramer of eight domains. It has previously been shown that a mutant of rat beta B2-crystallin, in which the bulk of the N- and C-terminal sequence extensions has been deleted, assembles into dimers and tetramers. Here we present the 3.0 A resolution X-ray structure of the tetramer, beta B2 delta NC1. The mutant tetramer has a very similar set of domain interactions to the native structure. However, the structures differ in the relative orientation of the two sets of four domains. The paired N- and C-terminal domain interface, which is at the heart of the dimer structure, is very similar to the native structure. However, the truncation of the C-terminal extension removes an important tryptophan residue, which prevents the extension from acting as a (non-covalent) linker, as it does in native beta B2. There is a knock-on structural effect that removes a contact between extension and covalent linker, and this appears to cause a small twist in the linker that is amplified into a 20 degrees rotation between sets of paired domains.
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Affiliation(s)
- B V Norledge
- Birkbeck College, Department of Crystallography, London, United Kingdom
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19
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Abstract
The Cks proteins are essential components of the cyclin-dependent protein kinases that regulate mitosis in all eukaryotes, but their precise function remains obscure. The crystal structures of several Cks proteins offer insights into their roles during the cell cycle.
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Affiliation(s)
- J Pines
- Wellcome/CRC Institute, Cambridge, UK
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