Protein reconstitution and three‐dimensional domain swapping: Benefits and constraints of covalency

The phenomena of protein reconstitution and three‐dimensional domain swapping reveal that highly similar structures can be obtained whether a protein is comprised of one or more polypeptide chains. In this review, we use protein reconstitution as a lens through which to examine the range of protein tolerance to chain interruptions and the roles of the primary structure in related features of protein structure and folding, including circular permutation, natively unfolded proteins, allostery, and amyloid fibril formation. The results imply that noncovalent interactions in a protein are sufficient to specify its structure under the constraints imposed by the covalent backbone.

[1]  R. Nussinov,et al.  Is allostery an intrinsic property of all dynamic proteins? , 2004, Proteins.

[2]  M. J. Conroy,et al.  Cystatin forms a tetramer through structural rearrangement of domain-swapped dimers prior to amyloidogenesis. , 2004, Journal of molecular biology.

[3]  P. S. Kim,et al.  The C-peptide helix from ribonuclease A considered as an autonomous folding unit. , 1987, Cold Spring Harbor symposia on quantitative biology.

[4]  A. Fersht,et al.  The structure of the transition state for the association of two fragments of the barley chymotrypsin inhibitor 2 to generate native-like protein: implications for mechanisms of protein folding. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[5]  K. Gunasekaran,et al.  Disallowed Ramachandran conformations of amino acid residues in protein structures. , 1996, Journal of molecular biology.

[6]  F. Richards,et al.  Degradation of ribonuclease by subtilisin. , 1955, Biochimica et biophysica acta.

[7]  F. Perler Protein splicing mechanisms and applications , 2005, IUBMB life.

[8]  Andrew L. Lee,et al.  Dynamic coupling and allosteric behavior in a nonallosteric protein. , 2006, Biochemistry.

[9]  B. Semler,et al.  Self-cleaving proteases. , 1991, Current opinion in cell biology.

[10]  David Eisenberg,et al.  Runaway domain swapping in amyloid-like fibrils of T7 endonuclease I. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[11]  A. Fersht,et al.  Protein fragments as models for events in protein folding pathways: protein engineering analysis of the association of two complementary fragments of the barley chymotrypsin inhibitor 2 (CI-2). , 1995, Biochemistry.

[13]  F. Richards ON THE ENZYMIC ACTIVITY OF SUBTILISIN-MODIFIED RIBONUCLEASE. , 1958, Proceedings of the National Academy of Sciences of the United States of America.

[14]  N. Nio,et al.  Complete amino acid sequence of the sweet protein monellin. , 1990, Agricultural and biological chemistry.

[15]  L. Wu,et al.  Autonomous protein folding units. , 2000, Advances in protein chemistry.

[16]  R. Sauer,et al.  Evolution of a protein fold in vitro. , 1999, Science.

[17]  D. Cram,et al.  The design of molecular hosts, guests, and their complexes , 1988, Science.

[18]  S. Linse,et al.  Reconstitution of calmodulin from domains and subdomains: Influence of target peptide. , 2006, Journal of molecular biology.

[19]  L M Amzel,et al.  Loss of translational entropy in binding, folding, and catalysis , 1997, Proteins.

[20]  A. Surolia,et al.  Protein stabilization through phage display , 2000, FEBS letters.

[21]  M. Bloom,et al.  Correlation between lipid plane curvature and lipid chain order. , 1996, Biophysical journal.

[22]  S. Linse,et al.  An extended hudrophobic core induces EF‐hand swapping , 2001, Protein science : a publication of the Protein Society.

[23]  L. Itzhaki,et al.  Three-dimensional domain swapping in p13suc1 occurs in the unfolded state and is controlled by conserved proline residues , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[24]  M. Juillerat,et al.  Complementation in folding and fragment exchange. , 1986, Methods in enzymology.

[25]  Y. Komeiji,et al.  Glycine 85 of the trp-repressor of E. coli is important in forming the hydrophobic tryptophan binding pocket: experimental and computational approaches. , 1994, Protein engineering.

[26]  Suganthi Balasubramanian,et al.  Protein alchemy: Changing β-sheet into α-helix , 1997, Nature Structural Biology.

[27]  W F van Gunsteren,et al.  Decomposition of the free energy of a system in terms of specific interactions. Implications for theoretical and experimental studies. , 1994, Journal of molecular biology.

[28]  Dill,et al.  Folding and binding. , 1996, Current opinion in structural biology.

[29]  D. Wiley,et al.  Structural characterization of a soluble and partially folded class I major histocompatibility heavy chain/β2m heterodimer , 1998, Nature Structural Biology.

[30]  N. Kobayashi,et al.  Conformational study on the IgG binding domain of protein G , 1993 .

[31]  M. A. Saper,et al.  Structure of the human class I histocompatibility antigen, HLA-A2 , 1987, Nature.

[32]  G. Rose,et al.  Protein folding--what's the question? , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[33]  Mitsuhiko Ikura,et al.  Genetic polymorphism and protein conformational plasticity in the calmodulin superfamily: Two ways to promote multifunctionality , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[34]  A. Joshua Wand,et al.  Dynamic activation of protein function: A view emerging from NMR spectroscopy , 2001, Nature Structural Biology.

[35]  O Jardetzky,et al.  Protein dynamics and conformational transitions in allosteric proteins. , 1996, Progress in biophysics and molecular biology.

[36]  R. Hantgan,et al.  Formation of a biologically active, ordered complex from two overlapping fragments of cytochrome c. , 1977, The Journal of biological chemistry.

[37]  D Eisenberg,et al.  The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-A resolution. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Pernilla Wittung-Stafshede,et al.  How do cofactors modulate protein folding? , 2005, Protein and peptide letters.

[39]  Denny G. A. Johansson,et al.  Autoproteolysis coupled to protein folding in the SEA domain of the membrane-bound MUC1 mucin , 2006, Nature Structural &Molecular Biology.

[40]  Mikael C. Bauer,et al.  Intra- versus intermolecular interactions in monellin: contribution of surface charges to protein assembly. , 2006, Journal of molecular biology.

[41]  C B Anfinsen,et al.  An experimental approach to the study of the folding of staphylococcal nuclease. , 1969, The Journal of biological chemistry.

[42]  Robert B. Gennis,et al.  Biomembranes: Molecular Structure and Function , 1988 .

[43]  D. Wiley,et al.  Structure of the human class I histocompatibility antigen, HLA-A2. , 2005, Journal of immunology.

[44]  B. Matthews,et al.  A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene , 1993, Nature.

[45]  D. Eisenberg,et al.  Domain swapping: entangling alliances between proteins. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[46]  Sara Linse,et al.  Coupling of ligand binding and dimerization of helix‐loop‐helix peptides: Spectroscopic and sedimentation analyses of calbindin D9k EF‐hands , 2002, Proteins.

[47]  S. Kim,et al.  Redesigning a sweet protein: increased stability and renaturability. , 1989, Protein engineering.

[48]  A. Holmgren Thioredoxin‐C′: Reconstitution of an active form of Escherichia coli thioredoxin from two noncovalently linked cyanogen bromide peptide fragments , 1972, FEBS letters.

[49]  P. Gettins Serpin structure, mechanism, and function. , 2002, Chemical reviews.

[50]  Zbigniew Grzonka,et al.  Human cystatin C, an amyloidogenic protein, dimerizes through three-dimensional domain swapping , 2001, Nature Structural Biology.

[51]  D. Shortle Structural analysis of non-native states of proteins by NMR methods. , 1996, Current opinion in structural biology.

[52]  R. L. Baldwin,et al.  The design and production of semisynthetic ribonucleases with increased thermostability by incorporation of S‐peptide analogues with enhanced helical stability , 1986, Proteins.

[53]  M. Newcomer,et al.  Protein folding and three-dimensional domain swapping: astrained relationship? , 2002 .

[54]  David Eisenberg,et al.  3D domain swapping: As domains continue to swap , 2002, Protein science : a publication of the Protein Society.

[55]  Roger A. Jones,et al.  Structural basis of RNA folding and recognition in an AMP–RNA aptamer complex , 1996, Nature.

[56]  L. Peltonen,et al.  Autoproteolytic activation of human aspartylglucosaminidase. , 2004, The Biochemical journal.

[57]  J. Carey,et al.  Structural organization in peptide fragments of cytochrome c by heme binding. , 1999, Journal of molecular biology.

[58]  H. K. Schachman,et al.  Random circular permutation of genes and expressed polypeptide chains: application of the method to the catalytic chains of aspartate transcarbamoylase. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[59]  J. Carey A systematic and general proteolytic method for defining structural and functional domains of proteins. , 2000, Methods in enzymology.

[60]  Gonzalo de Prat-Gay,et al.  Association of complementary fragments and the elucidation of protein folding pathways , 1996 .

[61]  G. Rose,et al.  A complete conformational map for RNA. , 1999, Journal of molecular biology.

[62]  David Eisenberg,et al.  A domain-swapped RNase A dimer with implications for amyloid formation , 2001, Nature Structural Biology.

[63]  Angela M Gronenborn,et al.  A protein contortionist: core mutations of GB1 that induce dimerization and domain swapping. , 2003, Journal of molecular biology.

[64]  Robert A. Grothe,et al.  Structure of the cross-β spine of amyloid-like fibrils , 2005, Nature.

[65]  A. Koide,et al.  High‐affinity fragment complementation of a fibronectin type III domain and its application to stability enhancement , 2005, Protein science : a publication of the Protein Society.

[66]  G. Weber Ligand binding and internal equilibria in proteins. , 1972, Biochemistry.

[67]  H. Berman,et al.  E. coli trp repressor forms a domain-swapped array in aqueous alcohol. , 2004, Structure.

[68]  L Serrano,et al.  The order of secondary structure elements does not determine the structure of a protein but does affect its folding kinetics. , 1995, Journal of molecular biology.

[69]  I. Ekiel,et al.  Folding-related Dimerization of Human Cystatin C (*) , 1996, The Journal of Biological Chemistry.

[70]  D. Shortle,et al.  Evidence for strained interactions between side-chains and the polypeptide backbone. , 1994, Journal of molecular biology.

[71]  M. L. Tasayco,et al.  Ordered self-assembly of polypeptide fragments to form nativelike dimeric trp repressor. , 1992, Science.

[72]  R. Nussinov,et al.  Folding and binding cascades: shifts in energy landscapes. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[73]  M. Newcomer,et al.  Protein folding and three-dimensional domain swapping: a strained relationship? , 2002, Current opinion in structural biology.

[74]  C. Dobson Protein misfolding, evolution and disease. , 1999, Trends in biochemical sciences.

[75]  S. R. Marana Molecular basis of substrate specificity in family 1 glycoside hydrolases , 2006, IUBMB life.

[76]  J. Rouvinen,et al.  Structural comparison of Ntn‐hydrolases , 2000, Protein science : a publication of the Protein Society.

[77]  C. Matthews,et al.  Testing the role of chain connectivity on the stability and structure of dihydrofolate reductase from E. coli: Fragment complementation and circular permutation reveal stable, alternatively folded forms , 2001, Protein science : a publication of the Protein Society.

[78]  S. Linse,et al.  Protein reconstitution and 3D domain swapping. , 2002, Current protein & peptide science.

[79]  H. Dyson,et al.  Coupling of folding and binding for unstructured proteins. , 2002, Current opinion in structural biology.

[80]  P. Schimmel,et al.  Functional assembly of a randomly cleaved protein. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[81]  M. Estes,et al.  X-ray structure of a native calicivirus: structural insights into antigenic diversity and host specificity. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[82]  J Yang,et al.  In vivo and in vitro studies of TrpR-DNA interactions. , 1996, Journal of molecular biology.

[83]  A. Murzin,et al.  A protein catalytic framework with an N-terminal nucleophile is capable of self-activation , 1995, Nature.

[84]  G. de Prat-Gay Association of complementary fragments and the elucidation of protein folding pathways. , 1996, Protein engineering.

[85]  M. Jaskólski,et al.  Prevention of Domain Swapping Inhibits Dimerization and Amyloid Fibril Formation of Cystatin C , 2004, Journal of Biological Chemistry.

[86]  R. Stenkamp,et al.  Thermodynamic and structural consequences of flexible loop deletion by circular permutation in the streptavidin‐biotin system , 1998, Protein science : a publication of the Protein Society.

[87]  W R Taylor,et al.  Three-dimensional domain duplication, swapping and stealing. , 1997, Current opinion in structural biology.

[88]  W. Xue,et al.  Multi‐method global analysis of thermodynamics and kinetics in reconstitution of monellin , 2004, Proteins.

[89]  L. Itzhaki,et al.  The unfolding story of three-dimensional domain swapping. , 2003, Structure.

[90]  J. R. Somoza,et al.  Two crystal structures of a potently sweet protein. Natural monellin at 2.75 A resolution and single-chain monellin at 1.7 A resolution. , 1993, Journal of molecular biology.

[91]  H. Dyson,et al.  Intrinsically unstructured proteins and their functions , 2005, Nature Reviews Molecular Cell Biology.

[92]  O. Jardetzky,et al.  AV77 hinge mutation stabilizes the helix-turn-helix domain of trp repressor. , 1996, Journal of molecular biology.

[93]  C. Birck,et al.  A novel protein fold and extreme domain swapping in the dimeric TorD chaperone from Shewanella massilia. , 2003, Structure.

[94]  P. Karplus Experimentally observed conformation‐dependent geometry and hidden strain in proteins , 1996, Protein science : a publication of the Protein Society.

[95]  S. Linse,et al.  Fragment complementation studies of protein stabilization by hydrophobic core residues. , 2001, Biochemistry.

[96]  Tom L. Blundell,et al.  High resolution structure of an oligomeric eye lens β-crystallin , 1991 .

[97]  Stress and strain in staphylococcal nuclease , 1993, Protein science : a publication of the Protein Society.

[98]  O. Jardetzky,et al.  The solution structures of the trp repressor-operator DNA complex. , 1994, Journal of molecular biology.

[99]  David Eisenberg,et al.  Deposition diseases and 3D domain swapping. , 2006, Structure.

[100]  Donald J. Cram The Design of Molecular Hosts, Guests, and Their Complexes (Nobel Lecture)† , 1988 .

[101]  Alexander Wlodawer,et al.  The domain-swapped dimer of cyanovirin-N is in a metastable folded state: reconciliation of X-ray and NMR structures. , 2002, Structure.

[102]  H. Paulus,et al.  Protein splicing and related forms of protein autoprocessing. , 2000, Annual review of biochemistry.

[103]  R. Hodges,et al.  Relative stabilities of synthetic peptide homo‐ and heterodimeric troponin‐C domains , 1994, Protein science : a publication of the Protein Society.

[104]  H. Uedaira,et al.  Complement assembly of two fragments of the streptococcal protein G B1 domain in aqueous solution , 1995, FEBS letters.

[105]  J. Veerkamp,et al.  Fatty acid binding and conformational stability of mutants of human muscle fatty acid-binding protein. , 1996, The Biochemical journal.

[106]  J. Feigon,et al.  Solution structure of an ATP-binding RNA aptamer reveals a novel fold. , 1997, RNA.

[107]  J. Veerkamp,et al.  Ligand specificity and conformational stability of human fatty acid-binding proteins. , 2001, The international journal of biochemistry & cell biology.

[108]  Witold K. Surewicz,et al.  Crystal structure of the human prion protein reveals a mechanism for oligomerization , 2002, Nature Structural Biology.

[109]  G. Schneider,et al.  Circular permutations of natural protein sequences: structural evidence. , 1997, Current opinion in structural biology.

[110]  H. Taniuchi,et al.  A study of core domains, and the core domain-domain interaction of cytochrome c fragment complex. , 1992, Archives of biochemistry and biophysics.

[111]  Lida K. Gifford,et al.  Domain organization of calbindin D28k as determined from the association of six synthetic EF‐hand fragments , 1997, Protein science : a publication of the Protein Society.

[112]  A. Fersht,et al.  Towards the complete structural characterization of a protein folding pathway: the structures of the denatured, transition and native states for the association/folding of two complementary fragments of cleaved chymotrypsin inhibitor 2. Direct evidence for a nucleation-condensation mechanism. , 1996, Folding & design.

[113]  G. Andria,et al.  The specific binding of three fragments of staphylococcal nuclease. , 1971, The Journal of biological chemistry.

[114]  D Eisenberg,et al.  Oligomer formation by 3D domain swapping: a model for protein assembly and misassembly. , 1997, Advances in protein chemistry.

[115]  P. S. Kim,et al.  Context-dependent secondary structure formation of a designed protein sequence , 1996, Nature.

[116]  David Eisenberg,et al.  Amyloid-like fibrils of ribonuclease A with three-dimensional domain-swapped and native-like structure , 2005, Nature.

[117]  A. Basak,et al.  Circular permutation of βB2‐crystallin changes the hierarchy of domain assembly , 1998, Protein science : a publication of the Protein Society.

[118]  D Szwajkajzer,et al.  Molecular and biological constraints on ligand-binding affinity and specificity. , 1997, Biopolymers.

[119]  K. Håkansson The strand-helix motif is a recurring theme in biological hydrolysis. Does the conformation of the Ramachandran outlier enhance its electrophilicity? , 2002, International journal of biological macromolecules.