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PDBsum entry 1bk2

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protein links
Sh3-domain PDB id
1bk2
Jmol
Contents
Protein chain
57 a.a. *
Waters ×42
* Residue conservation analysis
PDB id:
1bk2
Name: Sh3-domain
Title: A-spectrin sh3 domain d48g mutant
Structure: A-spectrin. Chain: a. Fragment: sh3-domain. Engineered: yes. Mutation: yes
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Cell_line: bl21. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.01Å     R-factor:   0.228     R-free:   0.325
Authors: J.C.Martinez,M.T.Pisabarro,L.Serrano
Key ref:
J.C.Martinez et al. (1998). Obligatory steps in protein folding and the conformational diversity of the transition state. Nat Struct Biol, 5, 721-729. PubMed id: 9699637 DOI: 10.1038/1418
Date:
14-Jul-98     Release date:   16-Feb-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07751  (SPTA2_CHICK) -  Spectrin alpha chain, non-erythrocytic 1
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2477 a.a.
57 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     endocytosis   1 term 

 

 
DOI no: 10.1038/1418 Nat Struct Biol 5:721-729 (1998)
PubMed id: 9699637  
 
 
Obligatory steps in protein folding and the conformational diversity of the transition state.
J.C.Martinez, M.T.Pisabarro, L.Serrano.
 
  ABSTRACT  
 
We have analyzed the existence of obligatory steps in the folding reaction of the alpha-spectrin SH3 domain by mutating Asp 48 (D48G), which is at position i+3 of an isolated two-residue type II' beta-turn. Calorimetry and X-ray analysis show an entropic stabilizing effect resulting from local changes at the dihedral angles of the beta-turn. Kinetic analysis of D48G shows that this beta-turn is fully formed in the transition state, while there is no evidence of its formation in an isolated fragment. Introduction of several mutations in the D48G protein reveals that the local stabilization has not significantly altered the transition state ensemble. All these results, together with previous analysis of other alpha-spectrin and src SH3 mutants, indicate that: (i) in the folding reaction there could be obligatory steps which are not necessarily part of the folding nucleus; (ii) transition state ensembles in beta-sheet proteins could be quite defined and conformationally restricted ('mechanic folding nucleus'); and (iii) transition state ensembles in some proteins could be evolutionarily conserved.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Schematic diagram for the folding reaction of the SH3 protein. Unfolded state: the protein in strong denaturing conditions. Denatured state: the denatured protein under native conditions. Transition state: the highest energy point in the folding reaction. Folded state: the native conformation. The stabilizing point mutation at position 48 is shown as an X and the -turn is shown as a bold curve. In the denatured state the hairpin may be folded in some of the conformations. Since the hairpin by itself is not folded in water, this means that only those compact conformations stabilizing the hairpin will be significantly represented. Stabilization of the turn will favor those conformations and produce, on average, a more compact denatured state. Folding will be initiated through a search of conformations until certain specific interactions, which act as a scaffold for subsequent contacts, are formed (folding nucleus). This implies formation of the distal hairpin in the -spectrin SH3 and, consequently, full formation of the distal -turn. Once this 'nucleus' is built, the protein passes over the transition state and then follows the downhill rapid cooperative formation of the folded structure.
Figure 7.
Figure 7. Schematic diagram showing three possible models for the transition state in protein folding. The breadth of the transition state ensemble is indicated by two opposing concave lines. a, The transition state is conformationally very diverse as exemplified by two very different conformations having different -hairpins folded. [‡-U] values between 1 and 0 indicate that in some molecules the interaction broken by mutagenesis is fully made, in others it is not made at all, and in another group it is partly made. In this case, a stabilization of a local interaction (X) present only in one conformation and close to a mutation with an intermediate [‡-U] value, will result in that conformation being more populated, with the consequent change in the intermediate [‡-U] value. This is shown by a vertical narrowing of the transition state and the presence of only the stabilized conformation in the transition state. b, The transition state is conformationally more homogeneous with some interactions fully present in all conformations of the transition state. Here, in passing over the transition state it is only necessary for the protein to make a certain number of non-specific interactions which compensate for the entropic cost of folding. Stabilization of a local interaction (X) present in all conformations shifts the transition state towards the denatured state (Hammond's postulate) and, as a consequence, the conformational ensemble is less structured on average. c, In order to pass the transition state, several residues of the protein (shown by gray circles) need obligatorily to come together and form a specific cluster. In this case, stabilization of a local interaction present between two of these residues will not affect the overall structure of the transition state.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1998, 5, 721-729) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21086517 V.Castillo, A.Espargaró, V.Gordo, J.Vendrell, and S.Ventura (2010).
Deciphering the role of the thermodynamic and kinetic stabilities of SH3 domains on their aggregation inside bacteria.
  Proteomics, 10, 4172-4185.  
19541614 A.A.Fuller, D.Du, F.Liu, J.E.Davoren, G.Bhabha, G.Kroon, D.A.Case, H.J.Dyson, E.T.Powers, P.Wipf, M.Gruebele, and J.W.Kelly (2009).
Evaluating beta-turn mimics as beta-sheet folding nucleators.
  Proc Natl Acad Sci U S A, 106, 11067-11072.
PDB code: 2kbu
19617233 A.M.Candel, E.S.Cobos, F.Conejero-Lara, and J.C.Martinez (2009).
Evaluation of folding co-operativity of a chimeric protein based on the molecular recognition between polyproline ligands and SH3 domains.
  Protein Eng Des Sel, 22, 597-606.  
19617547 E.Shakhnovich (2009).
Protein folding roller coaster, one molecule at a time.
  Proc Natl Acad Sci U S A, 106, 11823-11824.  
19956763 J.Liu, and J.Song (2009).
Insights into protein aggregation by NMR characterization of insoluble SH3 mutants solubilized in salt-free water.
  PLoS One, 4, e7805.  
19629713 V.Chevelkov, U.Fink, and B.Reif (2009).
Quantitative analysis of backbone motion in proteins using MAS solid-state NMR spectroscopy.
  J Biomol NMR, 45, 197-206.  
18223000 E.S.Cobos, A.M.Candel, and J.C.Martinez (2008).
An error analysis for two-state protein-folding kinetic parameters and phi-values: progress toward precision by exploring pH dependencies on Leffler plots.
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18625237 M.C.Baxa, K.F.Freed, and T.R.Sosnick (2008).
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18160276 R.Broglia, Y.Levy, and G.Tiana (2008).
HIV-1 protease folding and the design of drugs which do not create resistance.
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17705837 V.Parthiban, M.M.Gromiha, M.Abhinandan, and D.Schomburg (2007).
Computational modeling of protein mutant stability: analysis and optimization of statistical potentials and structural features reveal insights into prediction model development.
  BMC Struct Biol, 7, 54.  
17623848 X.Periole, M.Vendruscolo, and A.E.Mark (2007).
Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain.
  Proteins, 69, 536-550.  
16906862 A.Amatori, J.Ferkinghoff-Borg, G.Tiana, and R.A.Broglia (2006).
Thermodynamic features characterizing good and bad folding sequences obtained using a simplified off-lattice protein model.
  Phys Rev E Stat Nonlin Soft Matter Phys, 73, 061905.  
16362723 A.Marx, J.Müller, E.M.Mandelkow, A.Hoenger, and E.Mandelkow (2006).
Interaction of kinesin motors, microtubules, and MAPs.
  J Muscle Res Cell Motil, 27, 125-137.  
16522792 C.J.Wilson, D.Apiyo, and P.Wittung-Stafshede (2006).
Solvation of the folding-transition state in Pseudomonas aeruginosa azurin is modulated by metal: Solvation of azurin's folding nucleus.
  Protein Sci, 15, 843-852.  
16683745 E.Shakhnovich (2006).
Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet.
  Chem Rev, 106, 1559-1588.  
16648162 F.Cecconi, C.Guardiani, and R.Livi (2006).
Testing simplified proteins models of the hPin1 WW domain.
  Biophys J, 91, 694-704.  
16543273 G.Wainreb, N.Haspel, H.J.Wolfson, and R.Nussinov (2006).
A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly.
  Bioinformatics, 22, 1343-1352.  
16815916 L.Sutto, G.Tiana, and R.A.Broglia (2006).
Sequence of events in folding mechanism: beyond the Gō model.
  Protein Sci, 15, 1638-1652.  
16807295 M.Jäger, Y.Zhang, J.Bieschke, H.Nguyen, M.Dendle, M.E.Bowman, J.P.Noel, M.Gruebele, and J.W.Kelly (2006).
Structure-function-folding relationship in a WW domain.
  Proc Natl Acad Sci U S A, 103, 10648-10653.
PDB codes: 1zcn 2f21
16505376 M.O.Lindberg, E.Haglund, I.A.Hubner, E.I.Shakhnovich, and M.Oliveberg (2006).
Identification of the minimal protein-folding nucleus through loop-entropy perturbations.
  Proc Natl Acad Sci U S A, 103, 4083-4088.  
16214873 M.Qin, J.Zhang, and W.Wang (2006).
Effects of disulfide bonds on folding behavior and mechanism of the beta-sheet protein tendamistat.
  Biophys J, 90, 272-286.  
16857672 X.Li, Y.Chen, Y.Liu, J.Gao, F.Gao, M.Bartlam, J.Y.Wu, and Z.Rao (2006).
Structural basis of Robo proline-rich motif recognition by the srGAP1 Src homology 3 domain in the Slit-Robo signaling pathway.
  J Biol Chem, 281, 28430-28437.
PDB code: 2gnc
16121395 L.Ragona, G.Colombo, M.Catalano, and H.Molinari (2005).
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15469926 J.E.Ollerenshaw, H.Kaya, H.S.Chan, and L.E.Kay (2004).
Sparsely populated folding intermediates of the Fyn SH3 domain: matching native-centric essential dynamics and experiment.
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15281124 J.Lee, S.Y.Kim, K.Joo, I.Kim, and J.Lee (2004).
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15041678 S.Casares, M.Sadqi, O.López-Mayorga, F.Conejero-Lara, and N.A.van Nuland (2004).
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15146499 S.Selvaraj, and M.M.Gromiha (2004).
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15576508 T.R.Sosnick, R.S.Dothager, and B.A.Krantz (2004).
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  EMBO J, 22, 1518-1528.  
12548722 K.Ikeda, O.V.Galzitskaya, H.Nakamura, and J.Higo (2003).
beta-Hairpins, alpha-helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal beta-hairpin of SH3 domain.
  J Comput Chem, 24, 310-318.  
12824493 L.Spagnolo, S.Ventura, and L.Serrano (2003).
Folding specificity induced by loop stiffness.
  Protein Sci, 12, 1473-1482.  
12784211 T.Ichimaru, and T.Kikuchi (2003).
Analysis of the differences in the folding kinetics of structurally homologous proteins based on predictions of the gross features of residue contacts.
  Proteins, 51, 515-530.  
12829501 T.Srimathi, T.K.Kumar, K.M.Kathir, Y.H.Chi, S.Srisailam, W.Y.Lin, I.M.Chiu, and C.Yu (2003).
Structurally homologous all beta-barrel proteins adopt different mechanisms of folding.
  Biophys J, 85, 459-472.  
12001223 A.Fernández (2002).
Time-resolved backbone desolvation and mutational hot spots in folding proteins.
  Proteins, 47, 447-457.  
11959988 A.R.Viguera, C.Vega, and L.Serrano (2002).
Unspecific hydrophobic stabilization of folding transition states.
  Proc Natl Acad Sci U S A, 99, 5349-5354.
PDB code: 1hd3
12496119 F.Ding, N.V.Dokholyan, S.V.Buldyrev, H.E.Stanley, and E.I.Shakhnovich (2002).
Direct molecular dynamics observation of protein folding transition state ensemble.
  Biophys J, 83, 3525-3532.  
11835513 G.Colombo, D.Roccatano, and A.E.Mark (2002).
Folding and stability of the three-stranded beta-sheet peptide Betanova: insights from molecular dynamics simulations.
  Proteins, 46, 380-392.  
11786916 J.G.Northey, A.A.Di Nardo, and A.R.Davidson (2002).
Hydrophobic core packing in the SH3 domain folding transition state.
  Nat Struct Biol, 9, 126-130.  
12237457 J.Karanicolas, and C.L.Brooks (2002).
The origins of asymmetry in the folding transition states of protein L and protein G.
  Protein Sci, 11, 2351-2361.  
12368899 M.Lindberg, J.Tångrot, and M.Oliveberg (2002).
Complete change of the protein folding transition state upon circular permutation.
  Nat Struct Biol, 9, 818-822.  
11805324 M.S.Cheung, A.E.García, and J.N.Onuchic (2002).
Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse.
  Proc Natl Acad Sci U S A, 99, 685-690.  
12426369 T.G.Wendt, N.Volkmann, G.Skiniotis, K.N.Goldie, J.Müller, E.Mandelkow, and A.Hoenger (2002).
Microscopic evidence for a minus-end-directed power stroke in the kinesin motor ncd.
  EMBO J, 21, 5969-5978.  
11694889 B.A.Krantz, and T.R.Sosnick (2001).
Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil.
  Nat Struct Biol, 8, 1042-1047.  
11340663 G.M.Langdon, M.A.Jiménez, C.G.Genzor, S.Maldonado, J.Sancho, and M.Rico (2001).
Anabaena apoflavodoxin hydrogen exchange: on the stable exchange core of the alpha/beta(21345) flavodoxin-like family.
  Proteins, 43, 476-488.  
11606303 G.Settanni, A.Cattaneo, and A.Maritan (2001).
Role of native-state topology in the stabilization of intracellular antibodies.
  Biophys J, 81, 2935-2945.  
11179896 K.Gunasekaran, S.J.Eyles, A.T.Hagler, and L.M.Gierasch (2001).
Keeping it in the family: folding studies of related proteins.
  Curr Opin Struct Biol, 11, 83-93.  
11606790 L.Li, and E.I.Shakhnovich (2001).
Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations.
  Proc Natl Acad Sci U S A, 98, 13014-13018.  
11340064 L.Mirny, and E.Shakhnovich (2001).
Protein folding theory: from lattice to all-atom models.
  Annu Rev Biophys Biomol Struct, 30, 361-396.  
11687614 N.Ferguson, J.R.Pires, F.Toepert, C.M.Johnson, Y.P.Pan, R.Volkmer-Engert, J.Schneider-Mergener, V.Daggett, H.Oschkinat, and A.Fersht (2001).
Using flexible loop mimetics to extend phi-value analysis to secondary structure interactions.
  Proc Natl Acad Sci U S A, 98, 13008-13013.
PDB code: 1k5r
11248045 N.Sinha, and R.Nussinov (2001).
Point mutations and sequence variability in proteins: redistributions of preexisting populations.
  Proc Natl Acad Sci U S A, 98, 3139-3144.  
11258944 P.Schubert, D.Schnappinger, K.Pfleiderer, and W.Hillen (2001).
Identification of a stability determinant on the edge of the Tet repressor four-helix bundle dimerization motif.
  Biochemistry, 40, 3257-3263.  
11179898 R.Guerois, and L.Serrano (2001).
Protein design based on folding models.
  Curr Opin Struct Biol, 11, 101-106.  
11524678 S.B.Ozkan, I.Bahar, and K.A.Dill (2001).
Transition states and the meaning of Phi-values in protein folding kinetics.
  Nat Struct Biol, 8, 765-769.  
11179895 V.Grantcharova, E.J.Alm, D.Baker, and A.L.Horwich (2001).
Mechanisms of protein folding.
  Curr Opin Struct Biol, 11, 70-82.  
11226214 Y.Levy, J.Jortner, and O.M.Becker (2001).
Solvent effects on the energy landscapes and folding kinetics of polyalanine.
  Proc Natl Acad Sci U S A, 98, 2188-2193.  
  11206067 A.Rath, and A.R.Davidson (2000).
The design of a hyperstable mutant of the Abp1p SH3 domain by sequence alignment analysis.
  Protein Sci, 9, 2457-2469.  
11025541 B.Nölting, and K.Andert (2000).
Mechanism of protein folding.
  Proteins, 41, 288-298.  
10679463 D.J.Brockwell, D.A.Smith, and S.E.Radford (2000).
Protein folding mechanisms: new methods and emerging ideas.
  Curr Opin Struct Biol, 10, 16-25.  
  10739253 E.Cota, and J.Clarke (2000).
Folding of beta-sandwich proteins: three-state transition of a fibronectin type III module.
  Protein Sci, 9, 112-120.  
  11106173 H.M.Rodriguez, D.M.Vu, and L.M.Gregoret (2000).
Role of a solvent-exposed aromatic cluster in the folding of Escherichia coli CspA.
  Protein Sci, 9, 1993-2000.  
10639131 H.Nymeyer, N.D.Socci, and J.N.Onuchic (2000).
Landscape approaches for determining the ensemble of folding transition states: success and failure hinge on the degree of frustration.
  Proc Natl Acad Sci U S A, 97, 634-639.  
10869177 J.A.Bousquet, C.Garbay, B.P.Roques, and Y.Mély (2000).
Circular dichroic investigation of the native and non-native conformational states of the growth factor receptor-binding protein 2 N-terminal src homology domain 3: effect of binding to a proline-rich peptide from guanine nucleotide exchange factor.
  Biochemistry, 39, 7722-7735.  
10913274 K.Takano, Y.Yamagata, and K.Yutani (2000).
Role of amino acid residues at turns in the conformational stability and folding of human lysozyme.
  Biochemistry, 39, 8655-8665.
PDB codes: 1di3 1di4 1di5 1gaz
  11206053 M.C.Vega, J.C.Martínez, and L.Serrano (2000).
Thermodynamic and structural characterization of Asn and Ala residues in the disallowed II' region of the Ramachandran plot.
  Protein Sci, 9, 2322-2328.
PDB codes: 1qkw 1qkx
10737947 P.Ferrara, J.Apostolakis, and A.Caflisch (2000).
Computer simulations of protein folding by targeted molecular dynamics.
  Proteins, 39, 252-260.  
  11152127 S.M.Larson, and A.R.Davidson (2000).
The identification of conserved interactions within the SH3 domain by alignment of sequences and structures.
  Protein Sci, 9, 2170-2180.  
10841554 S.S.Plotkin, and J.N.Onuchic (2000).
Investigation of routes and funnels in protein folding by free energy functional methods.
  Proc Natl Acad Sci U S A, 97, 6509-6514.  
10860975 V.P.Grantcharova, D.S.Riddle, and D.Baker (2000).
Long-range order in the src SH3 folding transition state.
  Proc Natl Acad Sci U S A, 97, 7084-7089.  
  10386868 C.J.Tsai, S.Kumar, B.Ma, and R.Nussinov (1999).
Folding funnels, binding funnels, and protein function.
  Protein Sci, 8, 1181-1190.  
10047588 C.M.Dobson, and M.Karplus (1999).
The fundamentals of protein folding: bringing together theory and experiment.
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10322218 D.Thirumalai, and D.K.Klimov (1999).
Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models.
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10500172 E.Alm, and D.Baker (1999).
Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures.
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10322214 E.Alm, and D.Baker (1999).
Matching theory and experiment in protein folding.
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10508783 J.Clarke, E.Cota, S.B.Fowler, and S.J.Hamill (1999).
Folding studies of immunoglobulin-like beta-sandwich proteins suggest that they share a common folding pathway.
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10051587 J.M.Goldberg, and R.L.Baldwin (1999).
A specific transition state for S-peptide combining with folded S-protein and then refolding.
  Proc Natl Acad Sci U S A, 96, 2019-2024.  
10485889 L.B.Moran, J.P.Schneider, A.Kentsis, G.A.Reddy, and T.R.Sosnick (1999).
Transition state heterogeneity in GCN4 coiled coil folding studied by using multisite mutations and crosslinking.
  Proc Natl Acad Sci U S A, 96, 10699-10704.  
15012420 M.Gruebele (1999).
The fast protein folding problem.
  Annu Rev Phys Chem, 50, 485-516.  
10500171 O.V.Galzitskaya, and A.V.Finkelstein (1999).
A theoretical search for folding/unfolding nuclei in three-dimensional protein structures.
  Proc Natl Acad Sci U S A, 96, 11299-11304.  
10098403 R.L.Baldwin, and G.D.Rose (1999).
Is protein folding hierarchic? II. Folding intermediates and transition states.
  Trends Biochem Sci, 24, 77-83.  
10319810 S.E.Radford, and C.M.Dobson (1999).
From computer simulations to human disease: emerging themes in protein folding.
  Cell, 97, 291-298.  
10611302 T.Ternström, U.Mayor, M.Akke, and M.Oliveberg (1999).
From snapshot to movie: phi analysis of protein folding transition states taken one step further.
  Proc Natl Acad Sci U S A, 96, 14854-14859.  
9699621 M.Gruebele, and P.G.Wolynes (1998).
Satisfying turns in folding transitions.
  Nat Struct Biol, 5, 662-665.  
9699636 V.P.Grantcharova, D.S.Riddle, J.V.Santiago, and D.Baker (1998).
Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain.
  Nat Struct Biol, 5, 714-720.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.