Crystal Structure of the Repetitive Segments of Spectrin

Yan, Yong-Bin; Winograd, Enrique; Viel, Alain; Cronin, Timothy J.; Harrison, S.C.; Branton, Daniel

doi:10.1126/science.8266097

Cited by 338 publications

(309 citation statements)

References 31 publications

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“…The CksHs2 monomer was observed in solution and its inferred structure is the same as the crystallographic structure of CksHsl (81% identical) (Arvai et al, 1995). The a-spectrin dimer structure was determined crystallographically and the monomer was observed in solution (Yan et al, 1993). Singlechain Fv molecules form monomers, dimers, and higher oligomers in solution (Raag & Whitlow, 1995).…”

Section: Examples Of 3 D Domain Swapping In Proteinsmentioning

confidence: 65%

3D domain swapping: A mechanism for oligomer assembly

1995

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Abstract3D domain swapping is a mechanism for forming oligomeric proteins from their monomers. In 3D domain swapping, one domain of a monomeric protein is replaced by the same domain from an identical protein chain. The result is an intertwined dimer or higher oligomer, with one domain of each subunit replaced by the identical domain from another subunit. The swapped "domain" can be as large as an entire tertiary globular domain, or as small as an a-helix or a strand of a P-sheet. Examples of 3D domain swapping are reviewed that suggest domain swapping can serve as a mechanism for functional interconversion between monomers and oligomers, and that domain swapping may serve as a mechanism for evolution of some oligomeric proteins. Domain-swapped proteins present examples of a single protein chain folding into two distinct structures.Keywords: aggregation; complementation; oligomer evolution; protein dimerization Since Svedberg's discovery of functional molecules composed of two or more identical protein chains, much effort has been expended in studying their metabolic regulation (Monod et al., 1965;Koshland et al., 1966) and their assembly and disassembly (Kikuchi & King, 1975;Caspar, 1980;Jaenicke, 1995).Despite this progress, understanding the assembly of oligomeric proteins from monomers remains a challenge. A common observation is that disassembly of an oligomeric protein into its monomeric subunits is accompanied by irreversible unfolding and aggregation. This observation is often interpreted in terms of exposing apolar patches on the monomer surface that are covered in the oligomer, thereby providing binding energy from a hydrophobic interaction. Thus, the question remains of how the oligomer could have been assembled in the first place. We propose an answer to this question for some oligomers based on a mode of association that we have noticed in several proteins of Reprint requests to: David Eisenberg, Molecular Biology Institute, Department of Chemistry and Biochemistry, and UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, University of California-Los Angeles, Los Angeles, California 90095-1570; e-mail: david@pauling.rnbi.ucla.edu.Abbreviations: BS-RNase, bovine seminal ribonuclease; DT, diphtheria toxin; GM-CSF, granulocyte-macrophage colony-stimulating factor; GST, glutathione S-transferase; IF, interferon; IL, interleukin; RNase, ribonuclease. known structure. We term this mode of association 3 0 domain swapping, because oligomers are formed from stable monomers by exchanging domains.A problem related to the formation of oligomeric proteins in a cell is the problem of how oligomeric proteins evolved from monomeric precursor proteins. For an oligomer to evolve, random mutations must change the surface of the monomer so that sufficient free energy is released upon oligomerization to overcome the accompanying entropy loss of immobilizing the monomers. As we discuss in this review, single amino acid replacements must be fortuitous to provide an adequate free energy of interaction. But an ...

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Section: Examples Of 3 D Domain Swapping In Proteinsmentioning

confidence: 65%

3D domain swapping: A mechanism for oligomer assembly

1995

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“…Yet, the majority of the structural studies of spectrin are of its structural domains (e.g., 1AJ3 43 ; 2SPC 44 ; 3EDV 45 ; 3KBT/ 3KBU 32 ) or SH3 domain (2RMO 46 ; 2OAW 47 ; 1U06 48 ). For the tetramerization regions, many studies have focused on the N-terminal region of aI-and aII-spectrin, [15][16][17][18]30,31,42,48 but only a few have studied the Cterminal region of b-spectrin.…”

Section: Discussionmentioning

confidence: 99%

Apparent structural differences at the tetramerization region of erythroid and nonerythroid beta spectrin as discriminated by phage displayed scFvs

et al. 2011

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We have screened a human immunoglobulin single-chain variable fragment (scFv) phage library against the C-terminal tetramerization regions of erythroid and nonerythroid beta spectrin (bI-C1 and bII-C1, respectively) to explore the structural uniqueness of erythroid and nonerythroid b-spectrin isoforms. We have identified interacting scFvs, with clones ''G5'' and ''A2'' binding only to bI-C1, and clone ''F11'' binding only to bII-C1. The K d values, estimated by competitive enzyme-linked immunosorbent assay, of these scFvs with their target spectrin proteins were 0.1-0.3 lM. A more quantitative K d value from isothermal titration calorimetry experiments with the recombinant G5 and bI-C1 was 0.15 lM. The a-spectrin fragments (model proteins), aI-N1 and aII-N1, competed with the bI-C1, or bII-C1, binding scFvs, with inhibitory concentration (IC 50 ) values of~50 lM for aI-N1, and 0.5 lM for aII-N1. Our predicted structures of bI-C1 and bII-C1 suggest that the Helix B 0 of the Cterminal partial domain of bI differs from that of bII. Consequently, an unstructured region downstream of Helix B 0 in bI may interact specifically with the unstructured, complementarity determining region H1 of G5 or A2 scFv. The corresponding region in bII was helical, and bII did not bind G5 scFv. Our results suggest that it is possible for cellular proteins to differentially associate with the C-termini of different b-spectrin isoforms to regulate a-and b-spectrin association to form functional spectrin tetramers, and may sort b-spectrin isoforms to their specific cellular localizations.Keywords: beta spectrin; erythroid and nonerythroid; scFv; structural difference; affinity difference Abbreviations: aI-N1, a recombinant protein of aI-spectrin segment with residues 1-156; aI-spectrin, erythroid a-spectrin; aII-N1, a GST fusion protein of aII-spectrin segment with residues 1-147; aII-spectrin, nonerythroid a-spectrin; bI-C1, a GST fusion protein of bI-spectrin segment with residues 1898-2083; bI-C1D, a GST fusion protein of bI-spectrin segment with residues 1898-2070, that is, the residues 2071-2083 in bI-C1 were deleted; bI-spectrin, erythroid b-spectrin; bII-C1, a GST fusion protein of bII-spectrin segment with residues 1906-2093; bII-spectrin, nonerythroid b-spectrin; CD, circular dichroism; CDRs, complementarity determining regions; ELISA, enzyme-linked immunosorbent assay; EPR, electron paramagnetic resonance; GST, glutathione S-transferase; HRP, horseradish peroxidase; ITC, isothermal titration calorimetry; PBS, phosphate buffered saline at pH 7.4; rG5, recombinant G5, a single-chain variable fragment found to bind bI-C1; scFv, single-chain variable fragment.Yuanli Song's current address is

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“…Such features are observed in naturally occurring antiparallel coiled-coil trimers, such as the repetitive segments of spectrin. 34 This structure contains HIS at a, PHE at d, and TRP at d.…”

Section: Trimersmentioning

confidence: 99%

Computational analysis of residue contributions to coiled‐coil topology

Torre

Lazaridis

2011

Protein Science

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A variety of features are thought to contribute to the oligomeric and topological specificity of coiled coils. In previous work, we examined the determinants of oligomeric state. Here, we examine the energetic basis for the tendency of six coiled-coil peptides to align their a-helices in antiparallel orientation using molecular dynamics simulations with implicit solvation (EEF1.1). We also examine the effect of mutations known to disrupt the topology of these peptides. In agreement with experiment, ARG or LYS at a or d positions were found to stabilize the antiparallel configuration. The modeling suggests that this is not due to a-a 0 or d-d 0 repulsions but due to interactions with e 0 and g 0 residues. TRP at core positions also favors the antiparallel configuration. Residues that disfavor parallel dimers, such as ILE at d, are better tolerated in, and thus favor the antiparallel configuration. Salt bridge networks were found to be more stabilizing in the antiparallel configuration for geometric reasons: antiparallel helices point amino acid side chains in opposite directions. However, the structure with the largest number of salt bridges was not always the most stable, due to desolvation and configurational entropy contributions. In tetramers, the extent of stabilization of the antiparallel topology by core residues is influenced by the e 0 residue on a neighboring helix. Residues at b and c positions in some cases also contribute to stabilization of antiparallel tetramers. This work provides useful rules toward the goal of designing coiled coils with a well-defined and predictable three-dimensional structure.

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Crystal Structure of the Repetitive Segments of Spectrin

Cited by 338 publications

References 31 publications

3D domain swapping: A mechanism for oligomer assembly

3D domain swapping: A mechanism for oligomer assembly

Apparent structural differences at the tetramerization region of erythroid and nonerythroid beta spectrin as discriminated by phage displayed scFvs

Computational analysis of residue contributions to coiled‐coil topology

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