The Dominance of Symmetry in the Evolution of Homo-oligomeric Proteins

Schulz, Georg E.

doi:10.1016/j.jmb.2009.10.044

Cited by 27 publications

(19 citation statements)

References 25 publications

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“…Trimers and higher homo-oligomers of monotopic (and also of all other) membrane proteins should assume C n symmetry, which is rare for n greater than 2 because the development of such oligomers is entropically hampered. [31][32][33] In agreement with this rule, there is only 1 trimer (C 3 symmetry), 1 tetramer (C 4 symmetry) and no higher associations among the 34 distinct monotopic proteins. The observation corresponds well with soluble proteins, assuming rarely C n symmetry.…”

Section: Oligomerization and Asymmetric Contents Of Crystalssupporting

confidence: 62%

A New Classification of Membrane Protein Crystals

Schulz¹

2011

Journal of Molecular Biology

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Section: Oligomerization and Asymmetric Contents Of Crystalssupporting

confidence: 62%

A New Classification of Membrane Protein Crystals

Schulz¹

2011

Journal of Molecular Biology

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“…It was pointed out by Monod et al [10] that the effect of a single mutation in complexes with the close-packed form may be much greater than in complexes without dihedral symmetry. This effect may allow such complexes to evolve more readily by the efficient generation of favorable interactions, and this prediction has been supported by recent docking-simulation studies [11]–[13].…”

Section: Introductionmentioning

confidence: 71%

Influence of Structural Symmetry on Protein Dynamics

et al. 2012

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Structural symmetry in homooligomeric proteins has intrigued many researchers over the past several decades. However, the implication of protein symmetry is still not well understood. In this study, we performed molecular dynamics (MD) simulations of two forms of trp RNA binding attenuation protein (TRAP), the wild-type 11-mer and an engineered 12-mer, having two different levels of circular symmetry. The results of the simulations showed that the inter-subunit fluctuations in the 11-mer TRAP were significantly smaller than the fluctuations in the 12-mer TRAP while the internal fluctuations were larger in the 11-mer than in the 12-mer. These differences in thermal fluctuations were interpreted by normal mode analysis and group theory. For the 12-mer TRAP, the wave nodes of the normal modes existed at the flexible interface between the subunits, while the 11-mer TRAP had its nodes within the subunits. The principal components derived from the MD simulations showed similar mode structures. These results demonstrated that the structural symmetry was an important determinant of protein dynamics in circularly symmetric homooligomeric proteins.

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“…S3, B and C). In contrast, the vast majority of biological dimers are 2-fold symmetric (50,51) and also the 2:2 InlB/Met complex shows 2-fold symmetry. If this contact between two B-repeats were to stabilize a 2:2 InlB/Met complex, asymmetry would need to be introduced in the short linker between the end of the internalin domain and the start of the B-repeat, which is very unlikely.…”

Section: Resultsmentioning

confidence: 92%

Fold and Function of the InlB B-repeat

Ebbes

Bleymüller

Cernescu

et al. 2011

Journal of Biological Chemistry

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Host cell invasion by the facultative intracellular pathogen Listeria monocytogenes requires the invasion protein InlB in many cell types. InlB consists of an N-terminal internalin domain that binds the host cell receptor tyrosine kinase Met and C-terminal GW domains that bind to glycosaminoglycans (GAGs). Met binding and activation is required for host cell invasion, while the interaction between GW domains and GAGs enhances this effect. Soluble InlB elicits the same cellular phenotypes as the natural Met ligand hepatocyte growth factor/ scatter factor (HGF/SF), e.g. cell scatter. So far, little is known about the central part of InlB, the B-repeat. Here we present a structural and functional characterization of the InlB B-repeat. The crystal structure reveals a variation of the ␤-grasp fold that is most similar to small ubiquitin-like modifiers (SUMOs). However, structural similarity also suggests a potential evolutionary relation to bacterial mucin-binding proteins. The B-repeat defines the prototype structure of a hitherto uncharacterized domain present in over a thousand bacterial proteins. Generally, this domain probably acts as a spacer or a receptor-binding domain in extracellular multi-domain proteins. In cellular assays the B-repeat acts synergistically with the internalin domain conferring to it the ability to stimulate cell motility. Thus, the B-repeat probably binds a further host cell receptor and thereby enhances signaling downstream of Met.

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The Dominance of Symmetry in the Evolution of Homo-oligomeric Proteins

Cited by 27 publications

References 25 publications

A New Classification of Membrane Protein Crystals

A New Classification of Membrane Protein Crystals

Influence of Structural Symmetry on Protein Dynamics

Fold and Function of the InlB B-repeat

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