The ubiquitous buried water in the<scp>beta‐trefoil</scp>architecture contributes to the folding nucleus and ~20% of the folding enthalpy

Parker, Joseph B.; Tenorio, Connie A.; Blaber, Michael

doi:10.1002/pro.4192

Cited by 6 publications

(7 citation statements)

References 43 publications

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“…However, as a concatenated trimer, the folding nucleus of Symfoil‐4T is not distributed within each of the repeating trefoil motifs, rather, it spans the region from Turn IV through Turn IX (i.e., the central trefoil motif, plus preceding and following β‐hairpin turns) 30 . A recent mutational study, disrupting a conserved buried water within each of the three repeating trefoil motifs, showed that β‐hairpin structures preceding and following the central motif provide additional folding nucleation structure 36 . Such hairpins are not present in the first and third motif due to the structural “discontinuity” created by the N‐ and C‐termini.…”

Section: Discussionmentioning

confidence: 99%

“…30 A recent mutational study, disrupting a conserved buried water within each of the three repeating trefoil motifs, showed that β-hairpin structures preceding and following the central motif provide additional folding nucleation structure. 36 Such hairpins are not present in the first and third motif due to the structural "discontinuity" created by the N-and C-termini. The HSM1 and HSM2 proteins do not disrupt the preferred centrally-located folding nucleus, but the HSM3 mutation does.…”

Section: Discussionmentioning

confidence: 99%

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Functionalization of a symmetric protein scaffold: Redundant folding nuclei and alternative oligomeric folding pathways

2022

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Successful de novo protein design ideally targets specific folding kinetics, stability thermodynamics, and biochemical functionality, and the simultaneous achievement of all these criteria in a single step design is challenging. Protein design is potentially simplified by separating the problem into two steps: (a) an initial design of a protein “scaffold” having appropriate folding kinetics and stability thermodynamics, followed by (b) appropriate functional mutation—possibly involving insertion of a peptide functional “cassette.” This stepwise approach can also separate the orthogonal effects of the “stability/function” and “foldability/function” tradeoffs commonly observed in protein design. If the scaffold is a protein architecture having an exact rotational symmetry, then there is the potential for redundant folding nuclei and multiple equivalent sites of functionalization; thereby enabling broader functional adaptation. We describe such a “scaffold” and functional “cassette” design strategy applied to a β‐trefoil threefold symmetric architecture and a heparin ligand functionality. The results support the availability of redundant folding nuclei within this symmetric architecture, and also identify a minimal peptide cassette conferring heparin affinity. The results also identify an energy barrier of destabilization that switches the protein folding pathway from monomeric to trimeric, thereby identifying another potential advantage of symmetric protein architecture in de novo design.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Functionalization of a symmetric protein scaffold: Redundant folding nuclei and alternative oligomeric folding pathways

2022

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“…Establishment of this folding nucleus is the rate limiting step in folding, and once formed, serves to rapidly condense formation of the overall native structure. An isolated 42-mer trefoil motif (i.e., “Monofoil”) derived from the Symfoil protein spontaneously oligomerizes to yield an intact β-trefoil architecture ( Lee and Blaber, 2011 ; Lee et al, 2011 ); thus, a serviceable folding nucleus resides within each repeating motif in the Symfoil protein ( Blaber, 2020 ; Parker et al, 2021 ). However, phi-value analysis ( Fersht and Sato, 2004 ) indicates that the effective folding nucleus in the Symfoil protein, and the related fibroblast-growth factor-1 β-trefoil protein, while not identical, are both centrally-located and more expansive than an individual trefoil motif ( Longo et al, 2014 ; Xia et al, 2016 ).…”

Section: Discussionmentioning

confidence: 99%

Variable and Conserved Regions of Secondary Structure in the β-Trefoil Fold: Structure Versus Function

Blaber

2022

Front. Mol. Biosci.

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β-trefoil proteins exhibit an approximate C3 rotational symmetry. An analysis of the secondary structure for members of this diverse superfamily of proteins indicates that it is comprised of remarkably conserved β-strands and highly-divergent turn regions. A fundamental “minimal” architecture can be identified that is devoid of heterogenous and extended turn regions, and is conserved among all family members. Conversely, the different functional families of β-trefoils can potentially be identified by their unique turn patterns (or turn “signature”). Such analyses provide clues as to the evolution of the β-trefoil family, suggesting a folding/stability role for the β-strands and a functional role for turn regions. This viewpoint can also guide de novo protein design of β-trefoil proteins having novel functionality.

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“…Specifically, residues 52-69 and 77-87 from ECOD domain e4ow4A1 were used for the search motif. The rationale behind this choice of motif is discussed in greater detail in the section β-Trefoil-like Structure Motifs Occur in Just Two Ancient β-Protein Lineages, Including the IgG-like β-Sandwich, and relates to the rarity of this motif and its essentiality to β-trefoil structure and folding [31,32]. The search motif was aligned against all domains in the ECOD F99 database (version develop271) with TM-align [33].…”

Section: β-Trefoil-like (βTl) Motif Searchmentioning

confidence: 99%

“…The conserved water molecule forms hydrogen bonds to three distinct backbone sites, two β-strands and a loop, and is a hallmark structural feature that fundamentally enables the β-trefoil motif and architecture. Recently, the conserved water has been shown to make significant contributions to both the structure of the folding nucleus and the overall enthalpy of folding [32]. To search for β-trefoil-like motifs in other protein lineages, we focused on the conserved water molecule and the structural elements that interact with it, namely β-strands β1, β2, and the loop after β3 (canonical β-trefoil motif strand numbering).…”

Section: β-Trefoil-like Structure Motifs Occur In Just Two Ancient β-...mentioning

confidence: 99%

Evidence for the emergence of β-trefoils by ‘Peptide Budding’ from an IgG-like β-sandwich

2022

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As sequence and structure comparison algorithms gain sensitivity, the intrinsic interconnectedness of the protein universe has become increasingly apparent. Despite this general trend, β-trefoils have emerged as an uncommon counterexample: They are an isolated protein lineage for which few, if any, sequence or structure associations to other lineages have been identified. If β-trefoils are, in fact, remote islands in sequence-structure space, it implies that the oligomerizing peptide that founded the β-trefoil lineage itself arose de novo. To better understand β-trefoil evolution, and to probe the limits of fragment sharing across the protein universe, we identified both ‘β-trefoil bridging themes’ (evolutionarily-related sequence segments) and ‘β-trefoil-like motifs’ (structure motifs with a hallmark feature of the β-trefoil architecture) in multiple, ostensibly unrelated, protein lineages. The success of the present approach stems, in part, from considering β-trefoil sequence segments or structure motifs rather than the β-trefoil architecture as a whole, as has been done previously. The newly uncovered inter-lineage connections presented here suggest a novel hypothesis about the origins of the β-trefoil fold itself–namely, that it is a derived fold formed by ‘budding’ from an Immunoglobulin-like β-sandwich protein. These results demonstrate how the evolution of a folded domain from a peptide need not be a signature of antiquity and underpin an emerging truth: few protein lineages escape nature’s sewing table.

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The ubiquitous buried water in thebeta‐trefoilarchitecture contributes to the folding nucleus and ~20% of the folding enthalpy

Cited by 6 publications

References 43 publications

Functionalization of a symmetric protein scaffold: Redundant folding nuclei and alternative oligomeric folding pathways

Functionalization of a symmetric protein scaffold: Redundant folding nuclei and alternative oligomeric folding pathways

Variable and Conserved Regions of Secondary Structure in the β-Trefoil Fold: Structure Versus Function

Evidence for the emergence of β-trefoils by ‘Peptide Budding’ from an IgG-like β-sandwich

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