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Title: Synthetic Foldable Proteins Generated from Peptide Segments of Folding Nuclei of Reference Proteins.
Creator: Blaber, Michael, Longo, Liam
Date Issued: 2017-10-10
Identifier: FSU_uspto_9783587, 9783587, 941193, 14/707691, 6c9256d97d167832cbab694dc904bd27
Format: Citation

Title: Experimental support for the foldability-function tradeoff hypothesis: segregation of the folding nucleus and functional regions in fibroblast growth factor-1..
Creator: Longo, Liam, Lee, Jihun, Blaber, Michael
Abstract/Description: The acquisition of function is often associated with destabilizing mutations, giving rise to the stability-function tradeoff hypothesis. To test whether function is also accommodated at the expense of foldability, fibroblast growth factor-1 (FGF-1) was subjected to a comprehensive φ-value analysis at each of the 11 turn regions. FGF-1, a β-trefoil fold, represents an excellent model system with which to evaluate the influence of function on foldability: because of its threefold symmetric...
Show moreThe acquisition of function is often associated with destabilizing mutations, giving rise to the stability-function tradeoff hypothesis. To test whether function is also accommodated at the expense of foldability, fibroblast growth factor-1 (FGF-1) was subjected to a comprehensive φ-value analysis at each of the 11 turn regions. FGF-1, a β-trefoil fold, represents an excellent model system with which to evaluate the influence of function on foldability: because of its threefold symmetric structure, analysis of FGF-1 allows for direct comparisons between symmetry-related regions of the protein that are associated with function to those that are not; thus, a structural basis for regions of foldability can potentially be identified. The resulting φ-value distribution of FGF-1 is highly polarized, with the majority of positions described as either folded-like or denatured-like in the folding transition state. Regions important for folding are shown to be asymmetrically distributed within the protein architecture; furthermore, regions associated with function (i.e., heparin-binding affinity and receptor-binding affinity) are localized to regions of the protein that fold after barrier crossing (late in the folding pathway). These results provide experimental support for the foldability-function tradeoff hypothesis in the evolution of FGF-1. Notably, the results identify the potential for folding redundancy in symmetric protein architecture with important implications for protein evolution and design.
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Date Issued: 2012-12-01
Identifier: FSU_pmch_23047594, 10.1002/pro.2175, PMC3575920, 23047594, 23047594
Format: Citation

Title: Symmetric Protein Architecture in Protein Design.
Creator: Longo, Liam, Blaber, Michael
Abstract/Description: Top-down symmetric deconstruction (TDSD) is a joint experimental and computational approach to generate a highly stable, functionally benign protein scaffold for intended application in subsequent functional design studies. By focusing on symmetric protein folds, TDSD can leverage the dramatic reduction in sequence space achieved by applying a primary structure symmetric constraint to the design process. Fundamentally, TDSD is an iterative symmetrization process, in which the goal is to...
Show moreTop-down symmetric deconstruction (TDSD) is a joint experimental and computational approach to generate a highly stable, functionally benign protein scaffold for intended application in subsequent functional design studies. By focusing on symmetric protein folds, TDSD can leverage the dramatic reduction in sequence space achieved by applying a primary structure symmetric constraint to the design process. Fundamentally, TDSD is an iterative symmetrization process, in which the goal is to maintain or improve properties of thermodynamic stability and folding cooperativity inherent to a starting sequence (the “proxy”). As such, TDSD does not attempt to solve the inverse protein folding problem directly, which is computationally intractable. The present chapter will take the reader through all of the primary steps of TDSD--selecting a proxy, identifying potential mutations, establishing a stability/folding cooperativity screen--relying heavily on a successful TDSD solution for the common β-trefoil fold.
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Date Issued: 2014-08-20
Identifier: FSU_libsubv1_scholarship_submission_1456502653, 10.1007/978-1-4939-1486-9_8
Format: Citation

Title: Prebiotic Protein Design supports a Halophile Origin of Foldable Proteins.
Creator: Longo, Liam, Blaber, Michael
Abstract/Description: In this opinion article we argue for the following: 1) 10 of the common α-amino acids were likely available in the prebiotic world, produced by a variety of abiotic chemical syntheses; 2) although a highly-restricted set, experimental and theoretical considerations indicates this prebiotic alphabet of α-amino acids contains the requisite chemical information to comprise a foldable set (i.e., foldable polypeptides are possible having a composition only of the prebiotic alphabet); 3) a...
Show moreIn this opinion article we argue for the following: 1) 10 of the common α-amino acids were likely available in the prebiotic world, produced by a variety of abiotic chemical syntheses; 2) although a highly-restricted set, experimental and theoretical considerations indicates this prebiotic alphabet of α-amino acids contains the requisite chemical information to comprise a foldable set (i.e., foldable polypeptides are possible having a composition only of the prebiotic alphabet); 3) a comparison of the prebiotic alphabet with known proteomes predicts that polypeptides comprised of the prebiotic alphabet would have halophile properties – i.e., folding and solubility would be compatible with high salt. Recent experimental studies support this hypothesis; 4) proteogenesis (the emergence of polypeptides) – a key aspect of abiogenesis (the emergence of life from non-living molecules) – is likely to have occurred within the halophile environment.
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Date Issued: 2014-01-06
Identifier: FSU_libsubv1_scholarship_submission_1456502085, 10.3389/fmicb.2013.00418, PMC3880840
Format: Citation

Title: Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein.
Creator: Longo, Liam M, Lee, Jihun, Blaber, Michael
Abstract/Description: A compendium of different types of abiotic chemical syntheses identifies a consensus set of 10 "prebiotic" α-amino acids. Before the emergence of biosynthetic pathways, this set is the most plausible resource for protein formation (i.e., proteogenesis) within the overall process of abiogenesis. An essential unsolved question regarding this prebiotic set is whether it defines a "foldable set"--that is, does it contain sufficient chemical information to permit cooperatively folding polypeptides...
Show moreA compendium of different types of abiotic chemical syntheses identifies a consensus set of 10 "prebiotic" α-amino acids. Before the emergence of biosynthetic pathways, this set is the most plausible resource for protein formation (i.e., proteogenesis) within the overall process of abiogenesis. An essential unsolved question regarding this prebiotic set is whether it defines a "foldable set"--that is, does it contain sufficient chemical information to permit cooperatively folding polypeptides? If so, what (if any) characteristic properties might such polypeptides exhibit? To investigate these questions, two "primitive" versions of an extant protein fold (the β-trefoil) were produced by top-down symmetric deconstruction, resulting in a reduced alphabet size of 12 or 13 amino acids and a percentage of prebiotic amino acids approaching 80%. These proteins show a substantial acidification of pI and require high salt concentrations for cooperative folding. The results suggest that the prebiotic amino acids do comprise a foldable set within the halophile environment.
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Date Issued: 2013-02-05
Identifier: FSU_pmch_23341608, 10.1073/pnas.1219530110, PMC3568330, 23341608, 23341608, 1219530110
Format: Citation

Title: Ab initio Folding of a Trefoil-fold Motif Reveals Structural similarity with a β-propeller Blade Motif.
Creator: Tenorio, Connie, Longo, Liam, Parker, Joseph, Lee, Jihun, Blaber, Michael
Abstract/Description: Many protein architectures exhibit evidence of internal rotational symmetry postulated to be the result of gene duplication/fusion events involving a primordial polypeptide motif. A common feature of such structures is a domain-swapped arrangement at the interface of the N- and C-termini motifs and postulated to provide cooperative interactions that promote folding and stability. De novo designed symmetric protein architectures have demonstrated an ability to accommodate circular permutation...
Show moreMany protein architectures exhibit evidence of internal rotational symmetry postulated to be the result of gene duplication/fusion events involving a primordial polypeptide motif. A common feature of such structures is a domain-swapped arrangement at the interface of the N- and C-termini motifs and postulated to provide cooperative interactions that promote folding and stability. De novo designed symmetric protein architectures have demonstrated an ability to accommodate circular permutation of the N- and C-termini in the overall architecture; however, the folding requirement of the primordial motif are poorly understood, and tolerance to circular permutation is essentially unknown. The β-trefoil protein fold is a threefold symmetric architecture where the repeating ~42-mer “trefoil-fold” motif assembles via a domain-swapped arrangement. The trefoil-fold structure in isolation exposes considerable hydrophobic area that is otherwise buried in the intact β-trefoil trimeric assembly. The trefoil-fold sequence is not predicted to adopt the trefoil-fold architecture in ab initio folding studies; rather, the predicted fold is closely related to a compact “blade” motif from the β-propeller architecture. Expression of a trefoil-fold sequence and circular permutants shows that only the wild-type N-terminal motif definition yields an intact β-trefoil trimeric assembly, while permutants yield monomers. The results elucidate the folding requirements of the primordial trefoil-fold motif, and also suggest that this motif may sample a compact conformation that limits hydrophobic residue exposure, contains key trefoil-fold structural features, but is more structurally homologous to a β-propeller blade motif.
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Date Issued: 2020-03-03
Identifier: FSU_libsubv1_scholarship_submission_1583283654_54e07068, 10.1002/pro.3850
Format: Citation

Title: Evolution and design of protein structure by folding nucleus symmetric expansion.
Creator: Longo, Liam, Kumru, Ozan, Middaugh, Russell, Blaber, Michael
Abstract/Description: Models of symmetric protein evolution typically invoke gene duplication and fusion events, in which repetition of a structural motif generates foldable, stable symmetric protein architecture. Success of such evolutionary processes suggests that the duplicated structural motif must be capable of nucleating protein folding. If correct, symmetric expansion of a folding nucleus sequence derived from an extant symmetric fold may be an elegant and computationally tractable solution to de novo...
Show moreModels of symmetric protein evolution typically invoke gene duplication and fusion events, in which repetition of a structural motif generates foldable, stable symmetric protein architecture. Success of such evolutionary processes suggests that the duplicated structural motif must be capable of nucleating protein folding. If correct, symmetric expansion of a folding nucleus sequence derived from an extant symmetric fold may be an elegant and computationally tractable solution to de novo protein design. We report the efficient de novo design of a β-trefoil protein by symmetric expansion of a β-trefoil folding nucleus, previously identified by ɸ-value analysis. The resulting protein, having exact sequence symmetry, exhibits superior folding properties compared to its naturally evolved progenitor--with the potential for redundant folding nuclei. In principle, folding nucleus symmetric expansion can be applied to any given symmetric protein fold (that is, nearly 1/3 of the known proteome) provided information of the folding nucleus is available.
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Date Issued: 2014-10-07
Identifier: FSU_libsubv1_scholarship_submission_1456503265, 10.1016/j.str.2014.08.008
Format: Citation

Title: Mutation Choice to Eliminate Buried Free Cysteines in Protein Therapeutics.
Creator: Xia, Xue, Longo, Liam, Blaber, Michael
Abstract/Description: Buried free Cys residues can contribute to an irreversible unfolding pathway that promotes protein aggregation, increases immunogenic potential, and significantly reduces protein functional half-life. Consequently, mutation of buried free Cys residues can result in significant improvement in the storage, reconstitution, and pharmacokinetic properties of protein-based therapeutics. Mutational design to eliminate buried free Cys residues typically follows one of two common heuristics: either...
Show moreBuried free Cys residues can contribute to an irreversible unfolding pathway that promotes protein aggregation, increases immunogenic potential, and significantly reduces protein functional half-life. Consequently, mutation of buried free Cys residues can result in significant improvement in the storage, reconstitution, and pharmacokinetic properties of protein-based therapeutics. Mutational design to eliminate buried free Cys residues typically follows one of two common heuristics: either substitution by Ser (polar and isosteric), or substitution by Ala or Val (hydrophobic); however, a detailed structural and thermodynamic understanding of Cys mutations is lacking. We report a comprehensive structure and stability study of Ala, Ser, Thr and Val mutations at each of the three buried free Cys positions (Cys16, Cys83, and Cys117) in fibroblast growth factor-1 (FGF-1). Mutation was almost universally destabilizing, indicating a general optimization for the wild-type Cys, including van der Waals and H-bond interactions. Structural response to Cys mutation characteristically involved changes to maintain, or effectively substitute, local H-bond interactions -- by either structural collapse to accommodate the smaller oxygen radius of Ser/Thr, or conversely, expansion to enable inclusion of novel H-bonding solvent. Despite the diverse structural effects, the least destabilizing average substitution at each position was Ala, and not isosteric Ser.
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Date Issued: 2014-10-13
Identifier: FSU_libsubv1_scholarship_submission_1456504649, 10.1002/jps.24188
Format: Citation

Title: Simplified Protein Design Biased for Pre-Biotic Amino Acids Yields a Foldable, Halophilic Protein.
Creator: Longo, Liam, Lee, Jihun, Blaber, Michael
Abstract/Description: A compendium of different types of abiotic chemical syntheses identifies a consensus set of 10 “pre-biotic” -amino acids. Prior to the emergence of biosynthetic pathways this set is the most plausible resource for protein formation (i.e., proteogenesis) within the overall process of abiogenesis. An essential unsolved question regarding this pre-biotic set is whether it defines a “foldable set”? - that is, does it contain sufficient chemical information to permit cooperatively-folding...
Show moreA compendium of different types of abiotic chemical syntheses identifies a consensus set of 10 “pre-biotic” -amino acids. Prior to the emergence of biosynthetic pathways this set is the most plausible resource for protein formation (i.e., proteogenesis) within the overall process of abiogenesis. An essential unsolved question regarding this pre-biotic set is whether it defines a “foldable set”? - that is, does it contain sufficient chemical information to permit cooperatively-folding polypeptides? If so, what (if any) characteristic properties might such polypeptides exhibit? To investigate these questions two “primitive” versions of an extant protein fold (the β-trefoil) were produced by top-down symmetric deconstruction, resulting in a reduced alphabet size of 12 or 13 amino acids and a percentage of pre-biotic amino acids approaching 80%. These proteins show a substantial acidification of pI and require high salt concentrations for cooperative folding. The results suggest that the pre-biotic amino acids do comprise a foldable set within the halophile environment.
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Date Issued: 2012-12-19
Identifier: FSU_libsubv1_scholarship_submission_1456500856, 10.1073/pnas.1219530110
Format: Citation

Title: Characterization of binding of LARP6 to the 5' stem-loop of collagen mRNAs: implications for synthesis of type I collagen..
Creator: Stefanovic, Lela, Longo, Liam, Zhang, Yujie, Stefanovic, Branko
Abstract/Description: Type I collagen is composed of 2 polypeptides, α1(I) and α2(I), which fold into triple helix. Collagen α1(I) and α2(I) mRNAs have a conserved stem-loop structure in their 5' UTRs, the 5'SL. LARP6 binds the 5'SL to regulate type I collagen expression. We show that 5 nucleotides within the single stranded regions of 5'SL contribute to the high affinity of LARP6 binding. Mutation of individual nucleotides abolishes the binding in gel mobility shift assay. LARP6 binding to 5'SL of collagen α2(I)...
Show moreType I collagen is composed of 2 polypeptides, α1(I) and α2(I), which fold into triple helix. Collagen α1(I) and α2(I) mRNAs have a conserved stem-loop structure in their 5' UTRs, the 5'SL. LARP6 binds the 5'SL to regulate type I collagen expression. We show that 5 nucleotides within the single stranded regions of 5'SL contribute to the high affinity of LARP6 binding. Mutation of individual nucleotides abolishes the binding in gel mobility shift assay. LARP6 binding to 5'SL of collagen α2(I) mRNA is more stable than the binding to 5'SL of α1(I) mRNA, although the equilibrium binding constants are similar. The more stable binding to α2(I) mRNA may favor synthesis of the heterotrimeric type I collagen. LARP6 needs 2 domains to contact 5'SL, the La domain and the RRM. T133 in the La domain is critical for folding of the protein, while loop 3 in the RRM is critical for binding 5'SL. Loop 3 is also involved in the interaction of LARP6 and protein translocation channel SEC61. This interaction is essential for type I collagen synthesis, because LARP6 mutant which binds 5'SL but which does not interact with SEC61, suppresses collagen synthesis in a dominant negative manner. We postulate that LARP6 directly targets collagen mRNAs to the SEC61 translocons to facilitate coordinated translation of the 2 collagen mRNAs. The unique sequences of LARP6 identified in this work may have evolved to enable its role in type I collagen biosynthesis.
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Date Issued: 2014-01-01
Identifier: FSU_pmch_25692237, 10.1080/15476286.2014.996467, PMC4615758, 25692237, 25692237
Format: Citation

Title: Emergence of Symmetric Protein Architecture from a Simple Peptide Motif: Evolutionary Models.
Creator: Blaber, Michael, Lee, Jihun, Longo, Liam
Abstract/Description: Structural symmetry is observed in the majority of fundamental protein folds and gene duplication and fusion evolutionary processes are postulated to be responsible. However, convergent evolution leading to structural symmetry has also been proposed; additionally, there is debate regarding the extent to which exact primary structure symmetry is compatible with efficient protein folding. Issues of symmetry in protein evolution directly impact strategies for de novo protein design as symmetry...
Show moreStructural symmetry is observed in the majority of fundamental protein folds and gene duplication and fusion evolutionary processes are postulated to be responsible. However, convergent evolution leading to structural symmetry has also been proposed; additionally, there is debate regarding the extent to which exact primary structure symmetry is compatible with efficient protein folding. Issues of symmetry in protein evolution directly impact strategies for de novo protein design as symmetry can substantially simplify the design process. Additionally, when considering gene duplication and fusion in protein evolution, there are two competing models: ‘‘emergent architecture’’ and ‘‘conserved architecture’’. Recent experimental work has shed light on both the evolutionary process leading to symmetric protein folds as well as the ability of symmetric primary structure to efficiently fold. Such studies largely support a ‘‘conserved architecture’’ evolutionary model, suggesting that complex protein architecture was an early evolutionary achievement involving oligomerization of smaller polypeptides.
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Date Issued: 2012-06-26
Identifier: FSU_libsubv1_scholarship_submission_1464369511, 10.1007/s00018-012-1077-3
Format: Citation

Title: Alternative Folding Nuclei Definitions Facilitate the Evolution of a Symmetric Protein Fold from a Smaller Peptide Motif.
Creator: Longo, Liam, Lee, Jihun, Tenorio, Connie, Blaber, Michael
Abstract/Description: Protein 3° structure symmetry is a defining feature of nearly a third of protein folds and is generally thought to result from a combination of gene duplication, fusion, and truncation events. Such events represent major replication errors, involving substantial alteration of protein 3° structure as well as causing regions of exact repeating 1° structure, both of which are generally considered deleterious to protein folding. Thus, the prevalence of symmetric protein folds is counterintuitive...
Show moreProtein 3° structure symmetry is a defining feature of nearly a third of protein folds and is generally thought to result from a combination of gene duplication, fusion, and truncation events. Such events represent major replication errors, involving substantial alteration of protein 3° structure as well as causing regions of exact repeating 1° structure, both of which are generally considered deleterious to protein folding. Thus, the prevalence of symmetric protein folds is counterintuitive and suggests a specific, yet unexplained, robustness. Using a designed β-trefoil protein, we show that purely symmetric 1° structure enables utilization of alternative definitions of the critical folding nucleus in response to gross structural rearrangement. Thus, major replication errors producing 1° structure symmetry can conserve foldability. The results provide an explanation for the prevalence of symmetric protein folds, and highlight a critical role for 1° structure symmetry in protein evolution.
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Date Issued: 2013-10-17
Identifier: FSU_libsubv1_scholarship_submission_1456501539, 10.1016/j.str.2013.09.003
Format: Citation

Title: The Folding Nucleus Structure Persists in Thermally-Aggregated FGF-1.
Creator: Longo, Liam, Gao, Yuan, Tenorio, Connie, Wang, Gan, Paravastu, Anant, Blaber, Michael
Abstract/Description: An efficient protein folding pathway leading to target structure, and the avoidance of aggregation, is essential to protein evolution and de novo design; however, design details to achieve efficient folding and avoid aggregation are poorly understood. We report characterization of the thermally-induced aggregate of fibroblast growth factor-1 (FGF-1), a small globular protein, by solid-state NMR. NMR spectra are consistent with residual structure in the aggregate and provide evidence of a...
Show moreAn efficient protein folding pathway leading to target structure, and the avoidance of aggregation, is essential to protein evolution and de novo design; however, design details to achieve efficient folding and avoid aggregation are poorly understood. We report characterization of the thermally-induced aggregate of fibroblast growth factor-1 (FGF-1), a small globular protein, by solid-state NMR. NMR spectra are consistent with residual structure in the aggregate and provide evidence of a structured region that corresponds to the region of the folding nucleus. NMR data on aggregated FGF-1 also indicate the presence of unstructured regions that exhibit hydration-dependent dynamics and suggest that unstructured regions of aggregated FGF-1 lie outside the folding nucleus. Since it is known that regions outside the folding nucleus fold late in the folding pathway, we postulate that these regions unfold early in the unfolding pathway and that the partially folded state is more prone to intermolecular aggregation. This interpretation is further supported by comparison with a designed protein that shares the same FGF-1 folding nucleus sequence, but has different 1° structure outside the folding nucleus, and does not thermally aggregate. The results suggest that design of an efficient folding nucleus, and the avoidance of aggregation in the folding pathway, are potentially separable design criteria – the latter of which could principally focus upon the physicochemical properties of 1° structure outside the folding nucleus.
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Date Issued: 2017-10-23
Identifier: FSU_libsubv1_scholarship_submission_1509376995_85b5a7ca, 10.1002/pro.3332
Format: Citation

Title: Kallikrein-related Peptidase 6: A Biomarker for Traumatic Brain Injury.
Creator: Phipps, Helen, Longo, Liam, Blaber, Sachiko, Blaber, Michael, VanLandingham, Jacob
Abstract/Description: Establishment of a traumatic brain injury (TBI)-sensitive biomarker or identification of a key therapeutic agent would significantly improve clinicians’ efforts to diagnose and treat TBI, thereby promoting improved outcomes for patients. Numerous studies support the role of kallikrein-6 (Klk6) as a critical component of neuroinflammation and demyelination. This study assesses whether Klk6 is implicated in the secondary mechanisms of TBI and subsequently if serum levels of Klk6 are useable as...
Show moreEstablishment of a traumatic brain injury (TBI)-sensitive biomarker or identification of a key therapeutic agent would significantly improve clinicians’ efforts to diagnose and treat TBI, thereby promoting improved outcomes for patients. Numerous studies support the role of kallikrein-6 (Klk6) as a critical component of neuroinflammation and demyelination. This study assesses whether Klk6 is implicated in the secondary mechanisms of TBI and subsequently if serum levels of Klk6 are useable as a biomarker. Methods: The abundance of Klk6 following controlled cortical impact (CCI) of the medial prefrontal cortex to a depth of either 3.0 mm (severe) or 1.5 mm (moderate) was quantified. Uninjured and rats subjected to craniotomy-only were used as controls. Protein levels were quantified with Western-blotting, enzyme-linked immunosorbent assay and immunohistochemistry. Results: Severe and moderate CCI resulted in significant elevation of Klk6 in the contusion-core (12-fold-increase, p 5 0.0001) and serum (5-fold-increase, p 5 0.01) compared to controls. In all cases, Klk6 elevation was resolved within 72 hours. Conclusion: Serum levels of Klk6 are a statistically significant indicator of TBI 24 hours after CCI and thus may be of great utility to clinicians as a biomarker. These data strongly implicate Klk6 as a player in the neuroinflammation processes following CCI, although the specific mechanisms remain to be characterized.
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Date Issued: 2013-07-06
Identifier: FSU_libsubv1_scholarship_submission_1464402742, 10.3109/02699052.2013.823563
Format: Citation

Title: Evolution of a Protein Folding Nucleus.
Creator: Xia, Xue, Longo, Liam M., Sutherland, Mason A., Blaber, Michael
Abstract/Description: The folding nucleus (FN) is a cryptic element within protein primary structure that enables an efficient folding pathway and is the postulated heritable element in the evolution of protein architecture; however, almost nothing is known regarding how the FN structurally changes as complex protein architecture evolves from simpler peptide motifs. We report characterization of the FN of a designed purely symmetric β-trefoil protein by ϕ-value analysis. We compare the structure and folding...
Show moreThe folding nucleus (FN) is a cryptic element within protein primary structure that enables an efficient folding pathway and is the postulated heritable element in the evolution of protein architecture; however, almost nothing is known regarding how the FN structurally changes as complex protein architecture evolves from simpler peptide motifs. We report characterization of the FN of a designed purely symmetric β-trefoil protein by ϕ-value analysis. We compare the structure and folding properties of key foldable intermediates along the evolutionary trajectory of the β-trefoil. The results show structural acquisition of the FN during gene fusion events, incorporating novel turn structure created by gene fusion. Furthermore, the FN is adjusted by circular permutation in response to destabilizing functional mutation. FN plasticity by way of circular permutation is made possible by the intrinsic C3 cyclic symmetry of the β-trefoil architecture, identifying a possible selective advantage that helps explain the prevalence of cyclic structural symmetry in the proteome.
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Date Issued: 2015-12-10
Identifier: FSU_libsubv1_scholarship_submission_1464367133, 10.1002/pro.2848, PMC4918426
Format: Citation

Title: A Single Aromatic Core Mutation Converts a Designed "Primitive" Protein from Halophile to Mesophile Folding.
Creator: Longo, Liam, Tenorio, Conniee, Kumru, Ozan, Middaugh, Russell, Blaber, Michael
Abstract/Description: The halophile environment has a number of compelling aspects with regard to the origin of structured polypeptides (i.e., proteogenesis) and, instead of a curious niche that living systems adapted into, the halophile environment is emerging as a candidate “cradle” for proteogenesis. In this viewpoint, a subsequent halophile-to-mesophile transition was a key step in early evolution. Several lines of evidence indicate that aromatic amino acids were a late addition to the codon table and not part...
Show moreThe halophile environment has a number of compelling aspects with regard to the origin of structured polypeptides (i.e., proteogenesis) and, instead of a curious niche that living systems adapted into, the halophile environment is emerging as a candidate “cradle” for proteogenesis. In this viewpoint, a subsequent halophile-to-mesophile transition was a key step in early evolution. Several lines of evidence indicate that aromatic amino acids were a late addition to the codon table and not part of the original “prebiotic” set comprising the earliest polypeptides. We test the hypothesis that the availability of aromatic amino acids could facilitate a halophile-to-mesophile transition by hydrophobic core-packing enhancement. The effects of aromatic amino acid substitutions were evaluated in the core of a “primitive” designed protein enriched for the 10 prebiotic amino acids (A,D,E,G,I,L,P,S,T,V)--having an exclusively prebiotic core and requiring halophilic conditions for folding. The results indicate that a single aromatic amino acid substitution is capable of eliminating the requirement of halophile conditions for folding of a “primitive” polypeptide. Thus, the availability of aromatic amino acids could have facilitated a critical halophile-to-mesophile protein folding adaptation--identifying a selective advantage for the incorporation of aromatic amino acids into the codon table.
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Date Issued: 2014-10-25
Identifier: FSU_libsubv1_scholarship_submission_1456504194, 10.1002/pro.2580, PMC4282409
Format: Citation

Title: Symmetry and Simplicity in Protein Evolution and Design.
Creator: Longo, Liam M., Blaber, Michael, Steppan, Scott J., Logan, Timothy M., Stagg, Scott, Steinbock, Oliver, Florida State University, College of Arts and Sciences, Program in...
Show moreLongo, Liam M., Blaber, Michael, Steppan, Scott J., Logan, Timothy M., Stagg, Scott, Steinbock, Oliver, Florida State University, College of Arts and Sciences, Program in Molecular Biophysics
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Abstract/Description: The properties of proteins with reduced sequence complexity--either in the form of primary structure symmetry or restricted amino acid alphabets--are controversial. Studies of protein biophysics and sequence analyses suggest that simplified proteins lack fundamental features of foldability and stability (generally considered to be prerequisites for functional protein structures). Conversely, models of protein emergence and evolution freely invoke simplified proteins and presume them to be...
Show moreThe properties of proteins with reduced sequence complexity--either in the form of primary structure symmetry or restricted amino acid alphabets--are controversial. Studies of protein biophysics and sequence analyses suggest that simplified proteins lack fundamental features of foldability and stability (generally considered to be prerequisites for functional protein structures). Conversely, models of protein emergence and evolution freely invoke simplified proteins and presume them to be stable, foldable, and structured. To resolve this apparent contradiction, two model proteins with key features of sequence simplification were developed and their folding properties analyzed. The first model protein is characterized by a symmetric sequence and is derived from the folding nucleus of a human protein, fibroblast growth factor-1. The second model protein, which also has a symmetric sequence, is greatly enriched for the amino acids that were present at the origin of life. Studies of the stability, folding, and structure of these model proteins suggest that (1) the folding nucleus is a key element of protein evolution and design, (2) symmetric sequences are compatible with protein folding, and can confer robustness to structural reengagements that facilitate protein structure evolution, and (3) the amino acid diversity present on the early earth was likely sufficient to encode complex protein architecture, especially within a halophile environment. In total, the data presented here support a crucial role for proteins with sequence symmetry or amino acid alphabet simplification in key biological processes.
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Date Issued: 2014
Identifier: FSU_migr_etd-9210
Format: Thesis

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