Sequence- and structure-based approaches to deciphering enzyme evolution in the Haloalkonoate Dehalogenase superfamily

Understanding how changes in functional requirements of the cell select for changes in protein sequence and structure is a fundamental challenge in molecular evolution. This dissertation delineates some of the underlying evolutionary forces using as a model system, the Haloalkanoate Dehalogenase Superfamily (HADSF). HADSF members have unique cap-core architecture with the Rossmann-fold core domain accessorized by variable cap domain insertions (delineated by length, topology, and point of insertion). To identify the boundaries of variable domain insertions in protein sequences, I have developed a comprehensive computational strategy (CapPredictor or CP) using a novel sequence alignment algorithm in conjunction with a structure-guided sequence profile. Analysis of more than 40,000 HADSF sequences led to the following observations: (i) cap-type classes exhibit similar distributions across different phyla, indicating existence of all cap-types in the last universal common ancestor, and (ii) comparative analysis of the predicted cap-type and functional diversity indicated that cap-type does not dictate the divergence of substrate recognition and chemical pathway, and hence biological function. By analyzing a unique dataset of core- and cap-domain-only protein structures, I investigated the consequences of the accessory cap domain on the sequence-structure relationship of the core domain. The relationship between sequence and structure divergence in the core fold was shown to be monotonic and independent of the corresponding cap type. However, core domains with the same cap type bore a greater similarity than the core domains with different cap types, suggesting coevolution of the cap and core domains. Remarkably, a few degrees of freedom are needed to describe the structural diversity in the Rossmann fold accounting for the majority of the observed structural variance. Finally, I examined the location and role of conserved residue positions and co-evolving residue pairs in the core domain in the context of the cap domain. Positions critical for function were conserved while non-conserved positions mapped to highly mobile regions. Notably, we found exponential dependence of co-variance on inter-residue distance. Collectively, these novel algorithms and analyses contribute to an improved understanding of enzyme evolution, especially in the context of the use of domain insertions to expand substrate specificity and chemical mechanism

Consequences of domain insertion on sequence-structure divergence in a superfold.

Although the universe of protein structures is vast, these innumerable structures can be categorized into a finite number of folds. New functions commonly evolve by elaboration of existing scaffolds, for example, via domain insertions. Thus, understanding structural diversity of a protein fold evolving via domain insertions is a fundamental challenge. The haloalkanoic dehalogenase superfamily serves as an excellent model system wherein a variable cap domain accessorizes the ubiquitous Rossmann-fold core domain. Here, we determine the impact of the cap-domain insertion on the sequence and structure divergence of the core domain. Through quantitative analysis on a unique dataset of 154 core-domain-only and cap-domain-only structures, basic principles of their evolution have been uncovered. The relationship between sequence and structure divergence of the core domain is shown to be monotonic and independent of the corresponding type of domain insert, reflecting the robustness of the Rossmann fold to mutation. However, core domains with the same cap type share greater similarity at the sequence and structure levels, suggesting interplay between the cap and core domains. Notably, results reveal that the variance in structure maps to α-helices flanking the central β-sheet and not to the domain-domain interface. Collectively, these results hint at intramolecular coevolution where the fold diverges differentially in the context of an accessory domain, a feature that might also apply to other multidomain superfamilies

市民社会のプレーヤー交代劇と政治-仁平典宏の<贈与のパラドックス>論を読み解く-

千葉大学大学院人文社会科学研究科研究プロジェクト報告書第257集『都市コミュニティにおける相互扶助と次世代育成』水島治郎 編Sustainable Urban Communities: Communality and Generativity Report on the Research Projects No.25

Parafibromin Abnormalities in Ossifying Fibroma

Abstract Ossifying fibromas are very rare tumors that are sometimes seen as part of the hyperparathyroidism-jaw tumor syndrome (HPT-JT), which is caused by inactivating mutations of the HRPT2/CDC73 tumor suppressor gene. CDC73 mutations have been identified in a subset of sporadic cases but aberrant expression of the encoded protein, parafibromin, has not been demonstrated in ossifying fibroma. We sought to determine if loss of parafibromin regularly contributes to the development of sporadic, nonsyndromic ossifying fibroma. We examined a series of 9 ossifying fibromas, including ossifying, cemento-ossifying, and juvenile active variants, for parafibromin protein expression by immunohistochemistry and for CDC73 sequence abnormalities by Sanger sequencing and/or targeted AmpliSeq panel sequencing. Four ossifying fibromas showed a complete absence of nuclear parafibromin expression; loss of parafibromin expression was coupled with aberrant cytoplasmic parafibromin expression in 1 case. CDC73 mutations were detected in 2 cases with aberrant parafibromin expression. These results provide novel evidence, at the level of protein expression, that loss of the parathyroid CDC73/parafibromin tumor suppressor may play a role in the pathogenesis of a subset of ossifying fibromas.</jats:p

Divergence of Structure and Function in the Haloacid Dehalogenase Enzyme Superfamily: <i>Bacteroides thetaiotaomicron</i> BT2127 Is an Inorganic Pyrophosphatase

The explosion of protein sequence information requires that current strategies for function assignment must evolve to complement experimental approaches with computationally-based function prediction. This necessitates the development of strategies based on the identification of sequence markers in the form of specificity determinants and a more informed definition of orthologues. Herein, we have undertaken the function assignment of the unknown Haloalkanoate Dehalogenase superfamily member BT2127 (Uniprot accession # Q8A5V9) from Bacteroides thetaiotaomicron using an integrated bioinformatics/structure/mechanism approach. The substrate specificity profile and steady-state rate constants of BT2127 (with k(cat)/K(m) value for pyrophosphate of ∼1 × 10(5) M(−1) s(−1)), together with the gene context, supports the assigned in vivo function as an inorganic pyrophosphatase. The X-ray structural analysis of the wild-type BT2127 and several variants generated by site-directed mutagenesis shows that substrate discrimination is based, in part, on active site space restrictions imposed by the cap domain (specifically by residues Tyr76 and Glu47). Structure guided site directed mutagenesis coupled with kinetic analysis of the mutant enzymes identified the residues required for catalysis, substrate binding, and domain-domain association. Based on this structure-function analysis, the catalytic residues Asp11, Asp13, Thr113, and Lys147 as well the metal binding residues Asp171, Asn172 and Glu47 were used as markers to confirm BT2127 orthologues identified via sequence searches. This bioinformatic analysis demonstrated that the biological range of BT2127 orthologue is restricted to the phylum Bacteroidetes/Chlorobi. The key structural determinants in the divergence of BT2127 and its closest homologue β-phosphoglucomutase control the leaving group size (phosphate vs. glucose-phosphate) and the position of the Asp acid/base in the open vs. closed conformations. HADSF pyrophosphatases represent a third mechanistic and fold type for bacterial pyrophosphatases

Divergence of Structure and Function in the Haloacid Dehalogenase Enzyme Superfamily: <i>Bacteroides thetaiotaomicron</i> BT2127 Is an Inorganic Pyrophosphatase

The explosion of protein sequence information requires that current strategies for function assignment evolve to complement experimental approaches with computationally based function prediction. This necessitates the development of strategies based on the identification of sequence markers in the form of specificity determinants and a more informed definition of orthologues. Herein, we have undertaken the function assignment of the unknown haloalkanoate dehalogenase superfamily member BT2127 (Uniprot accession code Q8A5 V9) from Bacteroides thetaiotaomicron using an integrated bioinformatics–structure–mechanism approach. The substrate specificity profile and steady-state rate constants of BT2127 (with a kcat/Km value for pyrophosphate of ∼1 × 105 M–1 s–1), together with the gene context, support the assigned in vivo function as an inorganic pyrophosphatase. The X-ray structural analysis of wild-type BT2127 and several variants generated by site-directed mutagenesis shows that substrate discrimination is based, in part, on active site space restrictions imposed by the cap domain (specifically by residues Tyr76 and Glu47). Structure-guided site-directed mutagenesis coupled with kinetic analysis of the mutant enzymes identified the residues required for catalysis, substrate binding, and domain–domain association. On the basis of this structure–function analysis, the catalytic residues Asp11, Asp13, Thr113, and Lys147 as well the metal binding residues Asp171, Asn172, and Glu47 were used as markers to confirm BT2127 orthologues identified via sequence searches. This bioinformatic analysis demonstrated that the biological range of BT2127 orthologue is restricted to the phylum Bacteroidetes/Chlorobi. The key structural determinants in the divergence of BT2127 and its closest homologue, β-phosphoglucomutase, control the leaving group size (phosphate vs glucose phosphate) and the position of the Asp acid/base in the open versus closed conformations. HADSF pyrophosphatases represent a third mechanistic and fold type for bacterial pyrophosphatases

Markers of Initial and Long-Term Responses to Idecabtagene Vicleucel (Ide-Cel; bb2121) in the CRB-401 Study in Relapsed/Refractory Multiple Myeloma

†These authors contributed equally. Introduction Ide-cel, an anti-BCMA CAR T cell therapy, has demonstrated promising efficacy in the phase I CRB-401 trial in relapsed/refractory multiple myeloma (MM) (objective response rate, 85%; median progression-free survival [PFS], 11.8 months [95% CI: 6.2, 17.8]), but a subset of patients failed to respond and the duration of response varied across patients (Raje et al, N Engl J Med. 2019). A systematic examination of patient, product, and post-infusion correlates of overall and long-term response could offer biological insight into heterogeneous efficacy as well as provide biomarkers to guide post-CAR T disease management and future CAR T manufacturing and patient enrollment efforts. Soluble BCMA was of particular interest due to its expression on malignant and healthy plasma cells and its role as a composite measure of disease burden in MM. Methods We performed a retrospective analysis of 33 patients from the phase I CRB-401 study of ide-cel. The concentrations of ten immune-related factors in the blood (GMCSF, IFN-γ, IL-10, IL-1b, IL-2, IL-6, IL-8, MCP-1, TNF-α) and soluble BCMA were measured by ELISA before and after infusion with ide-cel along with 290 ide-cel CAR T-cell drug product attributes measured by flow cytometry and immunoassays. The absolute concentrations and fold-changes from baseline were assessed for correlation with overall and long-term response using univariate and multivariate (random forests) approaches. Results Several CAR T-cell drug product covariates nominally associated with longer PFS included reduced senescence phenotype in CD4 CAR T-cells and increased IL-2 and TNF-α production (P &lt; 0.05). Pre-infusion levels of soluble BCMA correlated with serum monoclonal protein (M-protein) levels in 20 of 33 patients for whom M-protein levels were measurable (ρ = .49; P = 0.03) and with concentrations of the involved free light chain (ρ = .59; P = 0.005) in 23 of 33 patients with measurable levels. Our investigation of soluble BCMA levels in patients achieving a partial response (PR) or better confirmed significant decreases in soluble BCMA levels relative to nonresponders (NR) as early as seven days post-infusion (median reduction of 50% for ≥ PR vs. median increase of 27% for NR, P = 0.02). The fold-change in soluble BCMA 1 month after infusion stratified patients who achieved a PR or better from those who did not (P = 0.0001). Notably, patients who maintained a response to ide-cel for ≥ 18 months (M18 R) experienced a greater depth of clearance of soluble BCMA at month 2 (median concentration of 1835 ng/L for M18 R vs. 6299 ng/L for M18 NR, P = 0.002). The induction of IL-6 and TNF-α in blood on days 1-9 post-infusion was also higher in patients with a PR or better in response to ide-cel (e.g. IL-6 median fold change increase at day 2 of 2.9 for ≥ PR vs. 0.7 for NR, P = 0.001), consistent with an active inflammatory response and higher levels of CAR T expansion. Conclusions These data from CRB-401 identify candidate drug product attributes and soluble factors that correlate with response to ide-cel and potentially MM-directed cellular therapies in general. These data suggest that changes in soluble BCMA may be a robust biomarker of both early and durable responses to ide-cel and the depth of clearance of soluble BCMA at 2 months post-infusion may identify patients at risk of progression before standard markers of myeloma progression have emerged. Further molecular characterization of drug product attributes, including CyTOF and RNA sequencing, is ongoing to identify additional biomarkers associated with clinical outcomes following ide-cel treatment. These data will help inform future strategies to improve the efficacy of ide-cel and validation in a larger cohort is ongoing. Disclosures Thompson: Celgene Corporation: Employment, Equity Ownership. Jiang:Juno Therapeutics, a Celgene Company: Employment, Equity Ownership. Campbell:Celgene Corporation: Employment, Equity Ownership. Fuller:Celgene Corporation: Employment, Equity Ownership. Kaiser:Celgene Corporation: Employment. Mashadi-Hossein:Celgene Corporation: Employment, Equity Ownership. Rytlewski:Adaptive Biotechnologies: Equity Ownership; Juno Therapeutics, a Celgene Company: Employment, Equity Ownership. Martin:Celgene Corporation: Employment, Equity Ownership. Finney:bluebird bio Inc.: Employment. Kleinsteuber:bluebird bio Inc.: Employment, Equity Ownership. Alonzo:bluebird bio Inc.: Employment, Equity Ownership. Pandya:bluebird bio Inc.: Employment. Agarwal:Celgene Corporation: Employment, Equity Ownership. Hege:Celgene Corporation: Employment, Equity Ownership, Patents &amp; Royalties; Arcus Biosciences: Membership on an entity's Board of Directors or advisory committees; Society for Immunotherapy of Cancer: Membership on an entity's Board of Directors or advisory committees; Mersana Therapuetics: Membership on an entity's Board of Directors or advisory committees. Raje:Merck: Consultancy; Takeda: Consultancy; Janssen: Consultancy; Celgene Corporation: Consultancy; Amgen Inc.: Consultancy; Bristol-Myers Squibb: Consultancy. Munshi:Celgene: Consultancy; Oncopep: Consultancy; Amgen: Consultancy; Janssen: Consultancy; Takeda: Consultancy; Abbvie: Consultancy; Adaptive: Consultancy. Hause:Juno Therapeutics, a Celgene Company: Employment, Equity Ownership. OffLabel Disclosure: ide-cel /bb2121 is an investigational agent and not yet approved in the US </jats:sec

Panoramic view of a superfamily of phosphatases through substrate profiling

Significance Here, we examine the activity profile of the haloalkanoic acid dehalogenase (HAD) superfamily by screening a customized library against &gt;200 enzymes from a broad sampling of the superfamily. From this dataset, we can infer the function of nearly 35% of the superfamily. Overall, the superfamily was found to show high substrate ambiguity, with 75% of the superfamily utilizing greater than five substrates. In addition, the HAD members with the least amount of structural accessorization of the Rossmann fold were found to be the most specific, suggesting that elaboration of the core domain may have led to increased substrate range of the superfamily.</jats:p