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1.
PLoS Biol ; 22(1): e3002462, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38289969

RESUMO

Mutations in the gene encoding Cu-Zn superoxide dismutase 1 (SOD1) cause a subset of familial amyotrophic lateral sclerosis (fALS) cases. A shared effect of these mutations is that SOD1, which is normally a stable dimer, dissociates into toxic monomers that seed toxic aggregates. Considerable research effort has been devoted to developing compounds that stabilize the dimer of fALS SOD1 variants, but unfortunately, this has not yet resulted in a treatment. We hypothesized that cyclic thiosulfinate cross-linkers, which selectively target a rare, 2 cysteine-containing motif, can stabilize fALS-causing SOD1 variants in vivo. We created a library of chemically diverse cyclic thiosulfinates and determined structure-cross-linking-activity relationships. A pre-lead compound, "S-XL6," was selected based upon its cross-linking rate and drug-like properties. Co-crystallographic structure clearly establishes the binding of S-XL6 at Cys 111 bridging the monomers and stabilizing the SOD1 dimer. Biophysical studies reveal that the degree of stabilization afforded by S-XL6 (up to 24°C) is unprecedented for fALS, and to our knowledge, for any protein target of any kinetic stabilizer. Gene silencing and protein degrading therapeutic approaches require careful dose titration to balance the benefit of diminished fALS SOD1 expression with the toxic loss-of-enzymatic function. We show that S-XL6 does not share this liability because it rescues the activity of fALS SOD1 variants. No pharmacological agent has been proven to bind to SOD1 in vivo. Here, using a fALS mouse model, we demonstrate oral bioavailability; rapid engagement of SOD1G93A by S-XL6 that increases SOD1G93A's in vivo half-life; and that S-XL6 crosses the blood-brain barrier. S-XL6 demonstrated a degree of selectivity by avoiding off-target binding to plasma proteins. Taken together, our results indicate that cyclic thiosulfinate-mediated SOD1 stabilization should receive further attention as a potential therapeutic approach for fALS.


Assuntos
Esclerose Lateral Amiotrófica , Animais , Camundongos , Esclerose Lateral Amiotrófica/tratamento farmacológico , Esclerose Lateral Amiotrófica/genética , Esclerose Lateral Amiotrófica/metabolismo , Cisteína/genética , Mutação , Superóxido Dismutase/genética , Superóxido Dismutase/química , Superóxido Dismutase/metabolismo , Superóxido Dismutase-1/genética
2.
Biochemistry ; 2024 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-38940639

RESUMO

Human ornithine transcarbamylase (hOTC) is a mitochondrial transferase protein involved in the urea cycle and is crucial for the conversion of toxic ammonia to urea. Structural analysis coupled with kinetic studies of Escherichia coli, rat, bovine, and other transferase proteins has identified residues that play key roles in substrate recognition and conformational changes but has not provided direct evidence for all of the active residues involved in OTC function. Here, computational methods were used to predict the likely active residues of hOTC; the function of these residues was then probed with site-directed mutagenesis and biochemical characterization. This process identified previously reported active residues, as well as distal residues that contribute to activity. Mutation of active site residue D263 resulted in a substantial loss of activity without a decrease in protein stability, suggesting a key catalytic role for this residue. Mutation of predicted second-layer residues H302, K307, and E310 resulted in significant decreases in enzymatic activity relative to that of wild-type (WT) hOTC with respect to l-ornithine. The mutation of fourth-layer residue H107 to produce the hOTC H107N variant resulted in a 66-fold decrease in catalytic efficiency relative to that of WT hOTC with respect to carbamoyl phosphate and a substantial loss of thermal stability. Further investigation identified H107 and to a lesser extent E98Q as key residues involved in maintaining the hOTC quaternary structure. This work biochemically demonstrates the importance of D263 in hOTC catalytic activity and shows that residues remote from the active site also play key roles in activity.

3.
Biochem J ; 480(19): 1553-1569, 2023 10 11.
Artigo em Inglês | MEDLINE | ID: mdl-37747786

RESUMO

Haloacid dehalogenases (HAD) are members of a large superfamily that includes many Structural Genomics proteins with poorly characterized functionality. This superfamily consists of multiple types of enzymes that can act as sugar phosphatases, haloacid dehalogenases, phosphonoacetaldehyde hydrolases, ATPases, or phosphate monoesterases. Here, we report on predicted functional annotations and experimental testing by direct biochemical assay for Structural Genomics proteins from the HAD superfamily. To characterize the functions of HAD superfamily members, nine representative HAD proteins and 21 structural genomics proteins are analyzed. Using techniques based on computed chemical and electrostatic properties of individual amino acids, the functions of five structural genomics proteins from the HAD superfamily are predicted and validated by biochemical assays. A dehalogenase-like hydrolase, RSc1362 (Uniprot Q8XZN3, PDB 3UMB) is predicted to be a dehalogenase and dehalogenase activity is confirmed experimentally. Four proteins predicted to be sugar phosphatases are characterized as follows: a sugar phosphatase from Thermophilus volcanium (Uniprot Q978Y6) with trehalose-6-phosphate phosphatase and fructose-6-phosphate phosphatase activity; haloacid dehalogenase-like hydrolase from Bacteroides thetaiotaomicron (Uniprot Q8A2F3; PDB 3NIW) with fructose-6-phosphate phosphatase and sucrose-6-phosphate phosphatase activity; putative phosphatase from Eubacterium rectale (Uniprot D0VWU2; PDB 3DAO) as a sucrose-6-phosphate phosphatase; and hypothetical protein from Geobacillus kaustophilus (Uniprot Q5L139; PDB 2PQ0) as a fructose-6-phosphate phosphatase. Most of these sugar phosphatases showed some substrate promiscuity.


Assuntos
Hidrolases , Monoéster Fosfórico Hidrolases , Monoéster Fosfórico Hidrolases/genética , Monoéster Fosfórico Hidrolases/metabolismo , Hidrolases/química , Proteínas , Genômica , Açúcares
4.
Chem Res Toxicol ; 36(11): 1789-1803, 2023 11 20.
Artigo em Inglês | MEDLINE | ID: mdl-37883788

RESUMO

DNA damage and repair have been widely studied in relation to cancer and therapeutics. Y-family DNA polymerases can bypass DNA lesions, which may result from external or internal DNA damaging agents, including some chemotherapy agents. Overexpression of the Y-family polymerase human pol kappa can result in tumorigenesis and drug resistance in cancer. This report describes the use of computational tools to predict the effects of single nucleotide polymorphism variants on pol kappa activity. Partial Order Optimum Likelihood (POOL), a machine learning method that uses input features from Theoretical Microscopic Titration Curve Shapes (THEMATICS), was used to identify amino acid residues most likely involved in catalytic activity. The µ4 value, a metric obtained from POOL and THEMATICS that serves as a measure of the degree of coupling between one ionizable amino acid and its neighbors, was then used to identify which protein mutations are likely to impact the biochemical activity. Bioinformatic tools SIFT, PolyPhen-2, and FATHMM predicted most of these variants to be deleterious to function. Along with computational and bioinformatic predictions, we characterized the catalytic activity and stability of 17 cancer-associated DNA pol kappa variants. We identified pol kappa variants R48I, H105Y, G147D, G154E, V177L, R298C, E362V, and R470C as having lower activity relative to wild-type pol kappa; the pol kappa variants T102A, H142Y, R175Q, E210K, Y221C, N330D, N338S, K353T, and L383F were identified as being similar in catalytic efficiency to WT pol kappa. We observed that POOL predictions can be used to predict which variants have decreased activity. Predictions from bioinformatic tools like SIFT, PolyPhen-2, and FATHMM are based on sequence comparisons and therefore are complementary to POOL but are less capable of predicting biochemical activity. These bioinformatic and computational tools can be used to identify SNP variants with deleterious effects and altered biochemical activity from a large data set.


Assuntos
DNA Polimerase Dirigida por DNA , Neoplasias , Humanos , Eletricidade Estática , DNA Polimerase Dirigida por DNA/genética , Neoplasias/genética , Aminoácidos , DNA
5.
Molecules ; 27(8)2022 Apr 14.
Artigo em Inglês | MEDLINE | ID: mdl-35458726

RESUMO

A diastereoselective synthesis of the ß-anomer of glycinamide ribonucleotide (ß-GAR) has been developed. The synthesis was accomplished in nine steps from D-ribose and occurred in 5% overall yield. The route provided material on the multi-milligram scale. The synthetic ß-GAR formed was remarkably resistant to anomerization both in solution and as a solid.


Assuntos
Hidroximetil e Formil Transferases , Glicina/análogos & derivados , Fosforribosilglicinamido Formiltransferase , Ribonucleotídeos
6.
J Chem Phys ; 154(19): 195101, 2021 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-34240918

RESUMO

Interactions in enzymes between catalytic and neighboring amino acids and how these interactions facilitate catalysis are examined. In examples from both natural and designed enzymes, it is shown that increases in catalytic rates may be achieved through elongation of the buffer range of the catalytic residues; such perturbations in the protonation equilibria are, in turn, achieved through enhanced coupling of the protonation equilibria of the active ionizable residues with those of other ionizable residues. The strongest coupling between protonation states for a pair of residues that deprotonate to form an anion (or a pair that accept a proton to form a cation) is achieved when the difference in the intrinsic pKas of the two residues is approximately within 1 pH unit. Thus, catalytic aspartates and glutamates are often coupled to nearby acidic residues. For an anion-forming residue coupled to a cation-forming residue, the elongated buffer range is achieved when the intrinsic pKa of the anion-forming residue is higher than the intrinsic pKa of the (conjugate acid of the) cation-forming residue. Therefore, the high pKa, anion-forming residues tyrosine and cysteine make good coupling partners for catalytic lysine residues. For the anion-cation pairs, the optimum difference in intrinsic pKas is a function of the energy of interaction between the residues. For the energy of interaction ε expressed in units of (ln 10)RT, the optimum difference in intrinsic pKas is within ∼1 pH unit of ε.


Assuntos
Aminoácidos/química , Glicosídeo Hidrolases/química , Aminoácidos/metabolismo , Biocatálise , Glicosídeo Hidrolases/metabolismo , Concentração de Íons de Hidrogênio , Eletricidade Estática
7.
J Biol Chem ; 294(1): 71-88, 2019 01 04.
Artigo em Inglês | MEDLINE | ID: mdl-30420425

RESUMO

Caspases are cysteine-aspartic proteases involved in the regulation of programmed cell death (apoptosis) and a number of other biological processes. Despite overall similarities in structure and active-site composition, caspases show striking selectivity for particular protein substrates. Exosites are emerging as one of the mechanisms by which caspases can recruit, engage, and orient these substrates for proper hydrolysis. Following computational analyses and database searches for candidate exosites, we utilized site-directed mutagenesis to identify a new exosite in caspase-6 at the hinge between the disordered N-terminal domain (NTD), residues 23-45, and core of the caspase-6 structure. We observed that substitutions of the tri-arginine patch Arg-42-Arg-44 or the R44K cancer-associated mutation in caspase-6 markedly alter its rates of protein substrate hydrolysis. Notably, turnover of protein substrates but not of short peptide substrates was affected by these exosite alterations, underscoring the importance of this region for protein substrate recruitment. Hydrogen-deuterium exchange MS-mediated interrogation of the intrinsic dynamics of these enzymes suggested the presence of a substrate-binding platform encompassed by the NTD and the 240's region (containing residues 236-246), which serves as a general exosite for caspase-6-specific substrate recruitment. In summary, we have identified an exosite on caspase-6 that is critical for protein substrate recognition and turnover and therefore highly relevant for diseases such as cancer in which caspase-6-mediated apoptosis is often disrupted, and in neurodegeneration in which caspase-6 plays a central role.


Assuntos
Caspase 6/química , Mutação de Sentido Incorreto , Proteínas de Neoplasias/química , Neoplasias/enzimologia , Doenças Neurodegenerativas/enzimologia , Substituição de Aminoácidos , Arginina/química , Arginina/genética , Arginina/metabolismo , Caspase 6/genética , Caspase 6/metabolismo , Humanos , Hidrólise , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Neoplasias/genética , Neoplasias/patologia , Doenças Neurodegenerativas/genética , Doenças Neurodegenerativas/patologia , Domínios Proteicos
8.
Biochemistry ; 57(7): 1063-1072, 2018 02 20.
Artigo em Inglês | MEDLINE | ID: mdl-29341605

RESUMO

The process of DNA replication is carried out with high efficiency and accuracy by DNA polymerases. The replicative polymerase in E. coli is DNA Pol III, which is a complex of 10 different subunits that coordinates simultaneous replication on the leading and lagging strands. The 1160-residue Pol III alpha subunit is responsible for the polymerase activity and copies DNA accurately, making one error per 105 nucleotide incorporations. The goal of this research is to determine the residues that contribute to the activity of the polymerase subunit. Homology modeling and the computational methods of THEMATICS and POOL were used to predict functionally important amino acid residues through their computed chemical properties. Site-directed mutagenesis and biochemical assays were used to validate these predictions. Primer extension, steady-state single-nucleotide incorporation kinetics, and thermal denaturation assays were performed to understand the contribution of these residues to the function of the polymerase. This work shows that the top 15 residues predicted by POOL, a set that includes the three previously known catalytic aspartate residues, seven remote residues, plus five previously unexplored first-layer residues, are important for function. Six previously unidentified residues, R362, D405, K553, Y686, E688, and H760, are each essential to Pol III activity; three additional residues, Y340, R390, and K758, play important roles in activity.


Assuntos
DNA Polimerase III/química , Escherichia coli/química , Domínio Catalítico , DNA Polimerase III/genética , DNA Polimerase III/metabolismo , Estabilidade Enzimática , Escherichia coli/genética , Escherichia coli/metabolismo , Infecções por Escherichia coli/microbiologia , Humanos , Mutagênese Sítio-Dirigida , Conformação Proteica
9.
Immunity ; 28(6): 774-86, 2008 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-18538591

RESUMO

As CD1 proteins recycle between the cell surface and endosomes, they show altered receptiveness to lipid antigen loading. We hypothesized that changes in proton concentration encountered within distinct endosomal compartments influence the charge state of residues near the entrance to the CD1 groove and thereby control antigen loading. Molecular dynamic models identified flexible areas of the CD1b heavy chain in the superior and lateral walls of the A' pocket. In these same areas, residues that carry charge in a pH-dependent manner (D60, E62) were found to tether the rigid alpha1 helix to flexible areas of the alpha2 helix and the 50-60 loop. After disruption of these tethers with acid pH or mutation, we observed increased association and dissociation of lipids with CD1b and preferential presentation of antigens with bulky lipid tails. We propose that ionic tethers act as molecular switches that respond to pH fluxes during endosomal recycling and regulate the conformation of the CD1 heavy chain to control the size and rate of antigens captured.


Assuntos
Apresentação de Antígeno , Antígenos/imunologia , Endossomos/metabolismo , Lipídeos/imunologia , Antígenos CD1/química , Antígenos CD1/imunologia , Antígenos CD1/metabolismo , Linhagem Celular , Endossomos/imunologia , Humanos , Concentração de Íons de Hidrogênio , Proteínas Mutantes/imunologia , Proteínas Mutantes/metabolismo , Conformação Proteica , Estrutura Terciária de Proteína
10.
Methods ; 93: 51-63, 2016 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-26564235

RESUMO

Thousands of protein structures of unknown or uncertain function have been reported as a result of high-throughput structure determination techniques developed by Structural Genomics (SG) projects. However, many of the putative functional assignments of these SG proteins in the Protein Data Bank (PDB) are incorrect. While high-throughput biochemical screening techniques have provided valuable functional information for limited sets of SG proteins, the biochemical functions for most SG proteins are still unknown or uncertain. Therefore, computational methods for the reliable prediction of protein function from structure can add tremendous value to the existing SG data. In this article, we show how computational methods may be used to predict the function of SG proteins, using examples from the six-hairpin glycosidase (6-HG) and the concanavalin A-like lectin/glucanase (CAL/G) superfamilies. Using a set of predicted functional residues, obtained from computed electrostatic and chemical properties for each protein structure, it is shown that these superfamilies may be sorted into functional families according to biochemical function. Within these superfamilies, a total of 18 SG proteins were analyzed according to their predicted, local functional sites: 13 from the 6-HG superfamily, five from the CAL/G superfamily. Within the 6-HG superfamily, an uncharacterized protein BACOVA_03626 from Bacteroides ovatus (PDB 3ON6) and a hypothetical protein BT3781 from Bacteroides thetaiotaomicron (PDB 2P0V) are shown to have very strong active site matches with exo-α-1,6-mannosidases, thus likely possessing this function. Also in this superfamily, it is shown that protein BH0842, a putative glycoside hydrolase from Bacillus halodurans (PDB 2RDY), has a predicted active site that matches well with a known α-L-galactosidase. In the CAL/G superfamily, an uncharacterized glycosyl hydrolase family 16 protein from Mycobacterium smegmatis (PDB 3RQ0) is shown to have local structural similarity at the predicted active site with the known members of the GH16 family, with the closest match to the endoglucanase subfamily. The method discussed herein can predict whether an SG protein is correctly or incorrectly annotated and can sometimes provide a reliable functional annotation. Examples of application of the method across folds, comparing active sites between two proteins of different structural folds, are also given.


Assuntos
Biologia Computacional/métodos , Bases de Dados de Proteínas , Glicosídeo Hidrolases/química , Glicosídeo Hidrolases/fisiologia , Previsões , Estrutura Secundária de Proteína , Proteínas/química , Proteínas/fisiologia
11.
BMC Bioinformatics ; 14 Suppl 3: S13, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23514271

RESUMO

BACKGROUND: The prediction of biochemical function from the 3D structure of a protein has proved to be much more difficult than was originally foreseen. A reliable method to test the likelihood of putative annotations and to predict function from structure would add tremendous value to structural genomics data. We report on a new method, Structurally Aligned Local Sites of Activity (SALSA), for the prediction of biochemical function based on a local structural match at the predicted catalytic or binding site. RESULTS: Implementation of the SALSA method is described. For the structural genomics protein PY01515 (PDB ID 2aqw) from Plasmodium yoelii, it is shown that the putative annotation, Orotidine 5'-monophosphate decarboxylase (OMPDC), is most likely correct. SALSA analysis of YP_001304206.1 (PDB ID 3h3l), a putative sugar hydrolase from Parabacteroides distasonis, shows that its active site does not bear close resemblance to any previously characterized member of its superfamily, the Concanavalin A-like lectins/glucanases. It is noted that three residues in the active site of the thermophilic beta-1,4-xylanase from Nonomuraea flexuosa (PDB ID 1m4w), Y78, E87, and E176, overlap with POOL-predicted residues of similar type, Y168, D153, and E232, in YP_001304206.1. The substrate recognition regions of the two proteins are rather different, suggesting that YP_001304206.1 is a new functional type within the superfamily. A structural genomics protein from Mycobacterium avium (PDB ID 3q1t) has been reported to be an enoyl-CoA hydratase (ECH), but SALSA analysis shows a poor match between the predicted residues for the SG protein and those of known ECHs. A better local structural match is obtained with Anabaena beta-diketone hydrolase (ABDH), a known ß-diketone hydrolase from Cyanobacterium anabaena (PDB ID 2j5s). This suggests that the reported ECH function of the SG protein is incorrect and that it is more likely a ß-diketone hydrolase. CONCLUSIONS: A local site match provides a more compelling function prediction than that obtainable from a simple 3D structure match. The present method can confirm putative annotations, identify misannotation, and in some cases suggest a more probable annotation.


Assuntos
Anotação de Sequência Molecular , Proteínas/fisiologia , Homologia Estrutural de Proteína , Anabaena/enzimologia , Sítios de Ligação , Domínio Catalítico , Biologia Computacional/métodos , Enoil-CoA Hidratase/química , Glicosídeo Hidrolases/química , Hidrolases/química , Orotidina-5'-Fosfato Descarboxilase/química , Proteínas/química , Proteínas/metabolismo
12.
Bioinformatics ; 28(15): 2078-9, 2012 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-22661648

RESUMO

SUMMARY: We present an automated web server for partial order optimum likelihood (POOL), a machine learning application that combines computed electrostatic and geometric information for high-performance prediction of catalytic residues from 3D structures. Input features consist of THEMATICS electrostatics data and pocket information from ConCavity. THEMATICS measures deviation from typical, sigmoidal titration behavior to identify functionally important residues and ConCavity identifies binding pockets by analyzing the surface geometry of protein structures. Both THEMATICS and ConCavity (structure only) do not require the query protein to have any sequence or structure similarity to other proteins. Hence, POOL is applicable to proteins with novel folds and engineered proteins. As an additional option for cases where sequence homologues are available, users can include evolutionary information from INTREPID for enhanced accuracy in site prediction. AVAILABILITY: The web site is free and open to all users with no login requirements at http://www.pool.neu.edu. CONTACT: m.ondrechen@neu.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Inteligência Artificial , Internet , Proteínas/química , Software , Biologia Computacional/métodos , Estrutura Terciária de Proteína , Eletricidade Estática
13.
Bioorg Med Chem ; 21(23): 7453-64, 2013 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-24126093

RESUMO

Molecular modeling techniques were applied to the design, synthesis and optimization of a new series of xanthine based adenosine A(2A) receptor antagonists. The optimized lead compound was converted to a PEG derivative and a functional in vitro bioassay used to confirm efficacy. Additionally, the PEGylated version showed enhanced aqueous solubility and was inert to photoisomerization, a known limitation of existing antagonists of this class.


Assuntos
Desenho de Fármacos , Antagonistas de Receptores Purinérgicos P1/química , Antagonistas de Receptores Purinérgicos P1/farmacologia , Receptor A2A de Adenosina/metabolismo , Xantina/química , Xantina/farmacologia , Linhagem Celular , Cristalografia por Raios X , Humanos , Hipóxia/terapia , Imunoterapia , Modelos Moleculares , Polietilenoglicóis/química , Polietilenoglicóis/farmacologia , Receptor A2A de Adenosina/química
14.
CBE Life Sci Educ ; 22(2): ar25, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-37058442

RESUMO

In-person undergraduate research experiences (UREs) promote students' integration into careers in life science research. In 2020, the COVID-19 pandemic prompted institutions hosting summer URE programs to offer them remotely, raising questions about whether undergraduates who participate in remote research can experience scientific integration and whether they might perceive doing research less favorably (i.e., not beneficial or too costly). To address these questions, we examined indicators of scientific integration and perceptions of the benefits and costs of doing research among students who participated in remote life science URE programs in Summer 2020. We found that students experienced gains in scientific self-efficacy pre- to post-URE, similar to results reported for in-person UREs. We also found that students experienced gains in scientific identity, graduate and career intentions, and perceptions of the benefits of doing research only if they started their remote UREs at lower levels on these variables. Collectively, students did not change in their perceptions of the costs of doing research despite the challenges of working remotely. Yet students who started with low cost perceptions increased in these perceptions. These findings indicate that remote UREs can support students' self-efficacy development, but may otherwise be limited in their potential to promote scientific integration.


Assuntos
COVID-19 , Estudantes , Humanos , Pandemias
15.
Curr Opin Struct Biol ; 74: 102384, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35533564

RESUMO

Understanding the biochemically active amino acids in proteins is a key factor to improve the knowledge of how enzymes work, to predict the function of newly discovered protein structures of unknown function, and to establish design principles for enzyme engineering. Here, we explore recently reported computational chemistry-based methods for the prediction of active amino acids in protein 3D structures, including biochemically important distal residues, and their implications for functional genomics, for enzyme design, and for enhancing understanding of the function of enzymes.


Assuntos
Química Computacional , Proteínas , Aminoácidos/química , Domínio Catalítico , Biologia Computacional/métodos , Enzimas/química , Proteínas/química
16.
Protein Sci ; 31(5): e4291, 2022 05.
Artigo em Inglês | MEDLINE | ID: mdl-35481659

RESUMO

The computed electrostatic and proton transfer properties are studied for 20 enzymes that represent all six major enzyme commission classes and a variety of different folds. The properties of aspartate, glutamate, and lysine residues that have been previously experimentally determined to be catalytically active are reported. The catalytic aspartate and glutamate residues studied here are strongly coupled to at least one other aspartate or glutamate residue and often to multiple other carboxylate residues with intrinsic pKa differences less than 1 pH unit. Sometimes these catalytic acidic residues are also coupled to a histidine residue, such that the intrinsic pKa of the acidic residue is higher than that of the histidine. All catalytic lysine residues studied here are strongly coupled to tyrosine or cysteine residues, wherein the intrinsic pKa of the anion-forming residue is higher than that of the lysine. Some catalytic lysines are also coupled to other lysines with intrinsic pKa differences within 1 pH unit. Some evidence of the possible types of interactions that facilitate nucleophilicity is discussed. The interactions reported here provide important clues about how side chain functional groups that are weak Brønsted acids or bases for the free amino acid in solution can achieve catalytic potency and become strong acids, bases or nucleophiles in the enzymatic environment.


Assuntos
Aminoácidos , Histidina , Aminoácidos/química , Ácido Aspártico , Glutamatos , Lisina/química , Eletricidade Estática
17.
Integr Comp Biol ; 61(6): 2082-2094, 2022 02 05.
Artigo em Inglês | MEDLINE | ID: mdl-34374780

RESUMO

Information, energy, and matter are fundamental properties of all levels of biological organization, and life emerges from the continuous flux of matter, energy, and information. This perspective piece defines and explains each of the three pillars of this nexus. We propose that a quantitative characterization of the complex interconversions between matter, energy, and information that comprise this nexus will help us derive biological insights that connect phenomena across different levels of biological organization. We articulate examples from multiple biological scales that highlight how this nexus approach leads to a more complete understanding of the biological system. Metrics of energy, information, and matter can provide a common currency that helps link phenomena across levels of biological organization. The propagation of energy and information through levels of biological organization can result in emergent properties and system-wide changes that impact other hierarchical levels. Deeper consideration of measured imbalances in energy, information, and matter can help researchers identify key factors that influence system function at one scale, highlighting avenues to link phenomena across levels of biological organization and develop predictive models of biological systems.


Assuntos
Biologia , Animais
18.
ACS Chem Biol ; 17(2): 395-403, 2022 02 18.
Artigo em Inglês | MEDLINE | ID: mdl-35060718

RESUMO

Members of the Crotonase superfamily, a mechanistically diverse family of proteins that share a conserved quaternary structure, can often catalyze more than one reaction. However, the spectrum of activity for its members has not been well studied. We report on measured crotonase and hydrolase activity for eight structural genomics (SG) proteins from the Crotonase superfamily plus two previously characterized proteins, intended as controls: human enoyl CoA hydratase (ECH) and Anabaena ß-diketone hydrolase. Like most of the 15,000+ SG protein structures deposited in the Protein Data Bank (PDB), the eight SG proteins are of unknown or uncertain biochemical function. The functional characterization of the eight SG proteins is guided by the Structurally Aligned Local Sites of Activity (SALSA), a local-structure-based computational approach to functional annotation. For human ECH, the turnover number for hydrolase activity is threefold higher than that for ECH activity, although the catalytic efficiency is 160-fold higher for ECH. Three SG proteins originally annotated as ECHs were predicted by SALSA to be hydrolases and are observed to have higher catalytic efficiencies for hydrolase activity than for ECH activity, on par with the previously characterized hydrolase. Among the five SG proteins predicted by SALSA to be ECHs, all but one also show some hydrolase activity; all five exhibit lower ECH activity than the human ECH with respect to the crotonyl-CoA substrate. Here, we show examples demonstrating that SALSA can correct functional misannotations even within enzyme families that display promiscuous activity.


Assuntos
Enoil-CoA Hidratase , Hidrolases , Catálise , Bases de Dados de Proteínas , Enoil-CoA Hidratase/química , Enoil-CoA Hidratase/metabolismo , Genômica , Humanos , Hidrolases/química
19.
Front Chem ; 10: 1017394, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36385993

RESUMO

Three protein targets from SARS-CoV-2, the viral pathogen that causes COVID-19, are studied: the main protease, the 2'-O-RNA methyltransferase, and the nucleocapsid (N) protein. For the main protease, the nucleophilicity of the catalytic cysteine C145 is enabled by coupling to three histidine residues, H163 and H164 and catalytic dyad partner H41. These electrostatic couplings enable significant population of the deprotonated state of C145. For the RNA methyltransferase, the catalytic lysine K6968 that serves as a Brønsted base has significant population of its deprotonated state via strong coupling with K6844 and Y6845. For the main protease, Partial Order Optimum Likelihood (POOL) predicts two clusters of biochemically active residues; one includes the catalytic H41 and C145 and neighboring residues. The other surrounds a second pocket adjacent to the catalytic site and includes S1 residues F140, L141, H163, E166, and H172 and also S2 residue D187. This secondary recognition site could serve as an alternative target for the design of molecular probes. From in silico screening of library compounds, ligands with predicted affinity for the secondary site are reported. For the NSP16-NSP10 complex that comprises the RNA methyltransferase, three different sites are predicted. One is the catalytic core at the conserved K-D-K-E motif that includes catalytic residues D6928, K6968, and E7001 plus K6844. The second site surrounds the catalytic core and consists of Y6845, C6849, I6866, H6867, F6868, V6894, D6895, D6897, I6926, S6927, Y6930, and K6935. The third is located at the heterodimer interface. Ligands predicted to have high affinity for the first or second sites are reported. Three sites are also predicted for the nucleocapsid protein. This work uncovers key interactions that contribute to the function of the three viral proteins and also suggests alternative sites for ligand design.

20.
J Med Chem ; 65(14): 9939-9954, 2022 07 28.
Artigo em Inglês | MEDLINE | ID: mdl-35802702

RESUMO

An array of triazolopyridines based on JNJ-46356479 (6) were synthesized as potential positron emission tomography radiotracers for metabotropic glutamate receptor 2 (mGluR2). The selected candidates 8-10 featured enhanced positive allosteric modulator (PAM) activity (20-fold max.) and mGluR2 agonist activity (25-fold max.) compared to compound 6 in the cAMP GloSensor assays. Radiolabeling of compounds 8 and 9 (mG2P026) was achieved via Cu-mediated radiofluorination with satisfactory radiochemical yield, >5% (non-decay-corrected); high molar activity, >180 GBq/µmol; and excellent radiochemical purity, >98%. Preliminary characterization of [18F]8 and [18F]9 in rats confirmed their excellent brain permeability and binding kinetics. Further evaluation of [18F]9 in a non-human primate confirmed its superior brain heterogeneity in mapping mGluR2 and higher affinity than [18F]6. Pretreatment with different classes of PAMs in rats and a primate led to similarly enhanced brain uptake of [18F]9. As a selective ligand, [18F]9 has the potential to be developed for translational studies.


Assuntos
Receptores de Glutamato Metabotrópico , Animais , Encéfalo/diagnóstico por imagem , Encéfalo/metabolismo , Ligantes , Tomografia por Emissão de Pósitrons , Compostos Radiofarmacêuticos , Ratos , Ratos Sprague-Dawley , Receptores de Glutamato Metabotrópico/metabolismo
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