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Toward mechanistic classification of enzyme functions

Daniel E Almonacid, Patricia C Babbitt
2011 Current Opinion in Chemical Biology  
Cummings JA, Fedorov AA, Xu C, Brown S, Fedorov E, Babbitt PC, Almo SC, Raushel FM.  ...  Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase Holliday GL, Almonacid DE, Mitchell JBO, Thornton  ... 
doi:10.1016/j.cbpa.2011.03.008 pmid:21489855 pmcid:PMC3551611 fatcat:yy6jwgqljrc7bpotr5bwfhxiei

QUALIDADE DO LENHO DE ÁRVORES DE SchizolobiumparahybaVAR. amazonicum, ACRE, BRASIL

Moisés Silveira Lobão, Daniel Pinto Costa, Marco Aurélio Arizapana Almonacid, Mario Tomazello Filho
2012 Floresta e Ambiente  
Floresta e Ambiente 2012 jul./set.; 19(3):374-384 http://dx.  ...  A caracterização anatômica e a delimitação da área de madeira juvenil-adulta do tronco das árvores permitiram indicar o uso múltiplo e sustentado da sua madeira.  ...  Lenho de Árvores de Schizolobium parahyba var. amazonicum... 381 Floresta e Ambiente 2012; 19(3):374-384 Qualidade do Lobão MS, Costa DP, Almonacid MAA, Tomazello Filho M Floresta e Ambiente 2012  ... 
doi:10.4322/floram.2012.044 fatcat:yq7vizgvkvb2lhswnnsgfvne6i

Using Reaction Mechanism to Measure Enzyme Similarity

Noel M. O'Boyle, Gemma L. Holliday, Daniel E. Almonacid, John B.O. Mitchell
2007 Journal of Molecular Biology  
The apparent dissimilarity of the mechanisms of M0069 30 and M0083 31,32 (Figure 2(e)) according to the EC system highlights a deficiency of the hierarchical nature of that system.  ... 
doi:10.1016/j.jmb.2007.02.065 pmid:17400244 pmcid:PMC3461574 fatcat:yzx56y2e2raqvlwx4sownabeny

MACiE: exploring the diversity of biochemical reactions

Gemma L. Holliday, Claudia Andreini, Julia D. Fischer, Syed Asad Rahman, Daniel E. Almonacid, Sophie T. Williams, William R. Pearson
2011 Nucleic Acids Research  
MACiE (which stands for Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms, and can be accessed from http://www.ebi.ac.uk/thornton-srv/databases/ MACiE/. This article presents the release of Version 3 of MACiE, which not only extends the dataset to 335 entries, covering 182 of the EC sub-subclasses with a crystal structure available (90%), but also incorporates greater chemical and structural detail. This version of MACiE represents a shift in
more » ... is for new entries, from nonhomologous representatives covering EC reaction space to enzymes with mechanisms of interest to our users and collaborators with a view to exploring the chemical diversity of life. We present new tools for exploring the data in MACiE and comparing entries as well as new analyses of the data and new searches, many of which can now be accessed via dedicated Perl scripts.
doi:10.1093/nar/gkr799 pmid:22058127 pmcid:PMC3244993 fatcat:byhlceunrncahhkl6jvj2ufohu

16S rRNA Gene Sequencing as a Clinical Diagnostic Aid for Gastrointestinal-related Conditions [article]

Daniel E Almonacid, Laurens Kraal, Francisco J Ossandon, Yelena V Budovskaya, Juan Pablo Cardenas, Jessica Richman, Zachary S Apte
2016 bioRxiv   pre-print
Accurate detection of the microorganisms underlying gut dysbiosis in the patient is critical to initiate the appropriate treatment. However, most clinical microbiology techniques used to detect gut bacteria were developed over a century ago and rely on culture-based approaches that are often laborious, unreliable, and subjective. Further, culturing does not scale well for multiple targets and detects only a minority of the microorganisms in the human gastrointestinal tract. Here we present a
more » ... nical test for gut microorganisms based on targeted sequencing of the prokaryotic 16S rRNA gene. We tested 46 clinical prokaryotic targets in the human gut, 28 of which can be identified by a bioinformatics pipeline that includes sequence analysis and taxonomic annotation. Using microbiome samples from a cohort of 897 healthy individuals, we established a reference range defining clinically relevant relative levels for each of the 28 targets. Our assay accurately quantified all 28 targets and correctly reflected 38/38 verification samples of real and synthetic stool material containing known pathogens. Thus, we have established a new test to interrogate microbiome composition and diversity, which will improve patient diagnosis, treatment and monitoring. More broadly, our test will facilitate epidemiological studies of the microbiome as it relates to overall human health and disease.
doi:10.1101/084657 fatcat:e24r4izkp5cazfv3pecqxgwy7e

Soil Microbial Composition and Structure Allow Assessment of Biological Product Effectiveness and Crop Yield Prediction [article]

Nabeel Imam, Ignacio Belda, Adrian J Duehl, James R Doroghazi, Daniel E Almonacid, Varghese P Thomas, Alberto Acedo
2021 bioRxiv   pre-print
Kõiv V, Roosaare M, Vedler E, Kivistik PA, Toppi K, Schryer DW, Remm M, Tenson T, 555 Mäe A. 2015.  ...  Rasche F, Hödl V, Poll C, Kandeler E, Gerzabek MH, Van Elsas JD, Sessitsch A. 2006b. 539 Rhizosphere bacteria affected by transgenic potatoes with antibacterial activities 540 compared with the effects  ... 
doi:10.1101/2021.02.09.430373 fatcat:6jcsz3qjtnc7vjkce6qwnw23ee

Measures of reproducibility in sampling and laboratory processing methods in high-throughput microbiome analysis [article]

Patricia Vera-Wolf, Juan P Cardenas, Amanda M Morton, Tomas Norambuena, Rafael Torres, Luis E. Leon, Elisabeth M Bik, Juan A Ugalde, Daniel E Almonacid, Jessica Richman, Zachary S Apte
2018 bioRxiv   pre-print
These samples were randomly selected from a group of 897 healthy subjects described in 359 Almonacid et al. (Almonacid et al. 2017). B.  ...  Apte, Z., Richman, J., Behbahani, S.R. and Almonacid, D. 2017.  ... 
doi:10.1101/322677 fatcat:tj2wg2a5yjbevlxxcrfjs25b2y

IDH1 and IDH2 mutants identified in cancer lose inhibition by isocitrate because of a change in their binding sites [article]

Juan P Bascur, Melissa Alegria-Arcos, Ingrid Araya-Duran, Ezequiel I Juritz, Fernando D Gonzalez-Nilo, Daniel E Almonacid
2018 bioRxiv   pre-print
The catalytic residues of IDH1 and IDH2 were mapped from the E. coli IDH sequence by alignments performed by PROMALS3D (Pei, Kim & Grishin, 2008) .  ...  The E. coli isocitrate dehydrogenase (IDH) catalytic residues were obtained from the entry M0007 of the Mechanism, Annotation and Classification in Enzymes (MACiE) database (Holliday et al., 2012) .  ... 
doi:10.1101/425025 fatcat:xqvcwjhrczcl7ilnp3qoug3flm

The Structure–Function Linkage Database

Eyal Akiva, Shoshana Brown, Daniel E. Almonacid, Alan E. Barber, Ashley F. Custer, Michael A. Hicks, Conrad C. Huang, Florian Lauck, Susan T. Mashiyama, Elaine C. Meng, David Mischel, John H. Morris (+7 others)
2013 Nucleic Acids Research  
Each node represents a single protein, and each edge indicates a BLAST E-value <1e À80 .  ...  Edges between representative nodes indicate a mean BLAST E-value, between all pairs of sequences in these nodes, <1e À43 .  ... 
doi:10.1093/nar/gkt1130 pmid:24271399 pmcid:PMC3965090 fatcat:wvrijuzn7jgshaqjjqa5mwseb4

Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function

Daniel E. Almonacid, Emmanuel R. Yera, John B. O. Mitchell, Patricia C. Babbitt, Christine A. Orengo
2010 PLoS Computational Biology  
Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond
more » ... changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56%) suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to refine definitions of EC sub-subclasses for improved discrimination in their classification of enzyme reactions. The results also indicate that mechanistic convergence of reaction steps is widespread, suggesting that quantitative measurement of mechanistic similarity can inform approaches for functional annotation.
doi:10.1371/journal.pcbi.1000700 pmid:20300652 pmcid:PMC2837397 fatcat:gzf6fvbshzh6xcg5xuxargqs4i

Gut microbiome composition and risk factors in a large cross-sectional IBS cohort

Melissa Agnello, Lauren N Carroll, Nabeel Imam, Rodolfo Pino, Christina Palmer, Ignacio Varas, Claire Greene, Maureen Hitschfeld, Sarah Gupta, Daniel E Almonacid, Michael C Hoaglin
2020 BMJ Open Gastroenterology  
ObjectiveIrritable bowel syndrome (IBS) is a common gastrointestinal disorder that is difficult to diagnose and treat due to its inherent heterogeneity and unclear aetiology. Although there is evidence suggesting the importance of the microbiome in IBS, this association remains poorly defined. In the current study, we aimed to characterise a large cross-sectional cohort of patients with self-reported IBS in terms of microbiome composition, demographics, and risk factors.DesignIndividuals who
more » ... previously submitted a stool sample for 16S microbiome sequencing were sent a comprehensive survey regarding IBS diagnosis, demographics, health history, comorbidities, family history, and symptoms. Log ratio-transformed abundances of microbial taxa were compared between individuals reporting a diagnosis of IBS without any comorbidities and individuals reporting no health conditions. Univariable testing was followed by a multivariable logistic regression model controlling for relevant confounders.ResultsOut of 6386 respondents, 1692 reported a diagnosis of IBS without comorbidities and 1124 reported no health conditions. We identified 3 phyla, 15 genera, and 19 species as significantly associated with IBS after adjustment for confounding factors. Demographic risk factors include a family history of gut disorders and reported use of antibiotics in the last year.ConclusionThe results of this study confirm important IBS risk factors in a large cohort and support a connection for microbiome compositional changes in IBS pathogenesis. The results also suggest clinical relevance in monitoring and investigating the microbiome in patients with IBS. Further, the exploratory models described here provide a foundation for future studies.
doi:10.1136/bmjgast-2019-000345 pmid:32518661 pmcid:PMC7254124 fatcat:pwpx4ms5hfflrgso6rewnwxoz4

Draft Genome Sequence of Blautia luti DSM 14534T, Isolated from Human Stool

Rodrigo L. Ortiz, Felipe Melis-Arcos, Paulo C. Covarrubias, Juan A. Ugalde, Zachary S. Apte, José Pérez-Donoso, Juan P. Cárdenas, Daniel E. Almonacid, David Rasko
2020 Microbiology Resource Announcements  
Here, we report the draft sequence of Blautia luti strain DSM 14534T, originally isolated from human feces. This draft contains 74 contigs, comprising 3,718,760 bp with a G+C content of 42.87%. The annotated draft contains 3,338 coding sequences (CDSs) and 110 RNA genes.
doi:10.1128/mra.00088-20 pmid:32381603 fatcat:p7xbr5alsjew7n7xkfxajqslne

Participation of the Salmonella OmpD Porin in the Infection of RAW264.7 Macrophages and BALB/c Mice

Francisco Ipinza, Bernardo Collao, Debbie Monsalva, Victor H. Bustamante, Roberto Luraschi, Melissa Alegría-Arcos, Daniel E. Almonacid, Daniel Aguayo, Iván L. Calderón, Fernando Gil, Carlos A. Santiviago, Eduardo H. Morales (+3 others)
2014 PLoS ONE  
Figure S2 shows the same network thersholded at an E-value of 1e 2155 , corresponding to the highest E-value where OmpD is still connected to other known superfamily members.  ...  The structures of OmpF from Salmonella Typhi (PDB: 3NSG) and E. coli (PDB: 2ZFG), and OmpC from E. coli (PDB: 2J1N) and Salmonella Typhi (PDB: 3UU2) were used as threedimensional templates.  ... 
doi:10.1371/journal.pone.0111062 pmid:25360745 pmcid:PMC4215857 fatcat:udedeyyrejhbjbqflwgju5j7uy

A semiempirical approach to the intra-phycocyanin and inter-phycocyanin fluorescence resonance energy-transfer pathways in phycobilisomes

Adelio R. Matamala, Daniel E. Almonacid, Maximiliano F. Figueroa, JosÉ Martínez-oyanedel, Marta C. Bunster
2007 Journal of Computational Chemistry  
The term S is given by: S ¼ È D D " A ; (5) where È D and D are the quantum efficiency and the life-time of the fluorescence process of the donor chromophore, respectively, and " A is the molar extinction  ... 
doi:10.1002/jcc.20628 pmid:17299727 fatcat:7bd3vivpv5e23jrzilxlpxn4im

Mental Health Symptom Reduction Using Digital Therapeutics Care Informed by Genomic SNPs and Gut Microbiome Signatures [article]

Inti Pedroso, Shreyas V. Kumbhare, Bharat Joshi, Santosh K. Saravanan, Dattatray S. Mongod, Simitha Singh-Rambiritch, Tejaswini Uday, Karthik M. Muthukumar, Carmel Irudayanathan, Chandana Reddy-Sinha, Parambir S. Dulai, Ranjan Sinha (+1 others)
2022 medRxiv   pre-print
E.  ...  Additionally, IRB Study #21141 was determined to be exempt from IRB review by E&I Review Services on 08/06/2021.  ... 
doi:10.1101/2022.04.27.22273901 fatcat:r5a2msbodnbyvdl2sown6d3wou
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