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1.
J Chem Inf Model ; 64(5): 1581-1592, 2024 03 11.
Artigo em Inglês | MEDLINE | ID: mdl-38373276

RESUMO

Metalloproteins play a fundamental role in molecular biology, contributing to various biological processes. However, the discovery of high-affinity ligands targeting metalloproteins has been delayed due, in part, to a lack of suitable tools and data. Molecular docking, a widely used technique for virtual screening of small-molecule ligand interactions with proteins, often faces challenges when applied to metalloproteins due to the particular nature of the ligand metal bond. To address these limitations associated with docking metalloproteins, we introduce a knowledge-driven docking approach known as "metalloprotein bias docking" (MBD), which extends the AutoDock Bias technique. We assembled a comprehensive data set of metalloprotein-ligand complexes from 15 different metalloprotein families, encompassing Ca, Co, Fe, Mg, Mn, and Zn metal ions. Subsequently, we conducted a performance analysis of our MBD method and compared it to the conventional docking (CD) program AutoDock4, applied to various metalloprotein targets within our data set. Our results demonstrate that MBD outperforms CD, significantly enhancing accuracy, selectivity, and precision in ligand pose prediction. Additionally, we observed a positive correlation between our predicted ligand free energies and the corresponding experimental values. These findings underscore the potential of MBD as a valuable tool for the effective exploration of metalloprotein-ligand interactions.


Assuntos
Metaloproteínas , Humanos , Metaloproteínas/química , Simulação de Acoplamento Molecular , Ligantes
2.
Ecol Evol ; 8(13): 6492-6504, 2018 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-30038751

RESUMO

Despite its economic, social, biological, and cultural importance, wild forms of the genus Phaseolus are not well represented in germplasm banks, and they are at great risk due to changes in land use as well as climate change. To improve our understanding of the potential geographical distribution of wild beans (Phaseolus spp.) from Mexico and support in situ and ex situ conservation programs, we determined the climatic adaptation ranges of 29 species and two subspecies of Phaseolus collected throughout Mexico. Based on five biotic and 117 abiotic variables obtained from different databases-WorldClim, Global-Aridity, and Global-PET-we performed principal component and cluster analyses. Germplasm was distributed among 12 climatic types from a possible 28. The general climatic ranges were as follows: 8-3,083 m above sea level; 12.07-26.96°C annual mean temperature; 10.33-202.68 mm annual precipitation; 9.33-16.56 W/m2 of net radiation; 11.68-14.23 hr photoperiod; 0.06-1.57 aridity index; and 10-1,728 mm/month of annual potential evapotranspiration. Most descriptive variables (25) clustered species into two groups: One included germplasm from semihot climates, and the other included germplasm from temperate climates. Species clustering showed 45% to 54% coincidence with species previously grouped using molecular data. The species P. filiformis, P. purpusii, and P. maculatus were found at low-humidity locations; these species could be used to improve our understanding of the extreme aridity adaptation mechanisms used by wild beans to avoid or tolerate climate change as well as to introgress favorable alleles into new cultivars adapted to hot, dry environments.

3.
Artigo em Inglês | MEDLINE | ID: mdl-27728988

RESUMO

The current understanding of the genetic diversity of the phytopathogenic fungus Ustilago maydis is limited. To determine the genetic diversity and structure of U. maydis, 48 fungal isolates were analyzed using mitochondrial simple sequence repeats (SSRs). Tumours (corn smut or 'huitlacoche') were collected from different Mexican states with diverse environmental conditions. Using bioinformatic tools, five microsatellites were identified within intergenic regions of the U. maydis mitochondrial genome. SSRMUM4 was the most polymorphic marker. The most common repeats were hexanucleotides. A total of 12 allelic variants were identified, with a mean of 2.4 alleles per locus. An estimate of the genetic diversity using analysis of molecular variance (AMOVA) revealed that the highest variance component is within states (84%), with moderate genetic differentiation between states (16%) (FST = 0.158). A dendrogram generated using the unweighted paired-grouping method with arithmetic averages (UPGMA) and the Bayesian analysis of population structure grouped the U. maydis isolates into two subgroups (K = 2) based on their shared SSRs.


Assuntos
Variação Genética , Genoma Mitocondrial , Repetições de Microssatélites , Ustilago/genética , Teorema de Bayes , Genoma Fúngico , México , Mitocôndrias/genética , Análise de Sequência de DNA
4.
Rev. cuba. med. gen. integr ; 13(5): 474-81, sept.-oct. 1997. tab
Artigo em Espanhol | LILACS | ID: lil-223723

RESUMO

Se realizó un estudio descriptivo del total de hipertensos que laboran en el Ministerio de la Industria Básica, en el período de enero a diciembre de 1995 con el objetivo de identificar los factores de riesgo que favorezcan la aparición de la hipertensión arterial y sus diferencias según el sexo. El grupo de edad más afectado fue el comprendido entre 50 y 59 añoos, con predominio del sexo masculino. La historia familiar de hipertensión arterial (96,5 porciento), la cardiopatía isquémica (32,60 porciento) y la hipercolesterolemia (30,60 porciento), estuvo presente aunque su relación con el sexo no fue significativa. La hipertensión arterial se vio relacionada de forma significativa con la obesidad en el sexo femenino y con el hábito de fumar, el sedentarismo y la categoría ocupacional de dirigente en el sexo masculino


Assuntos
Humanos , Masculino , Feminino , Adulto , Pessoa de Meia-Idade , Diabetes Mellitus/complicações , Exercício Físico , Hipertensão/etiologia , Hipercolesterolemia/complicações , Isquemia Miocárdica/complicações , Obesidade/complicações , Fatores de Risco , Fumar , Categorias de Trabalhadores
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