Making optimal use of empirical energy functions: Force‐field parameterization in crystal space

Krieger, Elmar; Darden, Tom; Nabuurs, Sander B.; Finkelstein, Alan; Vriend, Gert

doi:10.1002/prot.20251

Cited by 813 publications

(705 citation statements)

References 32 publications

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“…To evaluate the impact of NR5A1 nonsynonymous mutations at the tertiary protein structure, several structural models were built for wild‐type and mutated molecules in the YASARA suite (Krieger et al, 2004), using as templates the crystal structures of the human liver receptor homologue 1 (LRH‐1, NR5A2) DNA‐binding domain (DBD) in complex with the hCYP7A1 promoter (PDB accession code 2A66), and the human NR5A1 ligand‐binding domain (LBD) in complex with di‐pamitoyl‐3‐SN‐phosphatidylethanolamine (PDB accession code 1ZDT). Stereo chemical quality of generated structural models was accessed with MOLPROBITY (Davis et al, 2007).…”

Section: Molecular Analysismentioning

confidence: 99%

Wide spectrum of NR5A1‐related phenotypes in 46,XY and 46,XX individuals

Domenice¹,

Machado²,

Ferreira

et al. 2016

Birth Defects Research Pt C

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Steroidogenic factor 1 (NR5A1, SF‐1, Ad4BP) is a transcriptional regulator of genes involved in adrenal and gonadal development and function. Mutations in NR5A1 have been among the most frequently identified genetic causes of gonadal development disorders and are associated with a wide phenotypic spectrum. In 46,XY individuals, NR5A1‐related phenotypes may range from disorders of sex development (DSD) to oligo/azoospermia, and in 46,XX individuals, from 46,XX ovotesticular and testicular DSD to primary ovarian insufficiency (POI). The most common 46,XY phenotype is atypical or female external genitalia with clitoromegaly, palpable gonads, and absence of Müllerian derivatives. Notably, an undervirilized external genitalia is frequently seen at birth, while spontaneous virilization may occur later, at puberty. In 46,XX individuals, NR5A1 mutations are a rare genetic cause of POI, manifesting as primary or secondary amenorrhea, infertility, hypoestrogenism, and elevated gonadotropin levels. Mothers and sisters of 46,XY DSD patients carrying heterozygous NR5A1 mutations may develop POI, and therefore require appropriate counseling. Moreover, the recurrent heterozygous p.Arg92Trp NR5A1 mutation is associated with variable degrees of testis development in 46,XX patients. A clear genotype‐phenotype correlation is not seen in patients bearing NR5A1 mutations, suggesting that genetic modifiers, such as pathogenic variants in other testis/ovarian‐determining genes, may contribute to the phenotypic expression. Here, we review the published literature on NR5A1‐related disease, and discuss our findings at a single tertiary center in Brazil, including ten novel NR5A1 mutations identified in 46,XY DSD patients. The ever‐expanding phenotypic range associated with NR5A1 variants in XY and XX individuals confirms its pivotal role in reproductive biology, and should alert clinicians to the possibility of NR5A1 defects in a variety of phenotypes presenting with gonadal dysfunction. Birth Defects Research (Part C) 108:309–320, 2016. © 2016 The Authors Birth Defects Research Part C: Embryo Today: Reviews Published by Wiley Periodicals, Inc.

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Section: Molecular Analysismentioning

confidence: 99%

Wide spectrum of NR5A1‐related phenotypes in 46,XY and 46,XX individuals

Domenice¹,

Machado²,

Ferreira

et al. 2016

Birth Defects Research Pt C

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“…The homology models of the CHD7 protein were constructed using YASARA Structure version 11.4.18 using standard settings. A short combined steepest descent and simulated annealing minimization using constraints on aligned backbone atoms was performed, followed by a full unrestrained simulated annealing minimization for the entire model using the YASARA2 force field [Krieger et al, 2002;Krieger et al, 2004;Krieger et al, 2009]. Modeling of the CHD7 variants and the assessment of the effect on CHD7 stability was performed using the FoldX protein design algorithm [Guerois et al, 2002;Schymkowitz et al, 2005;Reis et al, 2010] as described previously [Alibes et al, 2010;Pey et al, 2007;Rakoczy et al, 2011;van der Sloot et al, 2006].…”

Section: Structural Model Of the Chd7 Chromo-and Helicase Domainsmentioning

confidence: 99%

A novel classification system to predict the pathogenic effects of CHD7 missense variants in CHARGE syndrome

et al. 2012

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CHARGE syndrome is characterized by the variable occurrence of multisensory impairment, congenital anomalies, and developmental delay, and is caused by heterozygous mutations in the CHD7 gene. Correct interpretation of CHD7 variants is essential for genetic counseling. This is particularly difficult for missense variants because most variants in the CHD7 gene are private and a functional assay is not yet available. We have therefore developed a novel classification system to predict the pathogenic effects of CHD7 missense variants that can be used in a diagnostic setting. Our classification system combines the results from two computational algorithms (PolyPhen-2 and Align-GVGD) and the prediction of a newly developed structural model of the chromo-and helicase domains of CHD7 with segregation and phenotypic data. The combination of different variables will lead to a more confident prediction of pathogenicity than was previously possible. We have used our system to classify 145 CHD7 missense variants. Our data show that pathogenic missense mutations are mainly present in the middle of the CHD7 gene, whereas benign variants are mainly clustered in the 5 and 3 regions. Finally, we show that CHD7 missense mutations are, in general, associated with a milder phenotype than truncating mutations.

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“…At this interaction site, RhoA protrudes into a concavity on the surface of LARG between residues N975 and R986; therefore, we hypothesized that a small molecule that bound in that concavity would reduce or prevent RhoA binding to LARG. From the docking screen of more than 4 million compounds in the ZINC library (22,23), the top scoring 49 chemicals predicted to bind to the LARG binding concavity were tested for their ability to inhibit the binding interaction between the DH-PH domain module of LARG and RhoA. Purified DH-PH domains of LARG, expressed as the (His) 6 -tagged proteins in Escherichia coli, were incubated with RhoA in the presence of a given compound at 100 μM concentration.…”

Section: Resultsmentioning

confidence: 99%

Small-molecule inhibitors targeting G-protein–coupled Rho guanine nucleotide exchange factors

Shang

Marchioni

Evelyn

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

127

100

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The G-protein-mediated Rho guanine nucleotide exchange factor (GEF)-Rho GTPase signaling axis has been implicated in human pathophysiology and is a potential therapeutic target. By virtual screening of chemicals that fit into a surface groove of the DH-PH domain of LARG, a G-protein-regulated Rho GEF involved in RhoA activation, and subsequent validations in biochemical assays, we have identified a class of chemical inhibitors represented by Y16 that are active in specifically inhibiting LARG binding to RhoA. Y16 binds to the junction site of the DH-PH domains of LARG with a ∼80 nM K d and suppresses LARG catalyzed RhoA activation dose dependently. It is active in blocking the interaction of LARG and related G-proteincoupled Rho GEFs with RhoA without a detectable effect on other DBL family Rho GEFs, Rho effectors, or a RhoGAP. In cells, Y16 selectively inhibits serum-induced RhoA activity and RhoA-mediated signaling, effects that can be rescued by a constitutively active RhoA or ROCK mutant. By suppressing RhoA activity, Y16 inhibits mammary sphere formation of MCF7 breast cancer cells but does not affect the nontransforming MCF10A cells. Significantly, Y16 works synergistically with Rhosin/G04, a Rho GTPase activation site inhibitor, in inhibiting LARG-RhoA interaction, RhoA activation, and RhoA-mediated signaling functions. Thus, our studies show that Rho GEFs can serve as selective targets of small chemicals and present a strategy of dual inhibition of the enzyme-substrate pair of GEF-RhoA at their binding interface that leads to enhanced efficacy and specificity.

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Making optimal use of empirical energy functions: Force‐field parameterization in crystal space

Cited by 813 publications

References 32 publications

Wide spectrum of NR5A1‐related phenotypes in 46,XY and 46,XX individuals

Wide spectrum of NR5A1‐related phenotypes in 46,XY and 46,XX individuals

A novel classification system to predict the pathogenic effects of CHD7 missense variants in CHARGE syndrome

Small-molecule inhibitors targeting G-protein–coupled Rho guanine nucleotide exchange factors

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