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1.
Commun Biol ; 7(1): 418, 2024 Apr 06.
Artículo en Inglés | MEDLINE | ID: mdl-38582945

RESUMEN

Fuchs endothelial corneal dystrophy (FECD) is a leading indication for corneal transplantation, but its molecular etiology remains poorly understood. We performed genome-wide association studies (GWAS) of FECD in the Million Veteran Program followed by multi-ancestry meta-analysis with the previous largest FECD GWAS, for a total of 3970 cases and 333,794 controls. We confirm the previous four loci, and identify eight novel loci: SSBP3, THSD7A, LAMB1, PIDD1, RORA, HS3ST3B1, LAMA5, and COL18A1. We further confirm the TCF4 locus in GWAS for admixed African and Hispanic/Latino ancestries and show an enrichment of European-ancestry haplotypes at TCF4 in FECD cases. Among the novel associations are low frequency missense variants in laminin genes LAMA5 and LAMB1 which, together with previously reported LAMC1, form laminin-511 (LM511). AlphaFold 2 protein modeling, validated through homology, suggests that mutations at LAMA5 and LAMB1 may destabilize LM511 by altering inter-domain interactions or extracellular matrix binding. Finally, phenome-wide association scans and colocalization analyses suggest that the TCF4 CTG18.1 trinucleotide repeat expansion leads to dysregulation of ion transport in the corneal endothelium and has pleiotropic effects on renal function.


Asunto(s)
Distrofia Endotelial de Fuchs , Humanos , Distrofia Endotelial de Fuchs/genética , Distrofia Endotelial de Fuchs/metabolismo , Estudio de Asociación del Genoma Completo , Factor de Transcripción 4/genética , Colágeno , Laminina/genética
2.
Res Sq ; 2023 May 03.
Artículo en Inglés | MEDLINE | ID: mdl-37205546

RESUMEN

Fuchs endothelial corneal dystrophy (FECD) is a leading indication for corneal transplantation, but its molecular pathophysiology remains poorly understood. We performed genome-wide association studies (GWAS) of FECD in the Million Veteran Program (MVP) and meta-analyzed with the previous largest FECD GWAS, finding twelve significant loci (eight novel). We further confirmed the TCF4 locus in admixed African and Hispanic/Latino ancestries, and found an enrichment of European-ancestry haplotypes at TCF4 in FECD cases. Among the novel associations are low frequency missense variants in laminin genes LAMA5 and LAMB1 which, together with previously reported LAMC1, form laminin-511 (LM511). AlphaFold 2 protein modeling suggests that mutations at LAMA5 and LAMB1 may destabilize LM511 by altering inter-domain interactions or extracellular matrix binding. Finally, phenome-wide association scans and co-localization analyses suggest that the TCF4 CTG18.1 trinucleotide repeat expansion leads to dysregulation of ion transport in the corneal endothelium and has pleiotropic effects on renal function.

3.
J Mass Spectrom ; 56(6): e4713, 2021 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-33942435

RESUMEN

Oxidative and nitrative stress have been implicated in the molecular mechanisms underlying a variety of biological processes and disease states including cancer, aging, cardiovascular disease, neurological disorders, diabetes, and alcohol-induced liver injury. One marker of nitrative stress is the formation of 3-nitrotyrosine, or protein tyrosine nitration (PTN), which has been observed during inflammation and tissue injury; however, the role of PTN in the progression or possibly the pathogenesis of disease is still unclear. We show in a model of alcohol-induced liver injury that an increase in PTN occurs in hepatocyte nuclei within the liver of wild-type male C57BL/6J mice following chronic ethanol exposure (28 days). High-resolution mass spectrometric analysis of isolated hepatic nuclei revealed several novel sites of tyrosine nitration on histone proteins. Histone nitration sites were validated by tandem mass spectrometry (MS/MS) analysis of representative synthetic nitropeptides equivalent in sequence to the respective nitrotyrosine sites identified in vivo. We further investigated the potential structural impact of the novel histone H3 Tyr41 (H3Y41) nitration site identified using molecular dynamics (MD) simulations. MD simulations of the nitrated and non-nitrated forms of histone H3Y41 showed significant structural changes at the DNA interface upon H3Y41 nitration. The results from this study suggest that, in addition to other known post-translational modifications that occur on histone proteins (e.g., acetylation and methylation), PTN could induce chromatin structural changes, possibly affecting gene transcription processes associated with the development of alcohol-induced liver injury.


Asunto(s)
Enfermedad Hepática Crónica Inducida por Sustancias y Drogas/metabolismo , Etanol/metabolismo , Histonas/análisis , Nitratos/metabolismo , Tirosina/análogos & derivados , Secuencia de Aminoácidos , Animales , Modelos Animales de Enfermedad , Histonas/metabolismo , Hígado , Masculino , Ratones , Ratones Endogámicos C57BL , Simulación de Dinámica Molecular , Estrés Oxidativo , Espectrometría de Masas en Tándem , Tirosina/análisis , Tirosina/metabolismo
4.
Proteins ; 89(9): 1134-1144, 2021 09.
Artículo en Inglés | MEDLINE | ID: mdl-33864655

RESUMEN

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused substantially more infections, deaths, and economic disruptions than the 2002-2003 SARS-CoV. The key to understanding SARS-CoV-2's higher infectivity lies partly in its host receptor recognition mechanism. Experiments show that the human angiotensin converting enzyme 2 (ACE2) protein, which serves as the primary receptor for both CoVs, binds to the receptor binding domain (RBD) of CoV-2's spike protein stronger than SARS-CoV's spike RBD. The molecular basis for this difference in binding affinity, however, remains unexplained from X-ray structures. To go beyond insights gained from X-ray structures and investigate the role of thermal fluctuations in structure, we employ all-atom molecular dynamics simulations. Microseconds-long simulations reveal that while CoV and CoV-2 spike-ACE2 interfaces have similar conformational binding modes, CoV-2 spike interacts with ACE2 via a larger combinatorics of polar contacts, and on average, makes 45% more polar contacts. Correlation analysis and thermodynamic calculations indicate that these differences in the density and dynamics of polar contacts arise from differences in spatial arrangements of interfacial residues, and dynamical coupling between interfacial and non-interfacial residues. These results recommend that ongoing efforts to design spike-ACE2 peptide blockers will benefit from incorporating dynamical information as well as allosteric coupling effects.


Asunto(s)
Enzima Convertidora de Angiotensina 2/química , Enzima Convertidora de Angiotensina 2/metabolismo , Simulación de Dinámica Molecular , SARS-CoV-2/química , SARS-CoV-2/metabolismo , Glicoproteína de la Espiga del Coronavirus/química , Glicoproteína de la Espiga del Coronavirus/metabolismo , Regulación Alostérica , Humanos , Mutación , Unión Proteica , Receptores Virales/química , Receptores Virales/metabolismo , Termodinámica
5.
Structure ; 27(10): 1601-1611.e2, 2019 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-31402221

RESUMEN

Complexity in understanding allosteric stimulation of the hemagglutinin-neuraminidase (HN) protein of paramyxoviruses by host sialic acids (SIAs) stems from (1) unavailability of structure in its SIA-bound state and (2) the observation that this process is temperature sensitive. To consider simultaneously SIA's effect on structure and thermal fluctuations, we use molecular dynamics and simulate the dimeric form of the Newcastle disease virus HN. We find that SIA induces only minor structural changes in individual monomers, yet it reorients dimer interface by 10°. Interface reorientation is accompanied by constriction of SIA binding groove and enhanced fluctuations of interfacial residues that disrupt hydrophobic interactions and favor creation of new salt bridges. Supervised machine learning analysis of non-equilibrium data reveals that the allosteric signal is not formed from a directed sequence of these events. Altogether, we propose a detailed model of the initial events of allosteric stimulation, consistent with experiments on engineered mutations.


Asunto(s)
Proteína HN/química , Proteína HN/metabolismo , Virus de la Enfermedad de Newcastle/metabolismo , Ácidos Siálicos/farmacología , Regulación Alostérica , Sitios de Unión , Cristalografía por Rayos X , Proteína HN/efectos de los fármacos , Interacciones Hidrofóbicas e Hidrofílicas , Modelos Moleculares , Simulación de Dinámica Molecular , Virus de la Enfermedad de Newcastle/química , Unión Proteica , Conformación Proteica/efectos de los fármacos , Multimerización de Proteína , Aprendizaje Automático Supervisado
6.
Langmuir ; 32(26): 6766-74, 2016 07 05.
Artículo en Inglés | MEDLINE | ID: mdl-27283467

RESUMEN

Recent advances in nanotechnology bring to the forefront a new class of extrinsic constraints for remodeling lipid bilayers. In this next-generation technology, membranes are supported over nanoporous substrates. The nanometer-sized pores in the substrate are too small for bilayers to follow the substrate topology; consequently, the bilayers hang over the pores. Experiments demonstrate that nanoporous substrates remodel lipid bilayers differently from continuous substrates. The underlying molecular mechanisms, however, remain largely undetermined. Here we use molecular dynamics (MD) simulations to probe the effects of silica-type hydroxylation and charge densities on adsorbed palmitoyl-oleoylphosphatidylcholine (POPC) bilayers. We find that a 50% porous substrate decorated with a surface density of 4.6 hydroxyls/nm(2) adsorbs a POPC bilayer at a distance of 4.5 Å, a result consistent with neutron reflectivity experiments conducted on topologically similar silica constructs under highly acidic conditions. Although such an adsorption distance suggests that the interaction between the bilayer and the substrate will be buffered by water molecules, we find that the substrate does interact directly with the bilayer. The substrate modifies several properties of the bilayer-it dampens transverse lipid fluctuations, reduces lipid diffusion rates, and modifies transverse charge densities significantly. Additionally, it affects lipid properties differently in the two leaflets. Compared to substrates functionalized with sparser surface hydroxylation densities, this substrate adheres to bilayers at smaller distances and also remodels POPC more extensively, suggesting a direct correspondence between substrate hydrophilicity and membrane properties. A partial deprotonation of surface hydroxyls, as expected of a silica substrate under mildly acidic conditions, however, produces an inverse effect: it increases the substrate-bilayer distance, which we attribute to the formation of an electric double layer over the negatively charged substrate, and restores, at least partially, leaflet asymmetry and headgroup orientations. Overall, this study highlights the intrinsic complexity of lipid-substrate interactions and suggests the prospect of making two surface attributes-dipole densities and charge densities-work antagonistically toward remodeling lipid bilayer properties.

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