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1.
J Neurol ; 271(3): 1133-1149, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38133801

RESUMO

BACKGROUND: Multiple sclerosis patients would benefit from machine learning algorithms that integrates clinical, imaging and multimodal biomarkers to define the risk of disease activity. METHODS: We have analysed a prospective multi-centric cohort of 322 MS patients and 98 healthy controls from four MS centres, collecting disability scales at baseline and 2 years later. Imaging data included brain MRI and optical coherence tomography, and omics included genotyping, cytomics and phosphoproteomic data from peripheral blood mononuclear cells. Predictors of clinical outcomes were searched using Random Forest algorithms. Assessment of the algorithm performance was conducted in an independent prospective cohort of 271 MS patients from a single centre. RESULTS: We found algorithms for predicting confirmed disability accumulation for the different scales, no evidence of disease activity (NEDA), onset of immunotherapy and the escalation from low- to high-efficacy therapy with intermediate to high-accuracy. This accuracy was achieved for most of the predictors using clinical data alone or in combination with imaging data. Still, in some cases, the addition of omics data slightly increased algorithm performance. Accuracies were comparable in both cohorts. CONCLUSION: Combining clinical, imaging and omics data with machine learning helps identify MS patients at risk of disability worsening.


Assuntos
Esclerose Múltipla , Humanos , Esclerose Múltipla/diagnóstico por imagem , Esclerose Múltipla/terapia , Estudos Prospectivos , Leucócitos Mononucleares , Imageamento por Ressonância Magnética/métodos , Gravidade do Paciente , Aprendizado de Máquina
2.
Commun Biol ; 6(1): 342, 2023 03 30.
Artigo em Inglês | MEDLINE | ID: mdl-36997638

RESUMO

Genome-wide association studies (GWAS) successfully identified multiple sclerosis (MS) susceptibility variants. Despite this notable progress, understanding the biological context of these associations remains challenging, due in part to the complexity of linking GWAS results to causative genes and cell types. Here, we aimed to address this gap by integrating GWAS data with single-cell and bulk chromatin accessibility data and histone modification profiles from immune and nervous systems. MS-GWAS associations are significantly enriched in regulatory regions of microglia and peripheral immune cell subtypes, especially B cells and monocytes. Cell-specific polygenic risk scores were developed to examine the cumulative impact of the susceptibility genes on MS risk and clinical phenotypes, showing significant associations with risk and brain white matter volume. The findings reveal enrichment of GWAS signals in B cell and monocyte/microglial cell-types, consistent with the known pathology and presumed targets of effective MS therapeutics.


Assuntos
Linfócitos B , Microglia , Monócitos , Esclerose Múltipla , Humanos , Linfócitos B/metabolismo , Células Sanguíneas/metabolismo , Cromatina , Elementos Facilitadores Genéticos , Epigênese Genética , Predisposição Genética para Doença , Estratificação de Risco Genético , Variação Genética , Microglia/metabolismo , Monócitos/metabolismo , Esclerose Múltipla/genética , Análise da Expressão Gênica de Célula Única , Encéfalo/citologia , Biobanco do Reino Unido
3.
Brain ; 146(2): 645-656, 2023 02 13.
Artigo em Inglês | MEDLINE | ID: mdl-35253861

RESUMO

Polygenic inheritance plays a pivotal role in driving multiple sclerosis susceptibility, an inflammatory demyelinating disease of the CNS. We developed polygenic risk scores (PRS) of multiple sclerosis and assessed associations with both disease status and severity in cohorts of European descent. The largest genome-wide association dataset for multiple sclerosis to date (n = 41 505) was leveraged to generate PRS scores, serving as an informative susceptibility marker, tested in two independent datasets, UK Biobank [area under the curve (AUC) = 0.73, 95% confidence interval (CI): 0.72-0.74, P = 6.41 × 10-146] and Kaiser Permanente in Northern California (KPNC, AUC = 0.8, 95% CI: 0.76-0.82, P = 1.5 × 10-53). Individuals within the top 10% of PRS were at higher than 5-fold increased risk in UK Biobank (95% CI: 4.7-6, P = 2.8 × 10-45) and 15-fold higher risk in KPNC (95% CI: 10.4-24, P = 3.7 × 10-11), relative to the median decile. The cumulative absolute risk of developing multiple sclerosis from age 20 onwards was significantly higher in genetically predisposed individuals according to PRS. Furthermore, inclusion of PRS in clinical risk models increased the risk discrimination by 13% to 26% over models based only on conventional risk factors in UK Biobank and KPNC, respectively. Stratifying disease risk by gene sets representative of curated cellular signalling cascades, nominated promising genetic candidate programmes for functional characterization. These pathways include inflammatory signalling mediation, response to viral infection, oxidative damage, RNA polymerase transcription, and epigenetic regulation of gene expression to be among significant contributors to multiple sclerosis susceptibility. This study also indicates that PRS is a useful measure for estimating susceptibility within related individuals in multicase families. We show a significant association of genetic predisposition with thalamic atrophy within 10 years of disease progression in the UCSF-EPIC cohort (P < 0.001), consistent with a partial overlap between the genetics of susceptibility and end-organ tissue injury. Mendelian randomization analysis suggested an effect of multiple sclerosis susceptibility on thalamic volume, which was further indicated to be through horizontal pleiotropy rather than a causal effect. In summary, this study indicates important, replicable associations of PRS with enhanced risk assessment and radiographic outcomes of tissue injury, potentially informing targeted screening and prevention strategies.


Assuntos
Estudo de Associação Genômica Ampla , Esclerose Múltipla , Humanos , Herança Multifatorial/genética , Esclerose Múltipla/genética , Epigênese Genética , População Europeia , Fatores de Risco , Predisposição Genética para Doença/genética , Fenótipo
4.
Mol Cell Neurosci ; 120: 103707, 2022 05.
Artigo em Inglês | MEDLINE | ID: mdl-35231567

RESUMO

The neuronal microtubule-associated protein tau undergoes multiple post-translational modifications, which dynamically modulate its molecular functions and biochemical features in space and time. Among them, we have recently reported that a conserved lysine residue mapping to the microtubule-binding domain of the protein (K306 in mouse and K317 in human) is differentially methylated in a model of chronic autoimmune demyelination. In contrast with other well-studied tau post-translational modifications such as phosphorylation, lysine methylation is far less investigated and its specific impact on tau biology is not fully understood. Here we performed a comprehensive analysis of the effects of K317 methylation on key tau features. By combining in silico simulations with in vitro biochemical assays and live-cell imaging, we show that methylated tau is more prone to self-assembly into insoluble structures. Moreover, we demonstrate that K317 methylation affects the stabilization activity of tau on microtubule dynamics. Lastly, we highlight a role for K317 methylation in regulating both neuronal differentiation and cell proliferation. Altogether, these findings shed light on the biology of an overlooked tau post-translational modification as well as on the fine tuning of tau functionality in health and disease.


Assuntos
Lisina , Proteínas tau , Animais , Lisina/metabolismo , Metilação , Camundongos , Neurônios/metabolismo , Fosforilação , Processamento de Proteína Pós-Traducional , Proteínas tau/metabolismo
5.
Arch Biochem Biophys ; 719: 109156, 2022 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-35218721

RESUMO

The human leukocyte antigen (HLA) locus encodes a large group of proteins governing adaptive and innate immune responses. Among them, HLA class II proteins form α/ß heterodimers on the membrane of professional antigen-presenting cells (APCs), where they display both, self and pathogen-derived exogenous antigens to CD4+ T lymphocytes. We have previously shown that a shorter HLA-DRA isoform (sHLA-DRA) lacking 25 amino acids can be presented onto the cell membrane via binding to canonical HLA-DR2 heterodimers. Here, we employed atomistic molecular dynamics simulations to decipher the binding position of sHLA-DRA and its structural impact on functional regions of the HLA-DR2 molecule. We show that a loop region exposed only in the short isoform (residues R69 to G83) is responsible for binding to the outer domain of the HLA-DR2 peptide-binding site, and experimentally validated the critical role of F76 in mediating such interaction. Additionally, sHLA-DRA allosterically modifies the peptide-binding pocket conformation. In summary, this study unravels key molecular mechanisms underlying sHLA-DRA function, providing important insights into the role of full-length proteins in structural modulation of HLA class II receptors.


Assuntos
Antígeno HLA-DR2 , Peptídeos , Sítios de Ligação , Cadeias alfa de HLA-DR , Antígeno HLA-DR2/química , Antígeno HLA-DR2/metabolismo , Humanos , Isoformas de Proteínas/metabolismo
6.
Front Immunol ; 12: 674778, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34025673

RESUMO

The KIR (killer-cell immunoglobulin-like receptor) region is characterized by structural variation and high sequence similarity among genes, imposing technical difficulties for analysis. We undertook the most comprehensive study to date of KIR genetic diversity in a large population sample, applying next-generation sequencing in 2,130 United States European-descendant individuals. Data were analyzed using our custom bioinformatics pipeline specifically designed to address technical obstacles in determining KIR genotypes. Precise gene copy number determination allowed us to identify a set of uncommon gene-content KIR haplotypes accounting for 5.2% of structural variation. In this cohort, KIR2DL4 is the framework gene that most varies in copy number (6.5% of all individuals). We identified phased high-resolution alleles in large multi-locus insertions and also likely founder haplotypes from which they were deleted. Additionally, we observed 250 alleles at 5-digit resolution, of which 90 have frequencies ≥1%. We found sequence patterns that were consistent with the presence of novel alleles in 398 (18.7%) individuals and contextualized multiple orphan dbSNPs within the KIR complex. We also identified a novel KIR2DL1 variant, Pro151Arg, and demonstrated by molecular dynamics that this substitution is predicted to affect interaction with HLA-C. No previous studies have fully explored the full range of structural and sequence variation of KIR as we present here. We demonstrate that pairing high-throughput sequencing with state-of-art computational tools in a large cohort permits exploration of all aspects of KIR variation including determination of population-level haplotype diversity, improving understanding of the KIR system, and providing an important reference for future studies.


Assuntos
Variação Estrutural do Genoma/genética , Receptores Imunológicos/genética , Receptores KIR/genética , Alelos , Estudos de Coortes , Genótipo , Haplótipos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , América do Norte , Polimorfismo Genético , Polimorfismo de Nucleotídeo Único , População Branca/genética
7.
Immunology ; 162(2): 194-207, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-32986852

RESUMO

Class II human leucocyte antigen (HLA) proteins are involved in the immune response by presenting pathogen-derived peptides to CD4+ T lymphocytes. At the molecular level, they are constituted by α/ß-heterodimers on the surface of professional antigen-presenting cells. Here, we report that the acceptor variant (rs8084) in the HLA-DRA gene mediates the transcription of an alternative version of the α-chain lacking 25 amino acids in its extracellular domain. Molecular dynamics simulations suggest this isoform undergoes structural refolding which in turn affects its stability and cellular trafficking. The short HLA-DRA isoform cannot reach the cell surface, although it is still able to bind the corresponding ß-chain. Conversely, it remains entrapped within the endoplasmic reticulum where it is targeted for degradation. Furthermore, we demonstrate that the short isoform can be transported to the cell membrane via interactions with the peptide-binding site of canonical HLA heterodimers. Altogether, our findings indicate that short HLA-DRA functions as a novel intact antigen for class II HLA molecules.


Assuntos
Cadeias alfa de HLA-DR/imunologia , Antígenos de Histocompatibilidade Classe II/imunologia , Isoformas de Proteínas/imunologia , Adulto , Idoso , Aminoácidos/imunologia , Células Apresentadoras de Antígenos/imunologia , Sítios de Ligação/imunologia , Linhagem Celular , Linhagem Celular Tumoral , Membrana Celular/imunologia , Retículo Endoplasmático/imunologia , Feminino , Células HEK293 , Células HeLa , Humanos , Leucócitos Mononucleares/imunologia , Masculino , Pessoa de Meia-Idade , Peptídeos/imunologia , T-Linfocitopenia Idiopática CD4-Positiva/imunologia
8.
Proc Natl Acad Sci U S A ; 117(38): 23742-23750, 2020 09 22.
Artigo em Inglês | MEDLINE | ID: mdl-32878998

RESUMO

Ataxin-1 (ATXN1) is a ubiquitous polyglutamine protein expressed primarily in the nucleus where it binds chromatin and functions as a transcriptional repressor. Mutant forms of ataxin-1 containing expanded glutamine stretches cause the movement disorder spinocerebellar ataxia type 1 (SCA1) through a toxic gain-of-function mechanism in the cerebellum. Conversely, ATXN1 loss-of-function is implicated in cancer development and Alzheimer's disease (AD) pathogenesis. ATXN1 was recently nominated as a susceptibility locus for multiple sclerosis (MS). Here, we show that Atxn1-null mice develop a more severe experimental autoimmune encephalomyelitis (EAE) course compared to wildtype mice. The aggravated phenotype is mediated by increased T helper type 1 (Th1) cell polarization, which in turn results from the dysregulation of B cell activity. Ataxin-1 ablation in B cells leads to aberrant expression of key costimulatory molecules involved in proinflammatory T cell differentiation, including cluster of differentiation (CD)44 and CD80. In addition, comprehensive phosphoflow cytometry and transcriptional profiling link the exaggerated proliferation of ataxin-1 deficient B cells to the activation of extracellular signal-regulated kinase (ERK) and signal transducer and activator of transcription (STAT) pathways. Lastly, selective deletion of the physiological binding partner capicua (CIC) demonstrates the importance of ATXN1 native interactions for correct B cell functioning. Altogether, we report a immunomodulatory role for ataxin-1 and provide a functional description of the ATXN1 locus genetic association with MS risk.


Assuntos
Ataxina-1/metabolismo , Linfócitos B/metabolismo , Encefalomielite Autoimune Experimental/metabolismo , Animais , Apresentação de Antígeno , Proliferação de Células , Encefalomielite Autoimune Experimental/fisiopatologia , Camundongos , Camundongos Knockout , Esclerose Múltipla , Transdução de Sinais
9.
J Immunol ; 205(5): 1323-1330, 2020 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-32709660

RESUMO

Immune dysfunction plays a role in the development of Parkinson disease (PD). NK cells regulate immune functions and are modulated by killer cell immunoglobulin-like receptors (KIR). KIR are expressed on the surface of NK cells and interact with HLA class I ligands on the surface of all nucleated cells. We investigated KIR-allelic polymorphism to interrogate the role of NK cells in PD. We sequenced KIR genes from 1314 PD patients and 1978 controls using next-generation methods and identified KIR genotypes using custom bioinformatics. We examined associations of KIR with PD susceptibility and disease features, including age at disease onset and clinical symptoms. We identified two KIR3DL1 alleles encoding highly expressed inhibitory receptors associated with protection from PD clinical features in the presence of their cognate ligand: KIR3DL1*015/HLA-Bw4 from rigidity (p c = 0.02, odds ratio [OR] = 0.39, 95% confidence interval [CI] 0.23-0.69) and KIR3DL1*002/HLA-Bw4i from gait difficulties (p c = 0.05, OR = 0.62, 95% CI 0.44-0.88), as well as composite symptoms associated with more severe disease. We also developed a KIR3DL1/HLA interaction strength metric and found that weak KIR3DL1/HLA interactions were associated with rigidity (pc = 0.05, OR = 9.73, 95% CI 2.13-172.5). Highly expressed KIR3DL1 variants protect against more debilitating symptoms of PD, strongly implying a role of NK cells in PD progression and manifestation.


Assuntos
Doença de Parkinson/genética , Polimorfismo Genético/genética , Receptores KIR3DL1/genética , Alelos , Feminino , Genótipo , Antígenos HLA-B/genética , Humanos , Células Matadoras Naturais/metabolismo , Ligantes , Masculino , Pessoa de Meia-Idade , Índice de Gravidade de Doença
10.
Biophys J ; 118(8): 1977-1991, 2020 04 21.
Artigo em Inglês | MEDLINE | ID: mdl-32191864

RESUMO

Integrin αIIbß3 is a predominant type of integrin abundantly expressed on the surface of platelets and its activation regulates the process of thrombosis. Talin and kindlin are cytoplasmic proteins that bind to integrin and modulate its affinity for extracellular ligands. Although the molecular details of talin-mediated integrin activation are known, the mechanism of kindlin involvement in this process remains elusive. Here, we demonstrate that the interplay between talin and kindlin promotes integrin activation. Our all-atomic molecular dynamics simulations on complete transmembrane and cytoplasmic domains of integrin αIIbß3, talin1 F2/F3 subdomains, and the kindlin2 FERM domain in an explicit lipid-water environment over a microsecond timescale unraveled the role of kindlin as an enhancer of the talin interaction with the membrane proximal region of ß-integrin. The cooperation of kindlin with talin results in a complete disruption of salt bridges between R995 on αIIb and D723/E726 on ß3. Furthermore, kindlin modifies the molecular mechanisms of inside-out activation by decreasing the crossing angle between transmembrane helices of integrin αIIbß3, which eventually results in parallelization of integrin dimer. In addition, our control simulation featuring integrin in complex with kindlin reveals that kindlin binding is not sufficient for unclasping the inner-membrane and outer-membrane interactions of integrin dimer, thus ruling out the possibility of solitary action of kindlin in integrin activation.


Assuntos
Proteínas de Membrana , Talina , Plaquetas/metabolismo , Proteínas de Membrana/metabolismo , Simulação de Dinâmica Molecular , Complexo Glicoproteico GPIIb-IIIa de Plaquetas/metabolismo , Ligação Proteica , Talina/metabolismo
11.
Mol Biol Cell ; 30(26): 3112-3122, 2019 12 15.
Artigo em Inglês | MEDLINE | ID: mdl-31693446

RESUMO

Tandem calponin homology (CH1-CH2) domains are common actin-binding domains in proteins that interact with and organize the actin cytoskeleton. Despite regions of high sequence similarity, CH1-CH2 domains can have remarkably different actin-binding properties, with disease-associated point mutants known to increase as well as decrease affinity for F-actin. To investigate features that affect CH1-CH2 affinity for F-actin in cells and in vitro, we perturbed the utrophin actin-binding domain by making point mutations at the CH1-CH2 interface, replacing the linker domain, and adding a polyethylene glycol (PEG) polymer to CH2. Consistent with a previous model describing CH2 as a steric negative regulator of actin binding, we find that utrophin CH1-CH2 affinity is both increased and decreased by modifications that change the effective "openness" of CH1 and CH2 in solution. We also identified interface mutations that caused a large increase in affinity without changing solution "openness," suggesting additional influences on affinity. Interestingly, we also observe nonuniform subcellular localization of utrophin CH1-CH2 that depends on the N-terminal flanking region but not on bulk affinity. These observations provide new insights into how small sequence changes, such as those found in diseases, can affect CH1-CH2 binding properties.


Assuntos
Citoesqueleto de Actina/metabolismo , Actinas/metabolismo , Proteínas de Ligação ao Cálcio/metabolismo , Proteínas dos Microfilamentos/metabolismo , Sítios de Ligação , Proteínas de Ligação ao Cálcio/genética , Linhagem Celular Tumoral , Cristalografia por Raios X , Células HEK293 , Células HeLa , Humanos , Proteínas dos Microfilamentos/genética , Modelos Moleculares , Ligação Proteica/fisiologia , Domínios Proteicos/genética , Domínios Proteicos/fisiologia , Homologia de Sequência de Aminoácidos , Utrofina/metabolismo , Calponinas
12.
Structure ; 27(9): 1443-1451.e6, 2019 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-31353240

RESUMO

Targeting both integrins αVß3 and α5ß1 simultaneously appears to be more effective in cancer therapy than targeting each one alone. The structural requirements for bispecific binding of ligand to integrins have not been fully elucidated. RGD-containing knottin 2.5F binds selectively to αVß3 and α5ß1, whereas knottin 2.5D is αVß3 specific. To elucidate the structural basis of this selectivity, we determined the structures of 2.5F and 2.5D as apo proteins and in complex with αVß3, and compared their interactions with integrins using molecular dynamics simulations. These studies show that 2.5D engages αVß3 by an induced fit, but conformational selection of a flexible RGD loop accounts for high-affinity selective binding of 2.5F to both integrins. The contrasting binding of the highly flexible low-affinity linear RGD peptides to multiple integrins suggests that a "Goldilocks zone" of conformational flexibility of the RGD loop in 2.5F underlies its selective binding promiscuity to integrins.


Assuntos
Miniproteínas Nó de Cistina/metabolismo , Integrina alfaVbeta3/química , Integrina alfaVbeta3/metabolismo , Receptores de Vitronectina/química , Receptores de Vitronectina/metabolismo , Sítios de Ligação , Humanos , Integrina alfaVbeta3/genética , Células K562 , Modelos Moleculares , Simulação de Dinâmica Molecular , Mutação , Ligação Proteica , Conformação Proteica , Receptores de Vitronectina/genética
13.
J Autoimmun ; 101: 56-69, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31010726

RESUMO

The molecular events underlying the transition from initial inflammatory flares to the progressive phase of multiple sclerosis (MS) remain poorly understood. Here, we report that the microtubule-associated protein (MAP) Tau exerts a gender-specific protective function on disease progression in the MS model experimental autoimmune encephalomyelitis (EAE). A detailed investigation of the autoimmune response in Tau-deficient mice excluded a strong immunoregulatory role for Tau, suggesting that its beneficial effects are presumably exerted within the central nervous system (CNS). Spinal cord transcriptomic data show increased synaptic dysfunctions and alterations in the NF-kB activation pathway upon EAE in Tau-deficient mice as compared to wildtype animals. We also performed the first comprehensive characterization of Tau post-translational modifications (PTMs) in the nervous system upon EAE. We report that the methylation levels of the conserved lysine residue K306 are significantly decreased in the chronic phase of the disease. By combining biochemical assays and molecular dynamics (MD) simulations, we demonstrate that methylation at K306 decreases the affinity of Tau for the microtubule network. Thus, the down-regulation of this PTM might represent a homeostatic response to enhance axonal stability against an autoimmune CNS insult. The results, altogether, position Tau as key mediator between the inflammatory processes and neurodegeneration that seems to unify many CNS diseases.


Assuntos
Regulação da Expressão Gênica , Esclerose Múltipla/etiologia , Esclerose Múltipla/metabolismo , Neurônios/metabolismo , Sinapses/genética , Sinapses/metabolismo , Proteínas tau/metabolismo , Animais , Autoimunidade , Linhagem Celular , Modelos Animais de Doenças , Encefalomielite Autoimune Experimental , Feminino , Redes Reguladoras de Genes , Masculino , Metilação , Camundongos , Camundongos Knockout , Modelos Moleculares , Esclerose Múltipla/patologia , Transdução de Sinais , Relação Estrutura-Atividade , Subpopulações de Linfócitos T/imunologia , Subpopulações de Linfócitos T/metabolismo , Transcrição Gênica , Proteínas tau/química
14.
J Biomech Eng ; 140(2)2018 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-29272321

RESUMO

Cells have evolved into complex sensory machines that communicate with their microenvironment via mechanochemical signaling. Extracellular mechanical cues trigger complex biochemical pathways in the cell, which regulate various cellular processes. Integrin-mediated focal adhesions (FAs) are large multiprotein complexes, also known as the integrin adhesome, that link the extracellular matrix (ECM) to the actin cytoskeleton, and are part of powerful intracellular machinery orchestrating mechanotransduction pathways. As forces are transmitted across FAs, individual proteins undergo structural and functional changes that involve a conversion of chemical to mechanical energy. The local composition of early adhesions likely defines the regional stress levels and determines the type of newly recruited proteins, which in turn modify the local stress distribution. Various approaches have been used for detecting and exploring molecular mechanisms through which FAs are spatiotemporally regulated, however, many aspects are yet to be understood. Current knowledge on the molecular mechanisms of mechanosensitivity in adhesion proteins is discussed herein along with important questions yet to be addressed, are discussed.


Assuntos
Moléculas de Adesão Celular/metabolismo , Integrinas/metabolismo , Estresse Mecânico , Fenômenos Biomecânicos , Adesão Celular
15.
Biophys J ; 113(4): 948-956, 2017 Aug 22.
Artigo em Inglês | MEDLINE | ID: mdl-28834730

RESUMO

Integrin-mediated signaling is crucial for cell-substrate adhesion and can be triggered from both intra- and extracellular interactions. Although talin binding is sufficient for inside-out activation of integrin, other cytoplasmic proteins such as α-actinin and filamin can directly interfere with talin-mediated integrin activation. Specifically, α-actinin plays distinct roles in regulating αIIbß3 versus α5ß1 integrin. It has been shown that α-actinin competes with talin for binding to the cytoplasmic tail of ß3-integrin, whereas it cooperates with talin for activating integrin α5ß1. In this study, molecular dynamics simulations were employed to compare and contrast molecular mechanisms of αIIbß3 and α5ß1 activation in the presence and absence of α-actinin. Our results suggest that α-actinin impairs integrin signaling by both undermining talin binding to the ß3-integrin cytoplasmic tail and inducing a kink in the transmembrane domain of ß3-integrin. Furthermore, we showed that α-actinin promote talin association with ß1-integrin by restricting the motion of the cytoplasmic tail and reducing the entropic barrier for talin binding. Taken together, our results showed that the interplay between talin and α-actinin regulates signal transmission via controlling the conformation of the transmembrane domain and altering natural response modes of integrins in a type-specific manner.


Assuntos
Actinina/metabolismo , Membrana Celular/metabolismo , Integrina beta3/química , Integrina beta3/metabolismo , Simulação de Dinâmica Molecular , Talina/metabolismo , Citoplasma/metabolismo , Integrina alfa5beta1/metabolismo , Cinética , Complexo Glicoproteico GPIIb-IIIa de Plaquetas/metabolismo , Ligação Proteica , Domínios Proteicos
16.
Biophys J ; 112(9): 1885-1893, 2017 May 09.
Artigo em Inglês | MEDLINE | ID: mdl-28494959

RESUMO

Extracellular matrix stiffness sensing by living cells is known to play a major role in a variety of cell mechanobiological processes, such as migration and differentiation. Various membrane and cytoplasmic proteins are involved in transmitting and transducing environmental signals to biochemical cascades. Protein kinases play a key role in regulating the activity of focal adhesion proteins. Recently, an interaction between mitogen-activated protein kinase (MAPK1) and vinculin was experimentally shown to mediate this process. Here, we adopt a molecular modeling approach to further investigate this interaction and its possible regulatory effects. Using a combination of data-driven flexible docking and molecular dynamics simulations guided by previous experimental studies, we predict the structure of the MAPK1-vinculin complex. Furthermore, by comparing the association of MAPK1 with open versus closed vinculin, we demonstrate that MAPK1 exhibits preferential binding toward the open conformation of vinculin, suggesting that the MAPK1-vinculin interaction is conformationally selective. Finally, we demonstrate that changes in the size of the D3-D4 cleft provide a structural basis for the conformational selectivity of the interaction.


Assuntos
Proteína Quinase 1 Ativada por Mitógeno/metabolismo , Vinculina/metabolismo , Animais , Humanos , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Ligação Proteica , Conformação Proteica , Ratos
17.
ACS Biomater Sci Eng ; 3(11): 2712-2726, 2017 Nov 13.
Artigo em Inglês | MEDLINE | ID: mdl-33418698

RESUMO

Signal modulation has been developed in living cells throughout evolution to promote utilizing the same machinery for multiple cellular functions. Chemical and mechanical modules of signal transmission and transduction are interconnected and necessary for organ development and growth. However, due to the high complexity of the intercommunication of physical intracellular connections with biochemical pathways, there are many missing details in our overall understanding of mechanotransduction processes, i.e., the process by which mechanical signals are converted to biochemical cascades. Cell-matrix adhesions are mechanically coupled to the nucleus through the cytoskeleton. This modulated and tightly integrated network mediates the transmission of mechanochemical signals from the extracellular matrix to the nucleus. Various experimental and computational techniques have been utilized to understand the basic mechanisms of mechanotransduction, yet many aspects have remained elusive. Recently, in silico experiments have made important contributions to the field of mechanobiology. Herein, computational modeling efforts devoted to understanding integrin-mediated mechanotransduction pathways are reviewed, and an outlook is presented for future directions toward using suitable computational approaches and developing novel techniques for addressing important questions in the field of mechanotransduction.

18.
Biophys J ; 110(6): 1444-55, 2016 Mar 29.
Artigo em Inglês | MEDLINE | ID: mdl-27028653

RESUMO

α-Actinin is an essential actin cross-linker involved in cytoskeletal organization and dynamics. The molecular conformation of α-actinin's actin-binding domain (ABD) regulates its association with actin and thus mutations in this domain can lead to severe pathogenic conditions. A point mutation at lysine 255 in human α-actinin-4 to glutamate increases the binding affinity resulting in stiffer cytoskeletal structures. The role of different ABD conformations and the effect of K255E mutation on ABD conformations remain elusive. To evaluate the impact of K255E mutation on ABD binding to actin we use all-atom molecular dynamics and free energy calculation methods and study the molecular mechanism of actin association in both wild-type α-actinin and in the K225E mutant. Our models illustrate that the strength of actin association is indeed sensitive to the ABD conformation, predict the effect of K255E mutation--based on simulations with the K237E mutant chicken α-actinin--and evaluate the mechanism of α-actinin binding to actin. Furthermore, our simulations showed that the calmodulin domain binding to the linker region was important for regulating the distance between actin and ABD. Our results provide valuable insights into the molecular details of this critical cellular phenomenon and further contribute to an understanding of cytoskeletal dynamics in health and disease.


Assuntos
Actinina/química , Actinina/metabolismo , Actinas/metabolismo , Proteínas de Ligação ao Cálcio/química , Proteínas dos Microfilamentos/química , Homologia Estrutural de Proteína , Citoesqueleto de Actina/metabolismo , Regulação Alostérica , Animais , Calmodulina/química , Galinhas , Simulação por Computador , Humanos , Modelos Biológicos , Modelos Moleculares , Proteínas Mutantes/química , Proteínas Mutantes/metabolismo , Mutação/genética , Ligação Proteica , Domínios Proteicos , Calponinas
19.
J Mater Chem B ; 4(7): 1324-1330, 2016 Feb 21.
Artigo em Inglês | MEDLINE | ID: mdl-32262987

RESUMO

Albumins are used biologically and pharmacologically as transport proteins to deliver molecules to cells. Albumins also efficiently coat single-wall carbon nanotubes (SWCNTs) and promote their entry into mammalian and immune cells by the millions. Here, we show SWCNTs dispersed with bovine serum albumin (BSA) that are pre-loaded with rhodamine B (RB), small hydrophobic dye molecules that we consider here as models for drugs, drastically increase delivery of RB to HeLa cells and macrophages in culture. We determine spatial and concentration distribution of RB by independently visualizing SWCNTs and RB within the cells using unique SWCNT NIR fluorescence and fluorescence lifetime imaging of RB. The SWCNTs-BSA-RB ternary complexes are stable in water for days, and RB is only released when BSA is thermally or enzymatically denatured. We demonstrate efficacy of this approach by delivering daunomycin, a fluorescent chemotherapeutic drug that reduces proliferation in HeLa cells. Furthermore, we use molecular dynamics simulations to identify separate regions in BSA for drug loading and binding to SWCNTs. Together, our results demonstrate a pathway to enhance the delivery of a wide variety of drugs to cells through SWCNTs coated with albumin pre-loaded with drug molecules.

20.
Biophys J ; 109(3): 501-9, 2015 Aug 04.
Artigo em Inglês | MEDLINE | ID: mdl-26244732

RESUMO

Numerous biological functions of a cell, including polarization, differentiation, division, and migration, rely on its ability to endure mechanical forces generated by the cytoskeleton on the nucleus. Coupling of the cytoskeleton and nucleoskeleton is ultimately mediated by LINC complexes that are formed via a strong interaction between SUN- and KASH-domain-containing proteins in the nuclear envelope. These complexes are mechanosensitive and essential for the transmission of forces between the cytoskeleton and nucleoskeleton, and the progression of cellular mechanotransduction. Herein, using molecular dynamics, we examine the effect of tension on the human SUN2-KASH2 complex and show that it is remarkably stable under physiologically relevant tensile forces and large strains. However, a covalent disulfide bond between two highly conserved cysteine residues of SUN2 and KASH2 is crucial for the stability of this interaction and the transmission of forces through the complex.


Assuntos
Dissulfetos/química , Peptídeos e Proteínas de Sinalização Intracelular/química , Proteínas de Membrana/química , Simulação de Dinâmica Molecular , Proteínas Nucleares/química , Sequência de Aminoácidos , Humanos , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Mecanotransdução Celular , Proteínas de Membrana/metabolismo , Dados de Sequência Molecular , Proteínas Nucleares/metabolismo , Ligação Proteica
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