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1.
ACS Appl Bio Mater ; 7(2): 579-587, 2024 Feb 19.
Artigo em Inglês | MEDLINE | ID: mdl-37058420

RESUMO

G-protein coupled receptors (GPCRs) are eukaryotic integral membrane proteins that regulate signal transduction cascade pathways implicated in a variety of human diseases and are consequently of interest as drug targets. For this reason, it is of interest to investigate the way in which specific ligands bind and trigger conformational changes in the receptor during activation and how this in turn modulates intracellular signaling. In the present study, we investigate the way in which the ligand Prostaglandin E2 interacts with three GPCRs in the E-prostanoid family: EP1, EP2, and EP3. We examine information transfer pathways based on long-time scale molecular dynamics simulations using transfer entropy and betweenness centrality to measure the physical transfer of information among residues in the system. We monitor specific residues involved in binding to the ligand and investigate how the information transfer behavior of these residues changes upon ligand binding. Our results provide key insights that enable a deeper understanding of EP activation and signal transduction functioning pathways at the molecular level, as well as enabling us to make some predictions about the activation pathway for the EP1 receptor, for which little structural information is currently available. Our results should advance ongoing efforts in the development of potential therapeutics targeting these receptors.


Assuntos
Dinoprostona , Receptores de Prostaglandina E , Humanos , Dinoprostona/metabolismo , Receptores de Prostaglandina E/química , Receptores de Prostaglandina E/metabolismo , Ligantes , Prostaglandinas , Receptores Acoplados a Proteínas G
2.
J Chem Theory Comput ; 17(5): 3168-3177, 2021 May 11.
Artigo em Inglês | MEDLINE | ID: mdl-33929855

RESUMO

We develop an approach by which reliable estimates of the transfer entropy can be obtained from the variance-covariance matrix of atomic fluctuations, which converges quickly and retains sensitivity to the full chemical profile of the biomolecular system. We validate our method on ERK2, a well-studied kinase involved in the MAPK signaling cascade for which considerable computational, experimental, and mutation data are available. We present the results of transfer entropy analysis on data obtained from molecular dynamics simulations of wild-type active and inactive ERK2, along with mutants Q103A, I84A, L73P, and G83A. We show that our method is systematically consistent within the context of other approaches for calculating transfer entropy, and we provide a method for interpreting networks of interconnected residues in the protein from a perspective of allosteric coupling. We introduce new insights about possible allosteric activity of the extreme N-terminal region of the kinase, and we describe evidence that suggests that activation may occur by different paths or routes in different mutants. Our results highlight systematic advantages and disadvantages of each method for calculating transfer entropy and show the important role of transfer entropy analysis for understanding allosteric behavior in biomolecular systems.


Assuntos
Entropia , Proteína Quinase 1 Ativada por Mitógeno/metabolismo , Regulação Alostérica , Substituição de Aminoácidos , Proteína Quinase 1 Ativada por Mitógeno/química , Simulação de Dinâmica Molecular , Conformação Proteica
3.
J Chem Inf Model ; 54(10): 2869-75, 2014 Oct 27.
Artigo em Inglês | MEDLINE | ID: mdl-25204850

RESUMO

The yeast protein GCN4 is a transcriptional activator in the basic leucine zipper (bZip) family, whose distinguishing feature is the "chopstick-like" homodimer of alpha helices formed at the DNA-binding interface. While experiments have shown that truncated versions of the protein retain biologically relevant DNA-binding affinity, we present the results of a computational study revealing that these variants show a wide variety of dynamical modes in their interaction with the target DNA sequence. We have performed all-atom molecular dynamics simulations of the full-length GCN4 protein as well as three truncated variants; our data indicate that the truncated mutants show dramatically different correlation patterns. We conclude that although the truncated mutants still retain DNA-binding ability, the bZip interface present in the full-length protein provides important stability for the protein-DNA complex.


Assuntos
Fatores de Transcrição de Zíper de Leucina Básica/química , DNA Fúngico/química , Simulação de Dinâmica Molecular , Domínios e Motivos de Interação entre Proteínas , Proteínas de Saccharomyces cerevisiae/química , Sequência de Aminoácidos , Fatores de Transcrição de Zíper de Leucina Básica/genética , Fatores de Transcrição de Zíper de Leucina Básica/metabolismo , Sítios de Ligação , DNA Fúngico/metabolismo , Ligação de Hidrogênio , Dados de Sequência Molecular , Mutação , Ligação Proteica , Estrutura Secundária de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Termodinâmica , Transcrição Gênica
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