It has long been understood that some proteins undergo conformational transitions en route to the Michaelis Complex to allow chemistry. Examination of crystal structures of glycosyltransferase ...enzymes in the GT-B structural class reveals that the presence of ligand in the active site triggers an open-to-closed conformation transition, necessary for their catalytic functions. Herein, we describe microsecond molecular dynamics simulations of two distantly related glycosyltransferases that are part of the GT-B structural superfamily, HepI and GtfA. Simulations were performed using the open and closed conformations of these unbound proteins, respectively, and we sought to identify the major dynamical modes and communication networks that interconnect the open and closed structures. We provide the first reported evidence within the scope of our simulation parameters that the interconversion between open and closed conformations is a hierarchical multistep process which can be a conserved feature of enzymes of the same structural superfamily. Each of these motions involves of a collection of smaller molecular reorientations distributed across both domains, highlighting the complexities of protein dynamic involved in the interconversion process. Additionally, dynamic cross-correlation analysis was employed to explore the potential effect of distal residues on the catalytic efficiency of HepI. Multiple distal nonionizable residues of the C-terminal domain exhibit motions anticorrelated to positively charged residues in the active site in the
-terminal domain involved in substrate binding. Mutations of these residues resulted in a reduction in negatively correlated motions and an altered enzymatic efficiency that is dominated by lower K
values with
effectively unchanged. The findings suggest that residues with opposing conformational motions involved in the opening and closing of the bidomain HepI protein can allosterically alter the population and conformation of the "closed" state, essential to the formation of the Michaelis complex. The stabilization effects of these mutations likely equally influence the energetics of both the ground state and the transition state of the catalytic reaction, leading to the unaltered
. Our study provides new insights into the role of conformational dynamics in glycosyltransferase's function and new modality to modulate enzymatic efficiency.
The TLQP-21 neuropeptide has been implicated in functions as diverse as lipolysis, neurodegeneration and metabolism, thus suggesting an important role in several human diseases. Three binding targets ...have been proposed for TLQP-21: C3aR1, gC1qR and HSPA8. The aim of this review is to critically evaluate the molecular identity of the TLQP-21 receptor and the proposed multi-receptor mechanism of action. Several studies confirm a critical role for C3aR1 in TLQP-21 biological activity and a largely conserved mode of binding, receptor activation and signaling with C3a, its first-identified endogenous ligand. Conversely, data supporting a role of gC1qR and HSPA8 in TLQP-21 activity remain limited, with no signal transduction pathways being described. Overall, C3aR1 is the only receptor for which a necessary and sufficient role in TLQP-21 activity has been confirmed thus far. This conclusion calls into question the validity of a multi-receptor mechanism of action for TLQP-21 and should inform future studies.
Structural and functional diversity of peptides and GPCR result from long evolutionary processes. Even small changes in sequence can alter receptor activation, affecting therapeutic efficacy. We ...conducted a structure-function relationship study on the neuropeptide TLQP-21, a promising target for obesity, and its complement 3a receptor (C3aR1). After having characterized the TLQP-21/C3aR1 lipolytic mechanism, a homology modeling and molecular dynamics simulation identified the TLQP-21 binding motif and C3aR1 binding site for the human (h) and mouse (m) molecules. mTLQP-21 showed enhanced binding affinity and potency for hC3aR1 compared with hTLQP-21. Consistently, mTLQP-21, but not hTLQP-21, potentiates lipolysis in human adipocytes. These findings led us to uncover five mutations in the C3aR1 binding pocket of the rodent Murinae subfamily that are causal for enhanced calculated affinity and measured potency of TLQP-21. Identifying functionally relevant peptide/receptor co-evolution mechanisms can facilitate the development of innovative pharmacotherapies for obesity and other diseases implicating GPCRs.
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•TLQP-21 binds to C3aR1 and potentiates lipolysis via intracellular calcium•A cluster of mutations was identified in C3aR1 and TLQP-21 in Murinae•These mutations result in enhanced binding affinity and pharmacological potency•Mouse TLQP-21 enhances adrenergic-receptor-induced lipolysis in human adipocytes
GPCRs and neuropeptide ligands are under intense evolutionary pressure and are major pharmacological targets. Sahu et al. identify a cluster of mutations within the C3aR1 receptor and the TLQP-21 peptide in the Murinae subfamily of rodents, resulting in enhanced binding affinity and potency, leading to potentiation of adrenergic-receptor-induced lipolysis.
A precise balance of DNA methylation and demethylation is required for epigenetic control of cell identity, development, and growth. DNA methylation marks are introduced by de novo DNA ...methyltransferases DNMT3a/b and are maintained throughout cell divisions by DNA methyltransferase 1 (DNMT1), which adds methyl groups to hemimethylated CpG dinucleotides generated during DNA replication. Ten eleven translocation (TET) dioxygenases oxidize 5-methylcytosine (mC) to 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxylcytosine (caC), a process known to induce DNA demethylation and gene reactivation. In this study, we investigated the catalytic activity of human DNMT1 in the presence of oxidized forms of mC. A mass spectrometry-based assay was employed to study the kinetics of DNMT1-mediated cytosine methylation in CG dinucleotides containing C, mC, hmC, fC, or caC across from the target cytosine. Homology modeling, coupled with molecular dynamics simulations, was used to explore the structural consequences of mC oxidation with regard to the geometry of protein-DNA complexes. The DNMT1 enzymatic activity was strongly affected by the oxidation status of mC, with the catalytic efficiency decreasing in the following order: mC > hmC > fC > caC. Molecular dynamics simulations revealed that DNMT1 forms an unproductive complex with DNA duplexes containing oxidized forms of mC as a consequence of altered interactions of the target recognition domain of the protein with the C-5 substituent on cytosine. Our results provide new structural and mechanistic insight into TET-mediated DNA demethylation.
Metallo‐β–lactamases (MBLs) are zinc‐containing carbapenemases that inactivate a broad range of β–lactam antibiotics. There is a lack of β–lactamase inhibitors for restoring existing β–lactam ...antibiotics arsenals against common bacterial infections. Fragment‐based screening of a non‐specific metal chelator library demonstrates 8‐hydroxyquinoline as a broad‐spectrum nanomolar inhibitor against VIM‐2 and NDM‐1. A hit‐based substructure search provided an early structure–activity relationship of 8‐hydroxyquinolines and identified 8‐hydroxyquinoline‐7‐carboxylic acid as a low‐cytotoxic β–lactamase inhibitor that can restore β–lactam activity against VIM‐2‐expressing E. coli. Molecular modeling further shed structural insight into its potential mode of binding within the dinuclear zinc active site. 8‐Hydroxyquinoline‐7‐carboxylic acid is highly stable in human plasma and human liver microsomal study, making it an ideal lead candidate for further development.
Here, we report the discovery 8‐hydroxyquinoline‐7‐carboxylic acid (8HQCA) as a low‐cytotoxic nanomolar metallo beta‐lactamase inhibitor that can restore β‐lactam activity against VIM‐2‐expressing E. coli. 8HQCA is highly stable in human plasma and human liver microsomes with desired pharmacokinetic properties, making it an ideal lead candidate for preclinical studies.
Pro-peptide precursors are processed into biologically active peptide hormones or neurotransmitters, each playing an essential role in physiology and disease. Genetic loss of function of a ...pro-peptide precursor results in the simultaneous ablation of all biologically-active peptides within that precursor, often leading to a composite phenotype that can be difficult to align with the loss of specific peptide components. Due to this biological constraint and technical limitations, mice carrying the selective ablation of individual peptides encoded by pro-peptide precursor genes, while leaving the other peptides unaffected, have remained largely unaddressed.
We developed and characterized a mouse model carrying the selective knockout of the TLQP-21 neuropeptide (ΔTLQP-21) encoded by the Vgf gene. To achieve this goal, we used a knowledge-based approach by mutating a codon in the Vgf sequence leading to the substitution of the C-terminal Arginine of TLQP-21, which is the pharmacophore as well as an essential cleavage site from its precursor, into Alanine (R21→A).
We provide several independent validations of this mouse, including a novel in-gel digestion targeted mass spectrometry identification of the unnatural mutant sequence, exclusive to the mutant mouse. ΔTLQP-21 mice do not manifest gross behavioral and metabolic abnormalities and reproduce well, yet they have a unique metabolic phenotype characterized by an environmental temperature-dependent resistance to diet-induced obesity and activation of the brown adipose tissue.
The ΔTLQP-21 mouse line can be a valuable resource to conduct mechanistic studies on the necessary role of TLQP-21 in physiology and disease, while also serving as a platform to test the specificity of novel antibodies or immunoassays directed at TLQP-21. Our approach also has far-reaching implications by informing the development of knowledge-based genetic engineering approaches to generate selective loss of function of other peptides encoded by pro-hormones genes, leaving all other peptides within the pro-protein precursor intact and unmodified.
•We developed a mouse model carrying the selective knockout of the TLQP-21 neuropeptide (ΔTLQP-21).•ΔTLQP-21 mice do not manifest gross behavioral and metabolic abnormalities and reproduce well.•ΔTLQP-21 mice manifest a temperature-dependent resistance to diet-induced obesity and activation of the brown adipose tissue.•Our approach can be applied to perform loss of function of peptides encoded by pro-hormones genes.
Human γ-Aminobutyric acid transporter 1 (hGAT1) is a Na+/Cl− dependent co-transporter that plays a key role in the inhibitory neurotransmission of GABA in the brain. Due to the lack of structural ...data, the exact co-transport mechanism of GABA reuptake by hGAT1 remains unclear. To examine the roles of the co-transport ions and the nature of their interactions with GABA, homology modeling and molecular dynamics simulations of the hGAT1 in the open-to-out conformation were carried out. Our study focused on the sequential preloading of Na+ and Cl− ions, followed by GABA binding. Our simulations showed pre-loading of ions maintains the transport ready state of hGAT1 in the open-to-out conformation essential for GABA binding. Of the four putative preloaded states, GABA binding to the fully loaded state is most favored. Binding of Na+ ion to the Na1 site helps to maintain the open-to-out conformation for GABA binding as compared to the Na2 site. GABA binding to the mono-sodium or the di-sodium loaded states leads to destabilization of Na+ ions within their binding sites. The two most prominent interactions required for GABA binding include interaction between carboxylate group of GABA with the bound Na+ ion in Na1 binding site and the hydroxyl group of Y140. Overall our results support the fully loaded state as the predominate state for GABA binding. Our study further illustrates that Na+ ion within the Na1 site is crucial for GABA recognition. Therefore, a revised mechanism is proposed for the initial step of hGAT1 translocation cycle.
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Human γ-Aminobutyric acid transporter 1 (
GAT1) is a Na
/Cl
dependent co-transporter that plays a key role in the inhibitory neurotransmission of GABA in the brain. Due to the lack of structural ...data, the exact co-transport mechanism of GABA reuptake by
GAT1 remains unclear. To examine the roles of the co-transport ions and the nature of their interactions with GABA, homology modeling and molecular dynamics simulations of the
GAT1 in the open-to-out conformation were carried out. Our study focused on the sequential preloading of Na
and Cl
ions, followed by GABA binding. Our simulations showed pre-loading of ions maintains the transport ready state of
GAT1 in the open-to-out conformation essential for GABA binding. Of the four putative preloaded states, GABA binding to the fully loaded state is most favored. Binding of Na
ion to the Na1 site helps to maintain the open-to-out conformation for GABA binding as compared to the Na2 site. GABA binding to the mono-sodium or the di-sodium loaded states leads to destabilization of Na
ions within their binding sites. The two most prominent interactions required for GABA binding include interaction between carboxylate group of GABA with the bound Na
ion in Na1 binding site and the hydroxyl group of Y140. Overall our results support the fully loaded state as the predominate state for GABA binding. Our study further illustrates that Na
ion within the Na1 site is crucial for GABA recognition. Therefore, a revised mechanism is proposed for the initial step of
GAT1 translocation cycle.
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