Role Of Other Residues Research Articles

Determining the Kinetics of Desferroxiamine D from Streptomyces coelicolor using Isothermal Titration Calorimetry

The long‐term objective for this research is to create a new class of antibiotics that targets the non‐ribosomal peptide synthetase independent siderophore (NIS) pathway in bacteria. The focus of my current research is to quantify the first and second order kinetic constants and obtain the kinetics curve of our model system, Desferroxiamine D (DesD), from Streptomyces coelicolor. DesD reacts with ATP as a cofactor, and either the small (hydroxysuccinylcadaverine, HSC), medium or large (desferrioxamine G, or dfoG) substrates in an iterative manner. We have so far collected activity curves with ATP and dfoG limiting, and are pursuing HSC curves. To do this we used Isothermal Titration Calorimetry (ITC) to collect data and GraphPad Prism 8.2 along with Malvern MicroCal Peaq ITC software to fit the kinetics curves and determine the kinetics constants. We successfully gathered and analyzed ITC data for both the catalytic (wild type, Wt) and non‐catalytic (mutant, R306Q) forms of DesD and determined the optimal buffer conditions for solubility. We also gathered data regarding the activity of our Wt DesD enzyme in order to determine the lifespan and the time of optimal catalytic activity. We have found that our enzyme is still active within 96 hours where it was previously thought to have a 36–48 hour catalytic lifespan.In conducting these experiments, we observed that an industry standard amount of magnesium chloride (MgCl2) in our solution caused an oscillating signal during equilibration of the ITC prior to enzyme injection. We hypothesized that the data reflects metal chelation of the Mg by our substrate (dfoG). We plan on conducting a binding experiment using the ITC in order to quantify the substrate (dfoG) and MgCl2 interaction, and ultimately recommend a new standard amount of MgCl2 to the field for future experiments. Other future directions include determining the kinetic constants of Wt DesD interacting with its small substrate HSC (which must be synthesized and purified,) and determining the catalytic role of other residues in the active site by site‐directed mutagenesis and ITC. This experimental assay and data will be the foundation for future drug design targeting DesD.Support or Funding InformationThis research was supported in part by the National Science Foundation (NSF‐RUI grant 1716986 to K.M.H.), and by the John Stauffer Charitable Trust.

Receptor activity‐modifying protein‐dependent effects of mutations in the calcitonin receptor‐like receptor: implications for adrenomedullin and calcitonin gene‐related peptide pharmacology

Background and PurposeReceptor activity-modifying proteins (RAMPs) define the pharmacology of the calcitonin receptor-like receptor (CLR). The interactions of the different RAMPs with this class B GPCR yield high-affinity calcitonin gene-related peptide (CGRP) or adrenomedullin (AM) receptors. However, the mechanism for this is unclear.Experimental ApproachGuided by receptor models, we mutated residues in the N-terminal helix of CLR, RAMP2 and RAMP3 hypothesized to be involved in peptide interactions. These were assayed for cAMP production with AM, AM2 and CGRP together with their cell surface expression. Binding studies were also conducted for selected mutants.Key ResultsAn important domain for peptide interactions on CLR from I32 to I52 was defined. Although I41 was universally important for binding and receptor function, the role of other residues depended on both ligand and RAMP. Peptide binding to CLR/RAMP3 involved a more restricted range of residues than that to CLR/RAMP1 or CLR/RAMP2. E101 of RAMP2 had a major role in AM interactions, and F111/W84 of RAMP2/3 was important with each peptide.Conclusions and ImplicationsRAMP-dependent effects of CLR mutations suggest that the different RAMPs control accessibility of peptides to binding residues situated on the CLR N-terminus. RAMP3 appears to alter the role of specific residues at the CLR-RAMP interface compared with RAMP1 and RAMP2.

Cell-penetrating fusion peptides OD1 and OD2 interact with Bcr–Abl and influence the growth and apoptosis of K562 cells

The Bcr-Abl oncoprotein is the cause of chronic myelogenous leukemia (CML). Crystal structure analysis suggests that Bcr30-63 is the core of the Bcr-Abl oligomerization interface for aberrant kinase activity; however, the precise role of other residues of Bcr1-72 excluding Bcr30-63 have not been evaluated. In this study, Bcr30-63 was named OD2 and other residues of Bcr1-72 were named OD1. Cytoplasmic transduction peptide (CTP) was used to carry molecules into cytoplasm. CTP-OD1 and CTP-OD2 fusion peptides were expressed from a cold-inducible expression system. Our results demonstrated that both fusion peptides could localize into the cytoplasm, specifically interact with the Bcr-Abl protein and further inhibit growth, induce apoptosis, and decrease the phosphorylation of Bcr-Abl in K562 cell lines. However, the viability of THP-1, a Bcr-Abl negative cell line, was unaffected. These results suggested that CTP-OD1 and CTP-OD2 may be an attractive therapeutic option to inhibit the activation of Bcr-Abl kinase in CML.

Mutation Analysis of Violaxanthin De-epoxidase Identifies Substrate-binding Sites and Residues Involved in Catalysis

Plants are able to deal with variable environmental conditions; when exposed to strong illumination, they safely dissipate excess energy as heat and increase their capacity for scavenging reacting oxygen species. Both these protection mechanisms involve activation of the xanthophyll cycle, in which the carotenoid violaxanthin is converted to zeaxanthin by violaxanthin de-epoxidase, using ascorbate as the source of reducing power. In this work, following determination of the three-dimensional structure of the violaxanthin de-epoxidase catalytic domain, we identified the putative binding sites for violaxanthin and ascorbate by in silico docking. Amino acid residues lying in close contact with the two substrates were analyzed for their involvement in the catalytic mechanism. Experimental results supported the proposed substrate-binding sites and point to two residues, Asp-177 and Tyr-198, which are suggested to participate in the catalytic mechanism, based on complete loss of activity in mutant proteins. The role of other residues and the mechanistic similarity to aspartic proteases and epoxide hydrolases are discussed.

Role of a strictly conserved residue in N‐glycosylic bond cleavage by human Thymine DNA Glycosylase

Thymine DNA glycosylase (TDG) promotes genomic integrity by removing thymine from mutagenic G·T mispairs arising from deamination of 5‐methylcytosine and follow‐on base excision repair enzymes restore a G·C pair. Previous studies suggested that Asn140, a strictly conserved active site residue is important, for base excision, yet its catalytic role had not been investigated rigorously. To further our understanding of the catalytic mechanism of TDG, here we determined the contribution of Asn140 to the substrate binding and chemical steps of the reaction. Isothermal titration calorimetry (ITC) experiments show that TDG‐N140A variant binds substrate analogs with the same tight affinity as wild‐type TDG, indicating Asn140 does not contribute to substrate binding. Single turnover kinetics experiments show that TDG‐N140A exhibits no detectable base excision activity for a G·T substrate, and its excision rate is vastly diminished (by ~104.4fold) for G·U, G·FU, and G·BrU substrates. Our findings indicate that Asn140 is essential for the chemical step, but does not contribute substantially to substrate binding. Thus N140A variant provides a useful platform for investigating the role of other residues in forming the reactive enzyme‐substrate complex. This work was supported by an NIH grant.

A comparative QM/MM study of the reaction mechanism of the Hepatitis C virus NS3/NS4A protease with the three main natural substrates NS5A/5B, NS4B/5A and NS4A/4B

The reaction mechanism of the NS3/NS4A protease with the NS4B/5A and NS4A/4B natural substrates has been investigated using the QM/MM (quantum mechanics/molecular mechanics) approach, and some calculations have been performed on the reaction with the NS5A/5B natural substrate. This study widely extends a previous contribution of our group on the reaction mechanism with the NS5A/5B substrate, the main goal here being to understand the differences found between the reaction mechanism of each natural substrate and the role played by the enzymatic residues in the catalytic cycle. This knowledge will ultimately help in developing new NS3/NS4A protease inhibitors. The two first steps of the mechanism have been considered: Acylation and breaking of the peptide bond, with emphasis on the former one (rate limiting process). Energy and free energy profiles for both steps have been calculated at the AM1/MM level and corrected by means of MP2 ab initio calculations, being evident the importance of correlation energy. Acylation is the rate limiting step in all cases and occurs through a tetracoordinated intermediate, as previously suggested for other serine proteases. Specificities in the NS4B/5A mechanism can be attributed to the presence of a Proline residue in the substrate P2 position. The analysis of structures and energies confirm the importance of the oxyanion hole in the electrostatic stabilization of the tetracoordinated intermediate. Finally, the role of other residues, e.g., Arg-155 and Asp-79, has been explained, and the viability of Arg-155 mutants and its resistance to some protease inhibitors has been understood thanks to virtual mutation studies.

Role of Non-phosphorylated Activation Loop Residues in Determining ERK2 Dephosphorylation, Activity, and Subcellular Localization

Extracellular signal-regulated kinases (ERKs) activity is regulated by MAPK/ERK kinases (MEKs), which phosphorylate the regulatory Tyr and Thr residues in ERKs activation loop, and by various phosphatases that remove the incorporated phosphates. Although the role of the phosphorylated residues in the activation loop of ERKs is well studied, much less is known about the role of other residues within this loop. Here we substituted several residues within amino acids 173-177 of ERK2 and studied their role in ERK2 phosphorylation, substrate recognition, and subcellular localization. We found that substitution of residues 173-175 and particularly Pro(174) to alanines reduces the EGF-induced ERK2 phosphorylation, without modifying its in vitro phosphorylation by MEK1. Examining the ability of these mutants to be dephosphorylated revealed that 173-5A mutants are hypersensitive to phosphatases, indicating that these residues are important for setting the phosphorylation/dephosphorylation balance of ERKs. In addition, 173-5A mutants reduced ERK2 activity toward Elk-1, without affecting the activity of ERK2 toward MBP, while substitution of residues 176-8 decreased ERK2 activity toward both substrates. Substitution of Asp(177) to alanine increased nuclear localization of the construct in MEK1-overexpressing cells, suggesting that this residue together with His(176) is involved in the dissociation of ERK2 from MEKs. Combining CRS/CD motif and the activation loop mutations revealed that these two regions cooperate in determining the net phosphorylation of ERK2, but the role of the CRS/CD motif predominates that of the activation loop residues. Thus, we show here that residues 173-177 of ERK2 join other regulatory regions of ERKs in governing ERK activity.

A quantum mechanics/molecular mechanics study of the reaction mechanism of the hepatitis C virus NS3 protease with the NS5A/5B substrate

Combined quantum mechanics and molecular mechanics (QM/MM) calculations were carried out to characterize the reaction mechanism of the NS3 protease with its preferred substrate (NS5A/5B). The main purpose of this study was to locate the barrier states and intermediates along the distinguished coordinate path (DCP) involved in this process. These structures, and in particular the one corresponding to the first barrier state and intermediate (B1 and I1), could be a starting point for the synthesis of inhibitors of this protease, which could be used to treat hepatitis C. The two first steps of the reaction mechanism were studied, i.e., the acylation step and the breaking of the peptide bond. The first step takes place through a tetracoordinated intermediate, as suggested from previous works on other Serine proteases. The importance of the different amino acid residues was also considered (perturbation study where the MM charges of each residue were set to zero independently). The residues of the oxyanion hole were confirmed as the most important for the electrostatic stabilization of the tetracoordinate intermediate. Moreover, the role of other residues, e.g., Arg-155 and Asp-79, was also explained.

Structural Determinants of L-type Channel Activation in Segment IIS6 Revealed by a Retinal Disorder

The mechanism of channel opening for voltage-gated calcium channels is poorly understood. The importance of a conserved isoleucine residue in the pore-lining segment IIS6 has recently been highlighted by functional analyses of a mutation (I745T) in the Ca(V)1.4 channel causing severe visual impairment (Hemara-Wahanui, A., Berjukow, S., Hope, C. I., Dearden, P. K., Wu, S. B., Wilson-Wheeler, J., Sharp, D. M., Lundon-Treweek, P., Clover, G. M., Hoda, J. C., Striessnig, J., Marksteiner, R., Hering, S., and Maw, M. A. (2005) Proc. Natl. Acad. Sci. U. S. A. 102, 7553-7558). In the present study we analyzed the influence of amino acids in segment IIS6 on gating of the Ca(V)1.2 channel. Substitution of Ile-781, the Ca(V)1.2 residue corresponding to Ile-745 in Ca(V)1.4, by residues of different hydrophobicity, size and polarity shifted channel activation in the hyperpolarizing direction (I781P > I781T > I781N > I781A > I781L). As I781P caused the most dramatic shift (-37 mV), substitution with this amino acid was used to probe the role of other residues in IIS6 in the process of channel activation. Mutations revealed a high correlation between the midpoint voltages of activation and inactivation. A unique kinetic phenotype was observed for residues 779-782 (LAIA) located in the lower third of segment IIS6; a shift in the voltage dependence of activation was accompanied by a deceleration of activation at hyperpolarized potentials, a deceleration of deactivation at all potentials (I781P and I781T), and decreased inactivation. These findings indicate that Ile-781 substitutions both destabilize the closed conformation and stabilize the open conformation of Ca(V)1.2. Moreover there may be a flexible center of helix bending at positions 779-782 of Ca(V)1.2. These four residues are completely conserved in high voltage-activated calcium channels suggesting that these channels may share a common mechanism of gating.

Role of the structurally disordered N- and C-terminal residues in the Janus-faced atracotoxins

The Janus-faced atracotoxins (J-ACTXs) are a family of insect-specific excitatory toxins isolated from the venom of Australian funnel-web spiders (genera Atrax and Hadronyche). In addition to a classical cystine knot motif, these toxins contain a rare vicinal disulfide bond. While the vicinal disulfide is known to be critical for insecticidal activity, the role of other residues in toxin function remains to be determined. In this study, we probed the role of the structurally disordered N- and C-terminal residues using a panel of recombinant mutants of the prototypic family member J-ACTX-Hv1c. We found that the structurally disordered C-terminal residues (Glu 36 and Pro 37) were dispensable for toxin function. However, whereas deletion of Ala 1 had minimal impact on toxin function, deletion of both Ala 1 and Ile 2 decreased insecticidal activity more than 70-fold. We propose that Ile 2 forms a part of the target binding site of J-ACTX-Hv1c.