Binding Sites For Ca2 Research Articles

Structural insight into the function of human peptidyl arginine deiminase 6

Peptidyl arginine deiminase 6 (PADI6 or PAD6) is vital for early embryonic development in mice and humans, yet its function remains elusive. PADI6 is less conserved than other PADIs and it is currently unknown whether it has a catalytic function. Here we show that human PADI6 dimerises like hPADIs 2–4, however, does not bind Ca2+ and is inactive in in vitro assays against standard PADI substrates. By determining the crystal structure of hPADI6, we show that hPADI6 is structured in the absence of Ca2+ where hPADI2 and hPADI4 are not, and the Ca-binding sites are not conserved. Moreover, we show that whilst the key catalytic aspartic acid and histidine residues are structurally conserved, the cysteine is displaced far from the active site centre and the hPADI6 active site pocket appears closed through a unique evolved mechanism in hPADI6, not present in the other PADIs. Taken together, these findings provide insight into how the function of hPADI6 may differ from the other PADIs based on its structure and provides a resource for characterising the damaging effect of clinically significant PADI6 variants.

A structure-based computational model of IP3R1 incorporating Ca and IP3 regulation

The inositol 1,4,5-triphosphate receptor (IP3R) mediates Ca release in many cell types and is pivotal to a wide range of cellular processes. High-resolution cryoelectron microscopy studies have provided new structural details of IP3R type 1 (IP3R1), showing that channel function is determined by the movement of various domains within and between each of its four subunits. Channel properties are regulated by ligands, such as Ca and IP3, which bind at specific sites and control the interactions between these domains. However, it is not known how the various ligand-binding sites on IP3R1 interact to control the opening of the channel. In this study, we present a coarse-grained model of IP3R1 that accounts for the channel architecture and the location of specific Ca- and IP3-binding sites. This computational model accounts for the domain-domain interactions within and between the four subunits that form IP3R1, and it also describes how ligand binding regulates these interactions. Using a kinetic model, we explore how two Ca-binding sites on the cytosolic side of the channel interact with the IP3-binding site to regulate the channel open probability. Our primary finding is that the bell-shaped open probability of IP3R1 provides constraints on the relative strength of these regulatory binding sites. In particular, we argue that a specific Ca-binding site, whose function has not yet been established, is very likely a channel antagonist. Additionally, we apply our model to show that domain-domain interactions between neighboring subunits exert control over channel cooperativity and dictate the nonlinear response of the channel to Ca concentration. This suggests that specific domain-domain interactions play a pivotal role in maintaining the channel’s stability, and a disruption of these interactions may underlie disease states associated with Ca dysregulation.

Both Las17-binding sites on Arp2/3 complex are important for branching nucleation and assembly of functional endocytic actin networks in S. cerevisiae

Arp2/3 complex nucleates branched actin filaments that drive membrane invagination during endocytosis and leading-edge protrusion in lamellipodia. Arp2/3 complex is maximally activated in vitro by binding of a WASP family protein to two sites—one on the Arp3 subunit and one spanning Arp2 and ARPC1—but the importance of each site in the regulation of force-producing actin networks is unclear. Here we identify mutations in budding yeast Arp2/3 complex that decrease or block engagement of Las17, the budding yeast WASP, at each site. As in the mammalian system, both sites are required for maximal activation in vitro. Dimerization of Las17 partially restores activity of mutations at both CA binding sites. Arp2/3 complexes defective at either site assemble force-producing actin networks in a bead motility assay, but their reduced activity hinders motility by decreasing actin assembly near the bead surface and by failing to suppress actin filament bundling within the networks. While even the most defective Las17 binding site mutants assembled actin filaments at endocytic sites, they showed significant internalization defects, potentially because they lack the proper architecture to drive plasma membrane remodeling. Together, our data indicate that both Las17 binding sites are important to assemble functional endocytic actin networks in budding yeast, but Arp2/3 complex retains some activity in vitro and in vivo even with a severe defect at either Las17 binding site.

Synthesis, X-Ray, Hirshfeld Surface, DFT, and Molecular Docking Investigation of N-(5H-Dibenzo[a,d][7]Annulen-5-Ylidene)-2-Methylpropane-2-Sulfinamide

Dibenzocycloheptene antidepressants are tricyclic antidepressants (TCAs) that contain the dibenzocycloheptene moiety in their chemical structures. They are used to treat major depressive disorder, anxiety disorders, chronic pain, and addiction. Herein, we report the synthesis of a pure tricyclic antidepressant containing dibenzocycloheptene moiety named N-(5H-dibenzo[a,d][7]annulen-5-ylidene)-2-methylpropane-2-sulfinamide (3) in high chemical yield through condensing (R)-tert-butanesulfinamide with a dibenzosuberon ketone. Its structure is elucidated by employing the X-ray technique, NMR spectroscopy characterization, and DFT calculations at the B3LYP/6-31++G(d,p) level of theory. The geometrical parameters are relatively well reproduced, and the optimized and X-ray geometries are relatively well superimposed. The interconnects in the crystalline form of 3 were identified through the analysis of its Hirshfeld surface (HS) and fingerprint plots. The highest interatomic contacts were found between H…H of 58.2% and C.H of 30.6%. Further, the ADMET (absorption, distribution, metabolism, excretion, and toxicity) pharmacokinetics, and physicochemical properties of 3 were determined, which showed that 3 may act as a carbonic Anhydrase I inhibitor. The binding affinity of 3 into the binding site of carbonic Anhydrase I is investigated using a molecular docking study. It forms a stable complex into the binding site of CA I with a binding energy of −7.12 kcal/mol.

Mechanism of inhibition of the oxygen-evolving complex of photosystem II by lanthanide cations

The process of the interaction of La3+and Tb3+ cations with the Ca-binding site of the oxygen-evolving complex of photosystem II samples depleted of calcium has been studied. The binding of cations to the Ca-binding site is irreversible and the bound cations cannot be washed out or replaced by Ca2+ cation. A feature of lanthanides to bind strongly to the Ca-binding site has been used to investigate if the bound Ln3+ cation has an effect on the high-affinity Mn-binding site of the oxygen-evolving complex. Therefore, in this work, hydroquinone was used for the extraction of manganese cations from the oxygen-evolving complex of the calcium-depleted photosystem II membranes with the Ca-binding site blocked by La3+ or Tb3+ and the activity of the high-affinity site was then examined using exogenous electron donors (Mn2+ + H2O2) and 1,5-di-phenylcarbazide. It was found that lanthanide cation bound to the Ca-binding site can significantly inhibit the oxidation rates of electron donors through the high-affinity Mn-binding site. The mechanism of the observed effect is discussed.

Structural basis for plastic glycolipid recognition of the C-type lectin Mincle

Mincle (macrophage-inducible C-type lectin, CLEC4E) is a C-type lectin immune-stimulatory receptor for cord factor, trehalose dimycolate (TDM), which serves as a potent component of adjuvants. The recognition of glycolipids by Mincle, especially their lipid parts, is poorly understood. Here, we performed nuclear magnetic resonance analysis, revealing that titration of trehalose harboring a linear short acyl chain showed a chemical shift perturbation of hydrophobic residues next to the Ca-binding site. Notably, there were split signalsfor Tyr201 upon complex formation, indicating two binding modes for the acyl chain. In addition, most Mincle residues close to the Ca-binding site showed no observable signals, suggesting their mobility on an ∼ ms scale even after complex formation. Mutagenesis study supported two putative lipid-bindingmodes for branched acyl-chain TDM binding. These results provide novel insights into the plastic-binding modes of Mincle toward a wide range of glycol- and glycerol-lipids, important for rational adjuvant development.

Investigation of the Plutonium(IV) Interactions with Two Variants of the EF-Hand Ca-Binding Site I of Calmodulin.

Due to its presence in the nuclear industry and its strong radiotoxicity, plutonium is an actinide of major interest in the event of internal contamination. To improve the understanding of its mechanisms of transport and accumulation in the body, the complexation of Pu(IV) to the most common protein calcium-binding motif found in cells, the EF-hand motif of calmodulin, was investigated. Visible and X-ray absorption spectroscopies (XAS) in solution made it possible to investigate the speciation of plutonium at physiological pH (pH 7.4) and pH 6 in two variants of the calmodulin Ca-binding site I and using Pu(IV) in different media: carbonate, chloride, or nitrate solutions. Three different species of Pu were identified in the samples, with formation of 1:1 Pu(IV):calmodulin peptide complexes, Pu(IV) reduction, and formation of peptide-mediated Pu(IV) hexanuclear cluster.

Effect of lanthanides on oxidation of Mn2+ cations via a high-affinity Mn-binding site in photosystem II membranes

Lanthanide cations (La3+ and Tb3+) bind to the Ca-binding site of the oxygen-evolving complex in Ca-depleted PSII membranes and irreversibly inhibit the oxygen evolution. Оn the other hand, EPR measurement of Mn2+ concentration in buffer revealed that lanthanide cations inhibit the light-dependent oxidation of Mn2+ cations via the high-affinity Mn-binding site in Mn-depleted PSII membranes, which suggests that they bind to and inhibit the high-affinity Mn-binding site of the oxygen-evolving complex. The inhibition is irreversible, bound Ln3+ cation could not be washed out from the sample. Calcium ion inhibits oxidation of Mn2+ (5 μM) at very high concentration (tens mM) and the inhibition is reversible. In this work we measured the reduction rate of exogenic electron acceptor 2,6-dichlorophenolindophenol during the oxidation of Mn2+ cations in the Ca-depleted PSII and in the Ca-depleted PSII treated with lanthanides after extraction of Mn cluster from these preparations. We found that irreversible binding of the lanthanide cation to the Ca-binding site in the Ca-depleted PSII membranes leads to a partial inhibition of the high-affinity Mn-binding site.

Identification of new 4-(6-oxopyridazin-1-yl)benzenesulfonamides as multi-target anti-inflammatory agents targeting carbonic anhydrase, COX-2 and 5-LOX enzymes: synthesis, biological evaluations and modelling insights

Multiple inhibitions of CA, COX-2 and 5-LOX enzymes has been recognised as a useful strategy for the development of anti-inflammatory drugs that can avoid the disadvantages of using NSAIDs alone. Here, we report new pyridazine-based sulphonamides (5a-c and 7a-f) as potential multi-target anti-inflammatory candidates. First, the furanone heterocycle in the dual CA/COX-2 inhibitor Polmacoxib was replaced with the pyridazinone one. Then, a hydrophobic tail was appended through benzylation of the 3-hydroxyl group of the pyridazinone scaffold to afford benzyloxy pyridazines 5a-c. Furthermore, the structures were adorned with the polar sulphonate functionality, in pyridazine sulphonates 7a-f, that are expected to be engaged in interactions with the hydrophilic half of the CA binding sites. All of the disclosed pyridazinones were tested for inhibitory activities against 4 hCA isoforms (I, II, IX, and XII), as well as against COX-1/2, and 5-LOX. Furthermore, in vivo anti-inflammatory and analgesic effects of pyridazinones 7a and 7b were examined.

Hydroxyapatite nucleation and growth modulated by amino acid-capped gold nanoparticles: An in vitro study

Surface modification of biomaterials significantly influences implantable materials' surface reactivity to induce an apatite-like layer formation. This study observed the bioactivity and surface reactivity of modified biomaterials (calcium-deficient hydroxyapatite [CDHA] on amino acid-capped AuNPs [AA-AuNPs]) through immersion in simulated body fluid (SBF). AuNPs capped with eight different amino acids (AA)—both charged and polar uncharged AAs—showed the ability to induce the biomimetic hydroxyapatite formation. The presence of a hydroxyapatite peak in the X-ray powder diffraction (XRD) pattern indicated hydroxyapatite formation after all samples’ immersion in SBF. Moreover, longer immersion time in SBF contributed to the nucleation and growth of hydroxyapatite shown by the changing of the crystal structure including lattice parameters, crystallinity index, and crystallite size. The XRD results confirmed that surface modification using AA-AuNPs significantly affected the orientation of the hydroxyapatite crystal, where AAs served as a binding site for Ca2+ and PO43− ions. Furthermore, grayscale analysis based on scanning electron microscope images showed that charged AAs exhibited a role in hydroxyapatite nucleation and growth while polar uncharged AAs only contributed to hydroxyapatite growth. The calculated Ca/P ratio also confirmed the formation of hydroxyapatite from CDHA. XRD and scanning electron microscopy/energy-dispersive X-ray spectroscopy results signify the bioactivity of CDHA-modulated AA-AuNPs in hydroxyapatite formation for new bone tissue regeneration.

Investigation of the carbonic anhydrase inhibitory activity of benzenesulfonamides incorporating substituted fused-pyrimidine tails.

Two new series of 2-thiocyclopenta[d]pyrimidine-benzenesulfonamides 12a-l and 2-thiotetrahydroquinazoline-benzenesulfonamides 13a-j were synthesized and evaluated for their carbonic anhydrase (CA, EC 4.2.1.1) inhibitory acivity and cytotoxic activity. The derivatives 12a and 12i exerted effective inhibition against CA II with Ki = 0.11 and 0.15 µM, while 12a, 12e, 12i, and 13d (Ki = 0.083-0.087 µM) were found to be the most potent against CA XII. In addition, higher selectivity toward CA II and CA XII over CA I and CA IX was observed for the majority of the synthesized conjugates. Analysis of the effect of the synthesized compounds on NCI cancer cell lines revealed that compounds 12b and 13d showed mean growth inhibitory effects of 53.59% and 49.25%, respectively. Docking of the synthesized hybrids in the CA II and CA XII binding pockets displayed the capability of the benzenesulfonamide derivatives to form, through their SO2 NH2 moiety, the characteristic interactions of the traditional CA inhibitors, besides additional interactions achieved by the tail with isoform-specific residues in the peripheral part of the CA binding sites.

Competitive metal-binding stoichiometry between calcium and strontium by cell wall proteins of Neurospora crassa.

Cell wall proteins from Neurospora crassa were isolated and evaluated to demonstrate their metal ability to bind Ca2+ /Sr2+ by loading the solubilized protein fraction on to immobilized metal affinity chromatography (IMAC) column pre-equilibrated with Ca2+ /Sr2+ . The sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis IMAC eluent, revealed ∼18 proteins with a similarity in the proteome pattern of Ca2+ /Sr2+ fractions. Diethyl aminoethyl chromatography showed five proteins in common in binding to Ca2+ and Sr2+ , were subjected to N-terminal sequencing. The sequence analysis was studied for the determination of metal-binding site prediction by CHED software indicating that all five were found to have a high affinity toward Ca2+ . From these five, two were randomly selected and denoted as CWP-A (possess five Ca binding sites of six metal-binding sites) and CWP-B (possess six binding sites of eight metal-binding sites). They were selected for further characterization studies to determine their Ca2+ bound Sr2+ binding properties. Surprisingly, these proteins were able to bind Sr2+ ions (29 μmol) with equal affinity as to Ca2+ ions (42 μmol) by means of direct binding, and/or by displacing calcium as observed in metal-dependent proteolytic protection, fluorescence-based metal exchange assays, and molecular simulation studies. From the results, we demonstrate for the first time, that there is a stoichiometry between Ca2+ (an essential macro elemental metal ion) and Sr2+ ions (a nonessential element for which no reported metabolic activity is reported) for the metal-binding sites on cell wall proteins. This stoichiometry could be due to similar atomic dimensions and metal-protein structure stabilizing properties of Sr2+ compared to Ca2+ .

Structural insights into the activation of human calcium-sensing receptor.

Human calcium-sensing receptor (CaSR) is a G-protein-coupled receptor that maintains Ca2+ homeostasis in serum. Here, we present the cryo-electron microscopy structures of the CaSR in the inactive and agonist+PAM bound states. Complemented with previously reported structures of CaSR, we show that in addition to the full inactive and active states, there are multiple intermediate states during the activation of CaSR. We used a negative allosteric nanobody to stabilize the CaSR in the fully inactive state and found a new binding site for Ca2+ ion that acts as a composite agonist with L-amino acid to stabilize the closure of active Venus flytraps. Our data show that agonist binding leads to compaction of the dimer, proximity of the cysteine-rich domains, large-scale transitions of seven-transmembrane domains, and inter- and intrasubunit conformational changes of seven-transmembrane domains to accommodate downstream transducers. Our results reveal the structural basis for activation mechanisms of CaSR and clarify the mode of action of Ca2+ ions and L-amino acid leading to the activation of the receptor.

Structural insights on the metal cross-linking of polymers from the first principles: Calcium – Polymethacrylic acid case study

Metal – polymer interactions are widely exploited for the formation of composite polymer materials, such as hydrogels. Despite the interest towards these systems, still few information is available about the atomistic structure of contacts formed at the interface between the polymer chains, as well as interactions responsible for their formation. In this work the interface formed through the interaction between a widely used polymer system – polymethacrylic acid (PMAA) and Ca2+ cation, as a frequently applied metal cross-linker, is investigated by an ab initio modeling. The local environment of Ca binding sites, including coordination patterns of carboxylic groups, the maximum number of chains cross-linked by one Ca cation, as well as the impact of the PMAA protonation state on the polymer cross-linking are studied. The dynamics of Ca cross-linking process in polymer-rich environment is analyzed. These findings shed the light on the mechanism of Ca – PMAA hydrogel formation and provide the atomistic scale insights on the structure of metal cross-links in the polymer environment, necessary for the optimization of experimental conditions required to obtain polymer composites with enhanced stability and targeted functional characteristics.

Crystal structures of Ca2+–calmodulin bound to NaV C-terminal regions suggest role for EF-hand domain in binding and inactivation

Voltage-gated sodium (NaV) and calcium channels (CaV) form targets for calmodulin (CaM), which affects channel inactivation properties. A major interaction site for CaM resides in the C-terminal (CT) region, consisting of an IQ domain downstream of an EF-hand domain. We present a crystal structure of fully Ca2+-occupied CaM, bound to the CT of NaV1.5. The structure shows that the C-terminal lobe binds to a site ∼90° rotated relative to a previous site reported for an apoCaM complex with the NaV1.5 CT and for ternary complexes containing fibroblast growth factor homologous factors (FHF). We show that the binding of FHFs forces the EF-hand domain in a conformation that does not allow binding of the Ca2+-occupied C-lobe of CaM. These observations highlight the central role of the EF-hand domain in modulating the binding mode of CaM. The binding sites for Ca2+-free and Ca2+-occupied CaM contain targets for mutations linked to long-QT syndrome, a type of inherited arrhythmia. The related NaV1.4 channel has been shown to undergo Ca2+-dependent inactivation (CDI) akin to CaVs. We present a crystal structure of Ca2+/CaM bound to the NaV1.4 IQ domain, which shows a binding mode that would clash with the EF-hand domain. We postulate the relative reorientation of the EF-hand domain and the IQ domain as a possible conformational switch that underlies CDI.

Functional analysis of the secondary HIV-1 capsid binding site in the host protein cyclophilin A

BackgroundEfficient HIV-1 replication depends on interaction of the viral capsid with the host protein cyclophilin A (CypA). CypA, a peptidylprolyl isomerase, binds to an exposed loop in the viral CA protein via the enzyme’s active site. Recent structural analysis of CypA in complex with CA tubes in conjunction with molecular dynamics simulations identified a secondary CA binding site on CypA that allows a bridging interaction with two hexameric subunits of the assembled CA lattice, leading to capsid stabilization (Liu et al. in Nat Commun 7:10714, 2016).ResultsWe performed mutational analysis of residues that have been proposed to mediate CA binding at the secondary binding site on CypA (A25, K27, P29 and K30) and tested the effects of the amino acid substitutions using interaction assays and HIV-1 infection assays in cells. The binding of recombinant CypA to self-assembled CA tubes or native HIV-1 capsids was measured in vitro using a quantitative fluorescence microscopy binding assay revealing that affinity and stoichiometry of CypA to the CA lattice was not affected by the substitutions. To test for functionality of the CypA secondary CA-binding site in HIV-1 infection, mutant CypA proteins were expressed in cells in which endogenous CypA was deleted, and the effects on HIV-1 infection were assayed. In normal HeLa-P4 cells, infection with HIV-1 bearing the A92E substitution in CA is inhibited by endogenous CypA and was inhibited to the same extent by expression of CypA mutants in CypA-null HeLa-P4 cells. Expression of the mutant CypA proteins in CypA-null Jurkat cells restored their permissiveness to infection by wild type HIV-1.ConclusionsThe amino acid changes at A25, K27, P29 and K30 did not affect the affinity of CypA for the CA lattice and did not impair CypA function in infection assays suggesting that these residues are not part of a secondary CA binding site on CypA.

Interaction of Terbium Cations with the Donor Side of Photosystem II in Higher Plants

Photosystem II (PSII) of higher plants provides photoinduced water oxidation and produces molecular oxygen as a by-product of this reaction followed by its release into the atmosphere. The oxygen-evolving complex (OEC) is located on the donor side of PSII and contains an Mn4CaO5 cluster catalyzing water oxidation. A cofactor of this reaction is a Ca2+ cation. Lanthanide ions are similar to Ca2+ ions in relation to some physical and chemical properties, such as the ionic radius and coordination number. In the case of calcium-binding proteins, Ca2+ substitution with these cations is possible. Some representatives of this group of cations are able to bind to the Ca-binding site of PSII. In this study, we investigated an interaction between the donor side of PSII and terbium, one of the least studied lanthanides. According to the obtained results, the incubation of native PSII preparations with Tb3+ cations caused an irreversible inhibition (by ~75% for 2 mM of Tb3+) of the oxygen evolving function. At the same time, changes in the electron transport at the acceptor side of PSII remained rather insignificant. Supplementation of an incubation buffer with 30 mM Ca2+ reduced the inhibiting effect of terbium almost two times. The obtained results agree with the fluorescence induction kinetics measurement in PSII preparations in the presence of exogenous Ca2+ and Tb3+ and allow for the supposition that terbium cations displace Ca2+ ions from OEC. This terbium-induced release of calcium from the catalytic center results in incomplete water oxidation producing H2O2 instead of molecular oxygen as it has been shown earlier for PSII in the absence of Ca2+ in OEC.

Characterization of the Ca2+-coordination structures of L- and T-plastins in combination with their synthetic peptide analogs by FTIR spectroscopy

FTIR spectroscopy was employed to characterize the coordination structures of divalent cations (M2+ = Ca2+ or Mg2+) bound by L- and T-plastins, which contain two EF-hand motifs. We focused on the N-terminal headpieces in the L- and T-plastins to analyze the regions of COO− stretching and amide-I in solution. The spectral profiles indicated that these headpieces have EF-hand calcium-binding sites because bands at 1551 cm−1 and 1555 cm−1 were observed for the bidentate coordination mode of Glu at the 12th position of the Ca2+-binding site of Ca2+-loaded L-plastin and T-plastin, respectively. The amide-I profile of the Mg2+-loaded L-plastin headpiece was identical with that of the apo L-plastin headpiece, meaning that L-plastin has a lower affinity for Mg2+. The amide-I profiles for apo, Mg2+-loaded and Ca2+-loaded T-plastin suggested that aggregation was generated in protein solution at a concentration of 1 mM. The implications of the FTIR spectral data for these plastin headpieces are discussed on the basis of data obtained for synthetic peptide analogs corresponding to the Ca2+-binding site.

Investigating the Conformation of S100β Protein Under Physiological Parameters Using Computational Modeling: A Clue for Rational Drug Design.

Background Physiochemical factors such as temperature, pH and cofactors are well known parameters that confer conformational changes in a protein structure. With S100β protein being a metal binding brain-specific receptor for both extracellular and intracellular functions, a change in conformation due to the above-mentioned factors, can compromise their cellular functions and therefore result in several pathological conditions such as Alzheimer's disease, Ischemic stroke, as well as Myocardial Infarction. Objective The studies conducted sought to elucidate the effect of these physiological factors on the conformational dynamics of S100β protein using computational modeling approaches. Method Temperature-dependent and protein-cofactor complexes molecular dynamics simulations were conducted by varying the temperature from 100 to 400K using GROMACS 5.0.3. Additionally, the conformational dynamics of the protein was studied by varying the pH at 5.0, 7.4 and 9.0 using Ambertools17. This was done by preparing the protein molecule, solvating and minimizing its energy level as well as heating it to the required temperature, equilibrating and simulating under desired conditions (NVT and NPT ensembles). Results The results show that the protein misfolds as a function of increasing temperature with alpha helical content at 100K and 400K being 57.8% and 43.3%, respectively. However, the binding sites of the protein was not appreciably affected by temperature variations. The protein displayed high conformational instability in acidic medium (pH ~5.0). The binding sites of Ca2+, Mg2+ and Zn2+ were identified and each exhibited different groupings of the secondary structural elements (binding motifs). The secondary structure analysis revealed different conformational changes with the characteristic appearance of two beta hairpins in the presence of Zn2+and Mg2+. Conclusion High temperatures, different cofactors and acidic pH confer conformational changes to the S100β structure and these results may inform the design of novel drugs against the protein.

Investigating the Conformation of S100β Protein Under Physiological Parameters Using Computational Modeling: A Clue for Rational Drug Design.

Background:Physiochemical factors such as temperature, pH and cofactors are well known parameters that confer conformational changes in a protein structure. With S100β protein being a metal binding brain-specific receptor for both extracellular and intracellular functions, a change in conformation due to the above-mentioned factors, can compromise their cellular functions and therefore result in several pathological conditions such as Alzheimer’s disease, Ischemic stroke, as well as Myocardial Infarction.Objective:The studies conducted sought to elucidate the effect of these physiological factors on the conformational dynamics of S100β protein using computational modeling approaches.Method:Temperature-dependent and protein-cofactor complexes molecular dynamics simulations were conducted by varying the temperature from 100 to 400K using GROMACS 5.0.3. Additionally, the conformational dynamics of the protein was studied by varying the pH at 5.0, 7.4 and 9.0 using Ambertools17. This was done by preparing the protein molecule, solvating and minimizing its energy level as well as heating it to the required temperature, equilibrating and simulating under desired conditions (NVT and NPT ensembles).Results:The results show that the protein misfolds as a function of increasing temperature with alpha helical content at 100K and 400K being 57.8% and 43.3%, respectively. However, the binding sites of the protein was not appreciably affected by temperature variations. The protein displayed high conformational instability in acidic medium (pH ~5.0). The binding sites of Ca2+, Mg2+ and Zn2+ were identified and each exhibited different groupings of the secondary structural elements (binding motifs). The secondary structure analysis revealed different conformational changes with the characteristic appearance of two beta hairpins in the presence of Zn2+and Mg2+.Conclusion:High temperatures, different cofactors and acidic pH confer conformational changes to the S100β structure and these results may inform the design of novel drugs against the protein.