Computational analysis of anti-cancer drug hydroxyurea adsorption on nanocages of gold, silver and copper: SERS and DFT assessment

The use of nanostructures in targeted drug delivery is effective in decreasing anticancer drug toxicity. Here, we discuss the theoretically predicted adsorption and interaction behavior of hydroxyurea [HU] with nano metal cages (nmC). HU interact the nmC through the N4 in primary amine with energies of -29.776, -30.684 and -22.105 kcal/mol for Au, Ag and Cu cage, respectively. As a result of reactivity studies, HU complexes with nmC (Au/Ag/Cu) are becoming more electrophilic and this gives the nmC system their bioactivity. It is suggested that nanocage is going to change the FMO's energy levels by means of absorption, so that it is used in drug administration. DOS and MEP were accomplished to gain additional understandings into the reactivity of proposed complexes. Method for improving the Raman signal of biomolecules is surface enhanced Raman scattering (SERS), which uses nanosized metal substrates. Chemical enhancement is evidenced by Mulliken charge distributions of all systems for detection and chemical compositions and exerts a significant role in determining them. In HU complexes containing nmC (Au/Ag/Cu), electron density was detected via ELF and LOL calculations. Based on the results of a non-covalent interaction (NCI) analysis, Van der Waals/hydrogen bonds/repulsive steric - interactions have been found. The title compound will also be analyzed in order to determine its bioactivity and drug likeness parameters, as a result, we will able to create a molecule with a highly favorable pharmacological profile and use the docking method to determine the values of the interaction energies for drug delivery. This study suggests that adsorption of drugs on nanocage surface occurs physically and functionalizing the nanocage has increased adsorption energy.

Reversal of Regioselectivity in Asymmetric C-H Bond Annulation with Bromoalkynes under Cobalt Catalysis

Metal-catalyzed asymmetric C-H bond annulation strategy offers a versatile platform, allowing the construction of complex P-chiral molecules through atom- and step-economical fashion. However, regioselective insertion of π-coupling partner between M-C bond with high enantio-induction remain elusive. Using commercially available Co(II) salt and chiral-Salox ligands, we demonstrate an unusual protocol for the regio-reversal, enantioselective C-H bond annulation of phosphinamide with bromoalkyne through desymmetrization. The reaction proceeds through ligand-assisted enantiodetermining cyclocobaltation followed by regioselective insertion of bromoalkyne between Co-C, subsequent reductive elimination, and halogen exchange with carboxylate resulted in P-stereogenic compounds in excellent ee (up to >99 %). The isolation of cobaltacycle involved in the catalytic cycle and the outcome of control experiments provide support for a plausible mechanism.

Multi-oligomeric and catalytically compromised serine acetyltransferase and cysteine regulatory complex of Mycobacterium tuberculosis

l-cysteine, a primary building block of mycothiol, plays an essential role in the defense mechanism of Mycobacterium tuberculosis (Mtb). However, it is unclear how Mtb regulates cysteine biosynthesis as no study has reported the cysteine regulatory complex (CRC) in Mtb. Serine acetyltransferase (SAT) and cysteine synthase (CS) interact to form CRC. Although MtCS has been characterized well, minimal information is available on MtSAT, which synthesizes, O-acetylserine (OAS), the precursor of cysteine. This study fills the gap and provides experimental evidence for the presence of MtCRC and a non-canonical multi-oligomeric MtSAT. We employed multiple analytical methods to characterize the oligomeric and kinetic properties of MtSAT and MtCRC. Results show that MtSAT, lacking >75 N-terminal amino acids exists in three different assembly states; trimer, hexamer, and dodecamer, compared to the single hexameric state of SAT of other bacteria. While hexamers display the highest catalytic turnover, the trimer is the least active. The predominance of trimers at low physiologically relevant concentrations suggests that MtSAT displays the lowest catalytic potential known. Further, the catalytic potential of MtSAT is also significantly reduced in CRC state, in contrast to enhanced activity of SAT in CRC of other organisms. Our study provides insights into multi-oligomeric MtSAT with reduced catalytic potential and demonstrates that both MtSAT and MtCS of Mycobacterium interact to form CRC, although with altered catalytic properties. We discuss our results in light of the altered biochemistry of the last step of canonical sulfate-dependent cysteine biosynthesis of Mycobacterium.

Mycobacterium tuberculosis H37Rv enolase (Rv1023)- expression, characterization and effect of host dependent modifications on protein functionality

Mycobacterium tuberculosis enolase is an essential glycolytic enzyme that catalyzes the conversion of 2, phosphoglycerate (PGA) to phosphoenol pyruvate (PEP). It is also a crucial link between glycolysis and the tricarboxylic acid (TCA) pathway. The depletion of PEP has recently been associated with the emergence of non-replicating drug resistant bacteria. Enolase is also known to exhibit multiple alternate functions, such as promoting tissue invasion via its role as a plasminogen (Plg) receptor. In addition, proteomic studies have identified the presence of enolase in the Mtb degradosome and in biofilms. However, the precise role in these processes has not been elaborated. The enzyme was recently identified as a target for 2-amino thiazoles - a novel class of anti-mycobacterials. In vitro assays and characterization of this enzyme were unsuccessful due to the inability to obtain functional recombinant protein. In the present study, we report the expression and characterization of enolase using Mtb H37Ra as a host strain. Our study demonstrates that the enzyme activity and alternate functions of this protein are significantly impacted by the choice of expression host (Mtb H37Ra or E. coli). Detailed analysis of the protein from each source revealed subtle differences in the post-translational modifications. Lastly, our study confirms the role of enolase in Mtb biofilm formation and describes the potential for inhibiting this process.

Structural, electronic, intermolecular interaction, reactivity, vibrational spectroscopy, charge transfer, Hirshfeld surface analysis, pharmacological and hydropathy plot on 5-Bromo nicotinic acid - Antiviral study (Hepatitis A, B, and C)

The therapeutic properties of 5-Bromonicotinatic acid (5BNA) were studied for antiviral illnesses like Hepatitis A, Hepatitis B and Hepatitis C and the influence of electron-donating and electron-withdrawing properties of functional groups on the nicotinic acid was evaluated and represented in this study using the DFT approach. The molecular parameters were determined for both gases as well as for various solvent phases. The reactive areas in the compound are examined utilising Fukui analysis. The molecular interactions are accomplished by recognising the different types of bonding found in the compound using the AIM, ELF, LOL, RDG and IRI. Solvation investigations were demonstrated to have an influence on molecular orbital energy, ESP, UV-Vis and NLO analyses. Electron-hole, NBO and Hirshfeld investigations are used to investigate the transfer of charges and interactions inside the molecule. The method of vibrational spectroscopy (IR and Raman) is used to differentiate and identify the various types of vibrations displayed by the compound. The hydropathy plots for the proteins 2A4O, 6CWD and 2OC8 associated with Hepatitis A, Hepatitis B and Hepatitis C illustrate the disquiet and attraction of the amino acids towards the water.

Improved Measurement of Solar Neutrinos from the Carbon-Nitrogen-Oxygen Cycle by Borexino and Its Implications for the Standard Solar Model

We present an improved measurement of the carbon-nitrogen-oxygen (CNO) solar neutrino interaction rate at Earth obtained with the complete Borexino Phase-III dataset. The measured rate, R_{CNO}=6.7_{-0.8}^{+2.0}  counts/(day×100  tonnes), allows us to exclude the absence of the CNO signal with about 7σ C.L. The correspondent CNO neutrino flux is 6.6_{-0.9}^{+2.0}×10^{8}  cm^{-2} s^{-1}, taking into account the neutrino flavor conversion. We use the new CNO measurement to evaluate the C and N abundances in the Sun with respect to the H abundance for the first time with solar neutrinos. Our result of N_{CN}=(5.78_{-1.00}^{+1.86})×10^{-4} displays a ∼2σ tension with the "low-metallicity" spectroscopic photospheric measurements. Furthermore, our result used together with the ^{7}Be and ^{8}B solar neutrino fluxes, also measured by Borexino, permits us to disfavor at 3.1σ C.L. the "low-metallicity" standard solar model B16-AGSS09met as an alternative to the "high-metallicity" standard solar model B16-GS98.

A dimeric proteomimetic prevents SARS-CoV-2 infection by dimerizing the spike protein

Protein tertiary structure mimetics are valuable tools to target large protein-protein interaction interfaces. Here, we demonstrate a strategy for designing dimeric helix-hairpin motifs from a previously reported three-helix-bundle miniprotein that targets the receptor-binding domain (RBD) of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Through truncation of the third helix and optimization of the interhelical loop residues of the miniprotein, we developed a thermostable dimeric helix-hairpin. The dimeric four-helix bundle competes with the human angiotensin-converting enzyme 2 (ACE2) in binding to RBD with 2:2 stoichiometry. Cryogenic-electron microscopy revealed the formation of dimeric spike ectodomain trimer by the four-helix bundle, where all the three RBDs from either spike protein are attached head-to-head in an open conformation, revealing a novel mechanism for virus neutralization. The proteomimetic protects hamsters from high dose viral challenge with replicative SARS-CoV-2 viruses, demonstrating the promise of this class of peptides that inhibit protein-protein interaction through target dimerization.

Rhodium-Catalyzed Annulations and Heck Coupling/Aza-Michael Addition for the Synthesis of Benzothiadiazinoisoquinoline 6,6-Dioxides and Benzothiadiazinoisoindole 5,5-Dioxides, Respectively

A new and efficient protocol has been demonstrated for the synthesis of benzothiadiazinoisoquinoline 6,6-dioxides and benzothiadiazinoisoindole 5,5-dioxides in good to excellent yields. These compounds are formed through a sequential Rh(III)-catalyzed C-H cyclization of dihydrophenylbenzothiadiazine 1,1-dioxides with alkynes and oxidative Heck coupling/aza-Michael addition of dihydrophenylbenzothiadiazine 1,1-dioxides with acrylates, respectively.

Microstructural correlation of cross rolling temperature of AT55 magnesium alloy in mechanical and formability behaviour

The development of magnesium alloy includes two key aspects, such as microstructure and texture, which play vital roles in mechanical and forming behaviour. In this study, cross-rolled Mg-5Al-5Sn alloy at various temperatures (350 °C, 400 °C, and 450 °C) with a 60% reduction in thickness was investigated. The effect of cross rolling temperature on the Mg-5Al-5Sn alloy microstructure, texture, tensile properties, and formability was studied. The yield strength increases from 114 MPa to 150 MPa with decreasing rolling temperature, which is attributed to grain refinement phenomena. This finding demonstrates that the AT55 Mg alloy possesses an impact on cross rolling temperature, viz. the formability increases with increases in cross rolling temperature. The alloy processed at 350 °C shows better strength and less formability than that of the alloy processed at 450 °C ( lower strength but good formability at room temperature, with an Erichsen value of 4.3 mm).

First Directional Measurement of Sub-MeV Solar Neutrinos with Borexino

We report the measurement of sub-MeV solar neutrinos through the use of their associated Cherenkov radiation, performed with the Borexino detector at the Laboratori Nazionali del Gran Sasso. The measurement is achieved using a novel technique that correlates individual photon hits of events to the known position of the Sun. In an energy window between 0.54 to 0.74 MeV, selected using the dominant scintillation light, we have measured 10 887_{-2103}^{+2386}(stat)±947(syst) (68% confidence interval) solar neutrinos out of 19 904 total events. This corresponds to a ^{7}Be neutrino interaction rate of 51.6_{-12.5}^{+13.9}  counts/(day·100  ton), which is in agreement with the standard solar model predictions and the previous spectroscopic results of Borexino. The no-neutrino hypothesis can be excluded with >5σ confidence level. For the first time, we have demonstrated the possibility of utilizing the directional Cherenkov information for sub-MeV solar neutrinos, in a large-scale, high light yield liquid scintillator detector. This measurement provides an experimental proof of principle for future hybrid event reconstruction using both Cherenkov and scintillation signatures simultaneously.

Development of nanobiomaterial for wound healing based on silver nanoparticles loaded on chitosan hydrogel

The objective of this study was to develop nanobiomaterial containing silver nanoparticles (AgNPs) for wound healing. AgNPs were synthesized using Saussurea lappa (Sl) aqueous root extract as reducing agent and were characterized physico-chemically using UV-vis spectral studies, XRD, FESEM, TEM, FTIR spectral analysis, DLS, and TG-DSC. Sl AgNPs production was optimized using response surface methodology. The cytotoxicity of Sl AgNPs was assessed by THP1 cell lines, which showed that Sl AgNPs were nontoxic with an IC50 of 151.10 μg/mL at 24 h. For topical application, Sl AgNPs was loaded on chitosan hydrogel was characterized through spreadability, in vitro release, antibacterial activity, swelling behavior, and SEM analysis. The chitosan Sl AgNPs hydrogel was subjected acute dermal toxicity test using Wistar albino rats and was found to be nontoxic. The excisional wound model was created along with Pseudomonas aeruginosa as an inoculant in Wistar albino rats. The chitosan Sl AgNPs hydrogel treated rats showed excellent wound healing qualities, lower bacterial counts, and enhanced production of connective tissues. Our findings strongly suggest that AgNPs synthesized from Saussurea lappa root extract loaded on chitosan hydrogel possibly applied for the remedy of infectious wounds at a concentration of 0.1 mg of Sl AgNPs/g of hydrogel.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03030-0.

Desolvation of Peptide Bond by O to S Substitution Impacts Protein Stability

Amino acid side chains are key to fine-tuning the microenvironment polarity in proteins composed of polar amide bonds. Here, we report that substituting an oxygen atom of the backbone amide bond with sulfur atom desolvates the thioamide bond, thereby increasing its lipophilicity. The impact of such local desolvation by O to S substitution in proteins was tested by synthesizing thioamidated variants of Pin1 WW domain. We observe that a thioamide acts in synergy with nonpolar amino acid side chains to reduce the microenvironment polarity and increase protein stability by more than 14 °C. Through favorable van der Waals and hydrogen bonding interactions, this single atom substitution significantly stabilizes proteins without altering the amino acid sequence and structure of the native protein.

Moonlighting Biochemistry of Cysteine Synthase: A Species-specific Global Regulator

Cysteine Synthase (CS), the enzyme that synthesizes cysteine, performs non-canonical regulatory roles by binding and modulating functions of disparate proteins. Beyond its role in catalysis and regulation in the cysteine biosynthesis pathway, it exerts its moonlighting effect by binding to few other proteins which possess a C-terminal "CS-binding motif", ending with a terminal ILE. Therefore, we hypothesized that CS might regulate many other disparate proteins with the "CS-binding motif". In this study, we developed an iterative sequence matching method for mapping moonlighting biochemistry of CS and validated our prediction by analytical and structural approaches. Using a minimal protein-peptide interaction system, we show that five previously unknown CS-binder proteins that participate in diverse metabolic processes interact with CS in a species-specific manner. Furthermore, results show that signatures of protein-protein interactions, including thermodynamic, competitive-inhibition, and structural features, highly match the known CS-Binder, serine acetyltransferase (SAT). Together, the results presented in this study allow us to map the extreme multifunctional space (EMS) of CS and reveal the biochemistry of moonlighting space, a subset of EMS. We believe that the integrated computational and experimental workflow developed here could be further modified and extended to study protein-specific moonlighting properties of multifunctional proteins.

Rh(III)-Catalyzed Oxidative C-2 Coupling of N-Pyridinylindoles with Benzo[b]thiophene 1,1-Dioxides via C-H Bond Activation

An efficient Rh(III)-catalyzed cross-dehydrogenative coupling of N-pyridinylindoles with benzo[b]thiophene 1,1-dioxides has been developed through directing-group-assisted C-H activation. This transformation constructs a new C-C bond from two inert C-H bonds in a one-pot reaction. The present reaction is compatible with various functional groups with respect to indoles and benzothiophene[b] 1,1-dioxides. Furthermore, the emission properties of synthesized compounds have been explored.

Molecular mechanism of selective substrate engagement and inhibitor disengagement of cysteine synthase

O-acetyl serine sulfhydrylase (OASS), referred to as cysteine synthase (CS), synthesizes cysteine from O-acetyl serine (OAS) and sulfur in bacteria and plants. The inherent challenge for CS is to overcome 4 to 6 log-folds stronger affinity for its natural inhibitor, serine acetyltransferase (SAT), as compared with its affinity for substrate, OAS. Our recent study showed that CS employs a novel competitive-allosteric mechanism to selectively recruit its substrate in the presence of natural inhibitor. In this study, we trace the molecular features that control selective substrate recruitment. To generalize our findings, we used CS from three different bacteria (Haemophilus, Salmonella, and Mycobacterium) as our model systems and analyzed structural and substrate-binding features of wild-type CS and its ∼13 mutants. Results show that CS uses a noncatalytic residue, M120, located 20 Å away from the reaction center, to discriminate in favor of substrate. M120A and background mutants display significantly reduced substrate binding, catalytic efficiency, and inhibitor binding. Results shows that M120 favors the substrate binding by selectively enhancing the affinity for the substrate and disengaging the inhibitor by 20 to 286 and 5- to 3-folds, respectively. Together, M120 confers a net discriminative force in favor of substrate by 100- to 858-folds.

Catalyst-free 1,6-conjugate addition of indoles and 4-hydroxycoumarins to para-quinone methides: synthesis of unsymmetrical triarylmethanes

The catalyst-free 1,6-conjugate addition of indoles and 4-hydroxycoumarins to para-quinone methides is reported. This protocol allowed us to access a range of unsymmetrical triarylmethanes in good to excellent yields. The outlined procedure is operationally simple, efficient, atom and step economical. The synthesized heterocyclic triarylmethanes were further converted into highly substituted indoloisoquinolines and pyranochromenones via metal-catalyzed C-H activation/annulation.

Magnetically recyclable CoFe2O4/ZnO nanocatalysts for the efficient catalytic degradation of Acid Blue 113 under ambient conditions

CoFe₂O₄/ZnO magnetic nanocatalysts were synthesized using a low-frequency ultrasound-assisted technique to enhance the optical, morphological, magnetic and catalytic properties of ZnO. The as-synthesized nanocatalysts were characterized by XRD, Raman, TEM, DR-UV-Vis and VSM analyses in order to confirm the expected modifications of the resulting nanocatalysts. The Raman spectral analysis revealed substitutional Zn²⁺ in the CoFe₂O₄/ZnO nanocatalyst. The as-synthesized material was tested for its catalytic activity in the degradation of Acid Blue (AB113), a known textile pollutant. The CoFe₂O₄ and CoFe₂O₄/ZnO nanocatalysts revealed the efficient catalytic degradation of AB113 in ambient conditions. The nanocatalyst dosage and the initial concentration of AB113 were varied by fixing one parameter as constant in order to determine the maximum catalytic efficiency with the minimum catalyst loading for AB113 degradation. The CoFe₂O₄/ZnO nanocatalyst demonstrated 10-fold enhanced mineralization of AB113 compared to the individual bare nanocatalysts, which could be achieved within 3 hours of catalytic degradation of AB113. The magnetic CoFe₂O₄/ZnO nanocatalyst was found to be stable for six consecutive recycles of AB113 degradation, which indicates that the catalytic efficiency of the nanocatalyst was retained after various numbers of cycles.

CoFe₂O₄/ZnO magnetic nanocatalysts were synthesized using a low-frequency ultrasound-assisted technique to enhance the optical, morphological, magnetic and catalytic properties of ZnO.

Impact of glycaemic control on fracture risk in 5368 people with newly diagnosed Type 1 diabetes: a time-dependent analysis

AIMS

To assess whether glycaemic control is associated with a lifelong increased risk of fracture in people with newly diagnosed Type 1 diabetes.

METHODS

People with newly diagnosed Type 1 diabetes between 1 January 1995 and 10 May 2016 were identified in The Health Improvement Network database. Longitudinal HbA_1c measurements from diagnosis to fracture or study end or loss to follow-up were collected. A Cox proportional hazards model with HbA_1c included as a time-dependent variable was fitted to these data.

RESULTS

Some 5368 people with newly diagnosed Type 1 diabetes were included. The estimated adjusted hazard ratio (aHR) for HbA_1c was statistically significant [aHR 1.007; 95% confidence interval (CI) 1.002-1.011 (mmol/mol) and aHR 1.07; 95% CI 1.03-1.12 (%)]. An incremental higher risk of fracture was observed with increasing levels of HbA_1c .

CONCLUSIONS

In people with newly diagnosed Type 1 diabetes, higher HbA_1c is associated with an increased risk for fractures.

Substrate-Induced Facilitated Dissociation of the Competitive Inhibitor from the Active Site of O-Acetyl Serine Sulfhydrylase Reveals a Competitive-Allostery Mechanism

By classical competitive antagonism, a substrate and competitive inhibitor must bind mutually exclusively to the active site. The competitive inhibition of O-acetyl serine sulfhydrylase (OASS) by the C-terminus of serine acetyltransferase (SAT) presents a paradox, because the C-terminus of SAT binds to the active site of OASS with an affinity that is 4-6 log-fold (10⁴-10⁶) greater than that of the substrate. Therefore, we employed multiple approaches to understand how the substrate gains access to the OASS active site under physiological conditions. Single-molecule and ensemble approaches showed that the active site-bound high-affinity competitive inhibitor is actively dissociated by the substrate, which is not consistent with classical views of competitive antagonism. We employed fast-flow kinetic approaches to demonstrate that substrate-mediated dissociation of full length SAT-OASS (cysteine regulatory complex) follows a noncanonical "facilitated dissociation" mechanism. To understand the mechanism by which the substrate induces inhibitor dissociation, we resolved the crystal structures of enzyme·inhibitor·substrate ternary complexes. Crystal structures reveal a competitive allosteric binding mechanism in which the substrate intrudes into the inhibitor-bound active site and disengages the inhibitor before occupying the site vacated by the inhibitor. In summary, here we reveal a new type of competitive allosteric binding mechanism by which one of the competitive antagonists facilitates the dissociation of the other. Together, our results indicate that "competitive allostery" is the general feature of noncanonical "facilitated/accelerated dissociation" mechanisms. Further understanding of the mechanistic framework of "competitive allosteric" mechanism may allow us to design a new family of "competitive allosteric drugs/small molecules" that will have improved selectivity and specificity as compared to their competitive and allosteric counterparts.

Structural and biochemical characterization of ligand recognition by CysB, the master regulator of sulfate metabolism

CysB, a member of LysR-type transcriptional regulators, up-regulates the expression of genes associated with sulfate metabolism and cysteine biosynthesis. CysB is activated under sulfur limiting conditions by O-acetylserine (OAS) and N-acetylserine (NAS), but the activation mechanism of CysB remain unknown. Here, we report four crystal structures of ligand binding domains of CysB (CysB-LBD) in apo form and in complex with sulfate, OAS, and NAS. Our results show that CysB has two distinct allosteric ligand binding sites; a sulfate and NAS specific site-1 and a second, NAS and OAS specific site-2. All three ligands bind through the induced-fit mechanism. Surprisingly, OAS remodels the site-1 by binding to site-2, suggesting that site-1 and site-2 are coupled allosterically. Using DNA binding and site-directed mutagenesis approach, we show that OAS enhances NAS mediated activation and mutation at site-1 has no effect on site-2 mediated OAS activation. Results indicate that inducer binding triggered signals from OAS-Specific site-2 are relayed to DBD through site-1. Together, results presented here suggest that induced-fit binding and allosteric coupling between two ligand binding sites and DBD underlie the key feature of CysB activation. Further, this study provides first structural glimpse into recognition of inducer ligands by CysB and provides a general framework to understand how LTTR family regulators respond to dual activators.

Radiofrequency-Assisted Body Piercing

The art of body piercing is ancient; however, nowadays it has evolved into a fashion statement. In the Indian subcontinent, ear and nose piercing hold religious and cultural significance in addition to being done for aesthetic reasons. Body piercing is routinely performed by railroading technique or by piercing guns; many modifications of the technique have emerged. Irrespective of the technique used, the main complications associated are intraoperative bleeding and postoperative infection. To overcome these problems, we describe a novel and simple technique of ear and nose piercing using the radio frequency cautery.

PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues

Background

In the past, many methods have been developed for peptide tertiary structure prediction but they are limited to peptides having natural amino acids. This study describes a method PEPstrMOD, which is an updated version of PEPstr, developed specifically for predicting the structure of peptides containing natural and non-natural/modified residues.

Results

PEPstrMOD integrates Forcefield_NCAA and Forcefield_PTM force field libraries to handle 147 non-natural residues and 32 types of post-translational modifications respectively by performing molecular dynamics using AMBER. AMBER was also used to handle other modifications like peptide cyclization, use of D-amino acids and capping of terminal residues. In addition, GROMACS was used to implement 210 non-natural side-chains in peptides using SwissSideChain force field library. We evaluated the performance of PEPstrMOD on three datasets generated from Protein Data Bank; i) ModPep dataset contains 501 non-natural peptides, ii) ModPep16, a subset of ModPep, and iii) CyclicPep contains 34 cyclic peptides. We achieved backbone Root Mean Square Deviation between the actual and predicted structure of peptides in the range of 3.81–4.05 Å.

Conclusions

In summary, the method PEPstrMOD has been developed that predicts the structure of modified peptide from the sequence/structure given as input. We validated the PEPstrMOD application using a dataset of peptides having non-natural/modified residues. PEPstrMOD offers unique advantages that allow the users to predict the structures of peptides having i) natural residues, ii) non-naturally modified residues, iii) terminal modifications, iv) post-translational modifications, v) D-amino acids, and also allows extended simulation of predicted peptides. This will help the researchers to have prior structural information of modified peptides to further design the peptides for desired therapeutic property. PEPstrMOD is freely available at http://osddlinux.osdd.net/raghava/pepstrmod/.

Reviewers

This article was reviewed by Prof Michael Gromiha, Dr. Bojan Zagrovic and Dr. Zoltan Gaspari.

Electronic supplementary material

The online version of this article (doi:10.1186/s13062-015-0103-4) contains supplementary material, which is available to authorized users.

Molecular basis of peptide recognition in metallopeptidase Dug1p from Saccharomyces cerevisiae

Dug1p, a M20 family metallopeptidase and human orthologue of carnosinase, hydrolyzes Cys-Gly dipeptide, the last step of glutathione (GSH) degradation in Saccharomyces cerevisiae. Molecular bases of peptide recognition by Dug1p and other M20 family peptidases remain unclear in the absence of structural information about enzyme-peptide complexes. We report the crystal structure of Dug1p at 2.55 Å resolution in complex with a Gly-Cys dipeptide and two Zn(2+) ions. The dipeptide is trapped in the tunnel-like active site; its C-terminus is held by residues at the S1' binding pocket, whereas the S1 pocket coordinates Zn(2+) ions and the N-terminus of the peptide. Superposition with the carnosinase structure shows that peptide mimics the inhibitor bestatin, but active site features are altered upon peptide binding. The space occupied by the N-terminus of bestatin is left unoccupied in the Dug1p structure, suggesting that tripeptides could bind. Modeling of tripeptides into the Dug1p active site showed tripeptides fit well. Guided by the structure and modeling, we examined the ability of Dug1p to hydrolyze tripeptides, and results show that Dug1p hydrolyzes tripeptides selectively. Point mutations of catalytic residues do not abolish the peptide binding but abolish the hydrolytic activity, suggesting a noncooperative mode in peptide recognition. In summary, results reveal that peptides are recognized primarily through their amino and carboxyl termini, but hydrolysis depends on the properties of peptide substrates, dictated by their respective sequences. Structural similarity between the Dug1p-peptide complex and the bestatin-bound complex of CN2 suggests that the Dug1p-peptide structure can be used as a template for designing natural peptide inhibitors.

Seasonal changes in selected immune response of Mystus gulio and Mystus vittatus

Estuaries are considered as highly potential area for that including feeding, spawning and nursery rearing of most of the finfishes and shellfishes. In the present investigation, two species of catfish (M. gulio and M. vittatus) were selected to study the impact of season on their immune organs (kidney and spleen) and selected immune response from Vellar estuary. The physico-chemical parameters (pH, temperature, salinity and rainfall) were measured during the sampling period 2009-10. The non-specific immune parameters (WBC count, lysozyme activity and NBT assay) were analyzed. The immune organs (head-kidney and spleen) variation was also observed by histological studies. Our results stated that the WBCs count of M. gulio and M. vittatus increased during summer (10.3 and 10.1 x 10(6) ml(-1)) season and decreased in monsoon (6.8 and 7.0 x 10(6) ml(-1)). In contrast, lysozyme activity was highest in post monsoon (1540 and 1525 U min(-1) ml(-1)) and lowest in summer (1000 and 960 U min(-1) ml(-1)). The activity of NBT was highest in monsoon (0.68 and 0.65 at 540 nm) and lowest in summer (0.012 and 0.2 at 540 nm). The histological observation implies that the cell variations were different in respect to different seasons.

Co-factor binding confers substrate specificity to xylose reductase from Debaryomyces hansenii

Binding of substrates into the active site, often through complementarity of shapes and charges, is central to the specificity of an enzyme. In many cases, substrate binding induces conformational changes in the active site, promoting specific interactions between them. In contrast, non-substrates either fail to bind or do not induce the requisite conformational changes upon binding and thus no catalysis occurs. In principle, both lock and key and induced-fit binding can provide specific interactions between the substrate and the enzyme. In this study, we present an interesting case where cofactor binding pre-tunes the active site geometry to recognize only the cognate substrates. We illustrate this principle by studying the substrate binding and kinetic properties of Xylose Reductase from Debaryomyces hansenii (DhXR), an AKR family enzyme which catalyzes the reduction of carbonyl substrates using NADPH as co-factor. DhXR reduces D-xylose with increased specificity and shows no activity towards "non-substrate" sugars like L-rhamnose. Interestingly, apo-DhXR binds to D-xylose and L-rhamnose with similar affinity (K(d)∼5.0-10.0 mM). Crystal structure of apo-DhXR-rhamnose complex shows that L-rhamnose is bound to the active site cavity. L-rhamnose does not bind to holo-DhXR complex and thus, it cannot competitively inhibit D-xylose binding and catalysis even at 4-5 fold molar excess. Comparison of K(d) values with K(m) values reveals that increased specificity for D-xylose is achieved at the cost of moderately reduced affinity. The present work reveals a latent regulatory role for cofactor binding which was previously unknown and suggests that cofactor induced conformational changes may increase the complimentarity between D-xylose and active site similar to specificity achieved through induced-fit mechanism.

Mass spectrometry assay for studying kinetic properties of dipeptidases: characterization of human and yeast dipeptidases

Chemical modifications of substrate peptides are often necessary to monitor the hydrolysis of small bioactive peptides. We developed an electrospray ionization mass spectrometry (ESI-MS) assay for studying substrate distributions in reaction mixtures and determined steady-state kinetic parameters, the Michaelis-Menten constant (K(m)), and catalytic turnover rate (V(max)/[E](t)) for three metallodipeptidases: two carnosinases (CN1 and CN2) from human and Dug1p from yeast. The turnover rate (V(max)/[E](t)) of CN1 and CN2 determined at pH 8.0 (112.3 and 19.5s(-1), respectively) suggested that CN1 is approximately 6-fold more efficient. The turnover rate of Dug1p for Cys-Gly dipeptide at pH 8.0 was found to be slightly lower (73.8s(-1)). In addition, we determined kinetic parameters of CN2 at pH 9.2 and found that the turnover rate was increased by 4-fold with no significant change in the K(m). Kinetic parameters obtained by the ESI-MS method are consistent with results of a reverse-phase high-performance liquid chromatography (RP-HPLC)-based assay. Furthermore, we used tandem MS (MS/MS) analyses to characterize carnosine and measured its levels in CHO cell lines in a time-dependent manner. The ESI-MS method developed here obviates the need for substrate modification and provides a less laborious, accurate, and rapid assay for studying kinetic properties of dipeptidases in vitro as well as in vivo.