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1.
J Mol Model ; 30(3): 91, 2024 Mar 01.
Article in English | MEDLINE | ID: mdl-38427116

ABSTRACT

CONTEXT: La2Mo2O9 is a potential electrolyte material for SOFC due to its higher oxygen conduction at high temperatures. However, La2Mo2O9 suffers from detrimental phase transition at high temperature from monoclinic α to cubic ß phase. This phase transition can be prevented by lowering the temperature. However, lowering the temperature reduces the ionic conductivity. Substitution of transition metal on Mo site is the best strategy for the suppression of phase transition. In the present work, the effect of substituting element on different sites has been investigated. From the result, it is observed that the band gap increases with concentration of Er. METHOD: For the assessment of mechanism behind the improved performance, the atomic insight is crucial. For that, we have employed ab initio DFT calculation. We have used PBE and grimme d3 dispersion correction for the accuracy of evaluated band gap and electrochemical stability. All DFT calculations have been performed using Quantum ESPRESSO pwscf code's and for the assessment of thermodynamical stability of La2Mo2O9 and the doped structures, an alternative descriptor, the global instability index (GII), which is based on the bond valance sum approach implemented in SoftBV was used. All the visualizations were done by XCrySDen and VESTA open source software.

2.
Mini Rev Med Chem ; 2024 Feb 23.
Article in English | MEDLINE | ID: mdl-38409693

ABSTRACT

BACKGROUND: Nigella sativa L. has been widely used in the Unani, Ayurveda, Chinese, and Arabic medicine systems and has a long history of medicinal and folk uses. Several phytoconstituents of the plant are reported to have excellent therapeutic properties. In-vitro and in-vivo studies have revealed that seed oil and thymoquinone have excellent inhibitory efficacy on a wide range of both pathogenic and non-pathogenic fungi. OBJECTIVE: The present review aims to undertake a comprehensive and systematic evaluation of the antifungal effects of different phytochemical constituents of black cumin. METHOD: An exhaustive database retrieval was conducted on PubMed, Scopus, ISI Web of Science, SciFinder, Google Scholar, and CABI to collect scientific information about the antifungal activity of N. sativa L. with 1990 to 2023 as a reference range using 'Nigella sativa,' 'Nigella oil,' 'antifungal uses,' 'dermatophytic fungi,' 'candidiasis,' 'anti-aflatoxin,' 'anti-biofilm' and 'biological activity' as the keywords. RESULTS: Black cumin seeds, as well as the extract of aerial parts, were found to exhibit strong antifungal activity against a wide range of fungi. Among the active compounds, thymoquinone exhibited the most potent antifungal effect. Several recent studies proved that black cumin inhibits biofilm formation and growth. CONCLUSION: The review provides an in-depth analysis of the antifungal activity of black cumin. This work emphasizes the need to expand studies on this plant to exploit its antifungal properties for biomedical applications.

3.
Food Chem X ; 20: 100910, 2023 Dec 30.
Article in English | MEDLINE | ID: mdl-38144773

ABSTRACT

Importance of nanotechnology may be seen by penetration of its application in diverse areas including the food sector. With investigations and advancements in nanotechnology, based on feedback from these diverse areas, ease, and efficacy are also increasing. The food sector may use nanotechnology to encapsulate smart foods for increased health, wellness, illness prevention, and effective targeted delivery. Such nanoencapsulated targeted delivery systems may further add to the economic and nutritional properties of smart foods like stability, solubility, effectiveness, safeguard against disintegration, permeability, and bioavailability of smart/bioactive substances. But in the way of application, the fabrication of nanomaterials/nanostructures has several challenges which range from figuring out the optimal technique for obtaining them to determining the most suitable form of nanostructure for a bioactive molecule of interest. This review precisely addresses concepts, recent advances in fabrication techniques as well as current challenges/glitches of nanoencapsulation with special reference to smart foods/bioactive components. Since dealing with food materials also raises the quest for safety and regulatory norms a brief overview of the safety and regulatory aspects of nanomaterials/nanoencapsulation is also presented.

4.
Front Plant Sci ; 14: 1238870, 2023.
Article in English | MEDLINE | ID: mdl-37719210

ABSTRACT

Introduction: This study explored the molecular characterization of 14 eggplant (brinjal) genotypes to evaluate their genetic diversity and the impact of heterosis. As eggplant is a vital horticultural crop with substantial economic and nutritional value, a comprehensive understanding of its genetic makeup and heterosis effects is essential for effective breeding strategies. Our aim was not only to dissect the genetic diversity among these genotypes but also to determine how genetic distance impacts heterotic patterns, which could ultimately help improve hybrid breeding programs. Methods: Genetic diversity was assessed using 20 SSR markers, and the parental lines were grouped into five clusters based on the Unweighted Pair Group Method of Arithmetic Means (UPGMA). Heterosis was examined through yield and yield-related traits among parents and hybrids. Results: Polymorphisms were detected in eight out of the twenty SSR markers across the parental lines. Notably, a high genetic distance was observed between some parents. The analysis of yield and yield-related traits demonstrated significant heterosis over mid, superior, and standard parents, particularly in fruit yield per plant. Two crosses (RKML-26 X PPC and RKML1 X PPC) displayed substantial heterosis over mid and better parents, respectively. However, the positive correlation between genetic distance and heterosis was only up to a certain threshold; moderate genetic distance often resulted in higher heterosis compared to very high genetic distance. Discussion: These findings emphasize the critical role of parental selection in hybrid breeding programs. The results contribute to the understanding of the relationship between genetic distance and heterosis, and it is suggested that future research should delve into the genetic mechanisms that drive heterosis and the effect of genetic distance variance on heterosis. The insights drawn from this study can be harnessed to enhance crop yield and economic value in breeding programs.

5.
JNMA J Nepal Med Assoc ; 61(262): 522-525, 2023 Jun 01.
Article in English | MEDLINE | ID: mdl-37464859

ABSTRACT

Introduction: Ageing predisposes to increased risk of infections which make these population vulnerable to high risk of various chronic co-morbidities, organ dysfunction and mortality. Increased frequency of infections has led to an increasing proportion of geriatric patient admission to hospitals, and antibiotics therapy has long been recognized as a cornerstone in the treatment of infections. The aim of this study was to find out the prevalence of antibiotic use among geriatric patients admitted to the Department of Medicine in a tertiary care centre. Methods: A descriptive cross-sectional study was conducted among geriatric patients admitted to Department of Medicine in a tertiary care centre from 1 May 2022 to 31 August 2022. Ethical approval was obtained from the Institutional Review Committee (Reference number: 17/22). Patients with the age of ≥60 years, admitted to the Department of Medicine who stayed for at least 24 hours was included as the study population. Convenience sampling method was used. Point estimate and 95% Confidence Interval were calculated. Results: Among 520 geriatric patients, antibiotics was used in 252 (48.46%) (44.16-52.76, 95% Confidence Interval) patients. Ceftriaxone was the most common antibiotic used in 165 (65.48%) patients, followed by oral azithromycin in 72 (28.57%). The mean antibiotics used per patient was 1.59±0.73. Conclusions: The prevalence of antibiotic use in the geriatric population was found to be lower than in the other studies done in similar settings. Keywords: aged; antibiotics; drug utilization.


Subject(s)
Anti-Bacterial Agents , Hospitalization , Humans , Aged , Middle Aged , Anti-Bacterial Agents/therapeutic use , Tertiary Care Centers , Cross-Sectional Studies , Ceftriaxone
6.
Photochem Photobiol ; 97(6): 1498-1506, 2021 11.
Article in English | MEDLINE | ID: mdl-34097757

ABSTRACT

An efficient photocatalytic regeneration of nicotinamide adenine dinucleotide (NADH) and nicotinamide adenine dinucleotide phosphate (NADPH) has been carried out by two-electron reduction and protonation of NAD+ /NADP+ , induced by photons in the visible light region. This functional artificial photosynthetic counterpart of the complete energy-trapping occurring in natural photosystem I (PS I) is achieved with nitrogen-enrich graphene quantum dot (N-EGQD) as the light-harvesting photocatalyst. In buffer aqueous solution, this compound photo catalytically recycles a rhodium hydride complex of the type [Cp*Rh(bpy)H]+ (Cp* = pentamethylcyclopentadienyl, bpy = 2,2'-bipyridine) which can mediate hydride transfer processes leading to nucleotide co-factor reduction. Very promising yields of 73.31%/78.45% of NADH/NADPH with the excellent thermal stability of N-EGQD photocatalyst is observed. Thus, in this work, an efficient light-harvesting photocatalyst is synthesized for the regeneration of nicotinamide cofactor that has pharmaceuticals application.


Subject(s)
Graphite , Quantum Dots , NAD/chemistry , NADP/chemistry , Oxidation-Reduction
7.
J Med Virol ; 93(1): 275-299, 2021 01.
Article in English | MEDLINE | ID: mdl-32617987

ABSTRACT

There have been over seven million cases and almost 413 372 deaths globally due to the novel coronavirus (2019-nCoV) associated disease COVID-19, as of 11 June 2020. Phylogenetic analysis suggests that there is a common source for these infections. The overall sequence similarities between the spike protein of 2019-nCoV and that of SARS-CoV are known to be around 76% to 78% and 73% to 76% for the whole protein and receptor-binding domain (RBD), respectively. Thus, they have the potential to serve as the drug and/or vaccine candidate. However, the individual response against 2019-nCoV differs due to genetic variations in the human population. Understanding the variations in angiotensin-converting enzyme 2 (ACE2) and human leukocyte antigen (HLA) that may affect the severity of 2019-nCoV infection could help in identifying individuals at a higher risk from the COVID-19. A number of potential drugs/vaccines as well as antibody/cytokine-based therapeutics are in various developmental stages of preclinical/clinical trials against SARS-CoV, MERS-CoV, and 2019-nCoV with substantial cross-reactivity, and may be used against COVID-19. For diagnosis, the reverse-transcription polymerase chain reaction is the gold standard test for initial diagnosis of COVID-19. A kit based on serological tests are also recommended for investigating the spread of COVID-19 but this is challenging due to the antibodies cross-reactivity. This review comprehensively summarizes the recent reports available regarding the host-pathogen interaction, morphological and genomic structure of the virus, and the diagnostic techniques as well as the available potential therapeutics against COVID-19.


Subject(s)
COVID-19/diagnosis , COVID-19/physiopathology , COVID-19/therapy , Host-Pathogen Interactions , SARS-CoV-2/genetics , Animals , Antibodies, Viral/immunology , Chiroptera/virology , Cross Reactions , Humans , Phylogeny , Receptors, Virus/chemistry , SARS-CoV-2/drug effects , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics
8.
Int J Biol Macromol ; 158: 159-179, 2020 Sep 01.
Article in English | MEDLINE | ID: mdl-32360460

ABSTRACT

Human malaria is a pathogenic disease mainly caused by Plasmodium falciparum, which was responsible for about 405,000 deaths globally in the year 2018. To date, several vaccine candidates have been evaluated for prevention, which failed to produce optimal output at various preclinical/clinical stages. This study is based on designing of polypeptide vaccines (PVs) against human malaria that cover almost all stages of life-cycle of Plasmodium and for the same 5 genome derived predicted antigenic proteins (GDPAP) have been used. For the development of a multi-immune inducer, 15 PVs were initially designed using T-cell epitope ensemble, which covered >99% human population as well as linear B-cell epitopes with or without adjuvants. The immune simulation of PVs showed higher levels of T-cell and B-cell activities compared to positive and negative vaccine controls. Furthermore, in silico cloning of PVs and codon optimization followed by enhanced expression within Lactococcus lactis host system was also explored. Although, the study has sound theoretical and in silico findings, the in vitro/in vivo evaluation seems imperative to warrant the immunogenicity and safety of PVs towards management of P. falciparum infection in the future.


Subject(s)
Epitopes/chemistry , Malaria Vaccines/chemistry , Molecular Docking Simulation , Plasmodium falciparum/immunology , Administration, Oral , Antibody Affinity , Binding Sites, Antibody , Epitopes/immunology , Humans , Immunogenicity, Vaccine , Malaria Vaccines/administration & dosage , Malaria Vaccines/immunology , Vaccines, Subunit/administration & dosage , Vaccines, Subunit/chemistry , Vaccines, Subunit/immunology
9.
Physiol Mol Biol Plants ; 24(6): 1209-1219, 2018 Nov.
Article in English | MEDLINE | ID: mdl-30425435

ABSTRACT

The Nigella sativa pharmacological properties are mainly ascribed to its volatile oil, of which thymoquinone is an important bioactive component. Surprisingly, till date, no standard formulation or thymoquinone rich N. sativa extract is under clinical use probably due to its poor extraction and lesser stability in the already used solvents. In the present investigation solubility, extraction, percent composition and total antioxidant activity from the seeds of N. sativa was explored using five solvents. An HPLC method was standardized in an isocratic system (C-18 column, flow rate of 1.0 ml/min, mobile phase-water:methanol: 30:70, detection wavelength-254 nm, retention time-8.77 min) for quantification of thymoquinone. To further confirm the presence of thymoquinone in the respective extracts absorbance spectra analysis has been carried out and compared with pure thymoquinone. Additionally total antioxidant activity of Nigella sativa extracts has been evaluated using ascorbic acid as standard. Our results showed maximum percentage yield in aqueous extract while methanol having the least yield and the ethanol, benzene and hexane extracts exhibited moderate yields. A linear standard calibration curve of thymoquinone showed R2 as 0.999 and % RSD as 7.166. The HPLC analysis revealed maximum percentage composition of thymoquinone in the benzene extract, whereas in the hexane and methanol extracts the content was less. Aqueous and ethanol extracts displayed insignificant thymoquinone content. Absorbance spectra analysis confirms the presence of thymoquinone peak in the benzene, hexane and methanol extracts while aqueous and ethanol extracts showed minimal absorbance. Maximum total antioxidant activity was observed in the aqueous extract while minimum was observed in the methanolic extract. Weak positive (+ 0.3676) correlation was established between percent composition of thymoquinone and antioxidant activity among different extracts indicating that thymoquinone may not be the only factor for antioxidant activity, but other phytochemicals might also contribute. However, we for the first time demonstrated that the benzene extract of N. sativa has better solubility and percent composition of thymoquinone as compared to other solvents. It can be concluded that the solubility, differential composition of bioactive components among these extracts may have diverse effects on the total antiradical activity. Thus, our study provides insights on optimization and standardization of bioactive rich formulation of N. sativa.

10.
Mitochondrial DNA A DNA Mapp Seq Anal ; 28(3): 442-450, 2017 05.
Article in English | MEDLINE | ID: mdl-27159686

ABSTRACT

Documentation of genetic differentiation among the populations of a species can provide useful information that has roles in conservation, breeding, and management plans. In the present study, we examined the genetic structure and phylogenetic relationships among the 149 individuals of Ompok bimaculatus belonging to 24 populations, collected from Indian waters, using cytochrome b gene. The combined analyses of data suggested that the Indian O. bimaculatus consist of three distinct mtDNA lineages with star-like haplotypes network, which exhibited high genetic variation and haplotypic diversity. Analysis of molecular variance indicated that most of the observed genetic variation was found among the populations suggesting restricted gene flow. Long-term interruption of gene flow was also evidenced by high overall Fst values (0.82367) that could be favored by the discontinuous distributions of the lineages.


Subject(s)
Catfishes/genetics , Genetic Variation , Phylogeny , Animals , Cytochromes b/genetics , Haplotypes , Phylogeography , Sequence Analysis, DNA
11.
ACS Chem Biol ; 11(7): 1805-9, 2016 07 15.
Article in English | MEDLINE | ID: mdl-27191252

ABSTRACT

Site-specific PEGylation is an important strategy for enhancing the pharmacokinetic properties of protein drugs, and has been enabled by the recent development of many chemoselective reactions for protein side-chain modification. However, the impact of these different conjugation strategies on the properties of PEG-protein conjugates is poorly understood. Here we show that the ability of PEG to enhance protein conformational stability depends strongly on the identity of the PEG-protein linker, with the most stabilizing linkers involving conjugation of PEG to planar polar groups near the peptide backbone. We also find that branched PEGs provide superior stabilization relative to their linear counterparts, suggesting additional applications for branched PEGs in protein stabilization.


Subject(s)
Polyethylene Glycols/chemistry , Proteins/chemistry , Circular Dichroism , Protein Conformation , Protein Stability
12.
Biotechnol Appl Biochem ; 63(1): 125-37, 2016.
Article in English | MEDLINE | ID: mdl-25594242

ABSTRACT

Topoisomerases (Topo I and II) have been looked as crucial targets against various types of cancers. In the present paper, 100 anticancerous alkaloids were subjected to in silico absorption, distribution, metabolism, excretion, and toxicity (ADMET) analyses to investigate their pharmacokinetic properties. Out of 100 alkaloids, only 18 were found to fulfill all the ADMET descriptors and obeyed the Lipinski's rule of five. All the 18 alkaloids were found to dock successfully within the active site of both Topo I and II. A comparison of the inhibitory potential of 18 screened alkaloids with those of selected drugs revealed that four alkaloids (oliveroline, coptisine, aristolactam, and piperine) inhibited Topo I, whereas six alkaloids (oliveroline, aristolactam, anonaine, piperine, coptisine, and liriodenine) inhibited Topo II more strongly than those of their corresponding drugs, topotecan and etoposide, respectively, with oliveroline being the outstanding. The stability of the complexes of Topo I and II with the best docked alkaloid, oliveroline, was further analyzed using 10 nSec molecular dynamics simulation and compared with those of the respective drugs, namely, topotecan and etoposide, which revealed stabilization of these complexes within 5 nSec of simulation with better stability of Topo II complex than that of Topo I.


Subject(s)
Alkaloids/chemistry , Alkaloids/pharmacology , Antineoplastic Agents/chemistry , Antineoplastic Agents/pharmacology , Topoisomerase Inhibitors/chemistry , Topoisomerase Inhibitors/pharmacology , Alkaloids/pharmacokinetics , Animals , Antineoplastic Agents/pharmacokinetics , Blood-Brain Barrier/metabolism , DNA Topoisomerases, Type I/metabolism , Humans , Intestinal Absorption , Molecular Docking Simulation , Molecular Dynamics Simulation , Neoplasms/drug therapy , Neoplasms/metabolism , Topoisomerase Inhibitors/pharmacokinetics
13.
J Am Chem Soc ; 136(50): 17547-60, 2014 Dec 17.
Article in English | MEDLINE | ID: mdl-25409346

ABSTRACT

PEGylation of protein side chains has been used for more than 30 years to enhance the pharmacokinetic properties of protein drugs. However, there are no structure- or sequence-based guidelines for selecting sites that provide optimal PEG-based pharmacokinetic enhancement with minimal losses to biological activity. We hypothesize that globally optimal PEGylation sites are characterized by the ability of the PEG oligomer to increase protein conformational stability; however, the current understanding of how PEG influences the conformational stability of proteins is incomplete. Here we use the WW domain of the human protein Pin 1 (WW) as a model system to probe the impact of PEG on protein conformational stability. Using a combination of experimental and theoretical approaches, we develop a structure-based method for predicting which sites within WW are most likely to experience PEG-based stabilization, and we show that this method correctly predicts the location of a stabilizing PEGylation site within the chicken Src SH3 domain. PEG-based stabilization in WW is associated with enhanced resistance to proteolysis, is entropic in origin, and likely involves disruption by PEG of the network of hydrogen-bound solvent molecules that surround the protein. Our results highlight the possibility of using modern site-specific PEGylation techniques to install PEG oligomers at predetermined locations where PEG will provide optimal increases in conformational and proteolytic stability.


Subject(s)
Polyethylene Glycols/chemistry , Protein Stability , Proteins/chemistry , Amino Acid Sequence , Binding Sites , Molecular Sequence Data , Protein Conformation , Thermodynamics
14.
Biomacromolecules ; 15(12): 4643-7, 2014 Dec 08.
Article in English | MEDLINE | ID: mdl-25387132

ABSTRACT

PEGylation is an important strategy for enhancing the pharmacokinetic properties of protein drugs. Modern chemoselective reactions now enable specific placement of a single PEG at any site on a protein surface. However, few rational structure-based guidelines exist for selecting optimal PEGylation sites. Here, we explore the impact of PEGylation on the conformational stability of α-helices using an α-helical coiled coil as a model system. We find that maleimide-based PEGylation of a solvent-exposed i position Cys can stabilize coiled-coil quaternary structure when Lys residues occupy both the i + 3 and i + 4 positions, due to favorable interactions between the PEG-maleimide and the Lys residues. Applying this Cys(i)-Lys(i+3)-Lys(i+4) triad to a solvent-exposed position within the C-terminal helix of the villin headpiece domain leads to similar PEG-based increases in conformational stability, highlighting the possibility of using the Cys(i)-Lys(i+3)-Lys(i+4) triad as a general strategy for PEG-based stabilization of helical proteins.


Subject(s)
Cysteine/chemistry , Lysine/chemistry , Polyethylene Glycols/chemistry , Proteins/chemistry , Amino Acid Sequence , Molecular Sequence Data , Protein Structure, Secondary
15.
Appl Biochem Biotechnol ; 172(7): 3414-23, 2014 Apr.
Article in English | MEDLINE | ID: mdl-24532464

ABSTRACT

A cinnamyl alcohol dehydrogenase (CAD) from the secondary xylem of Leucaena leucocephala has been purified to homogeneity through successive steps of ammonium sulfate fractionation, DEAE cellulose, Sephadex G-75, and Blue Sepharose CL-6B affinity column chromatographies. CAD was purified to 514.2 folds with overall recovery of 13 % and specific activity of 812. 5 nkat/mg. Native and subunit molecular masses of the purified enzyme were found to be ∼76 and ∼38 kDa, respectively, suggesting it to be a homodimer. The enzyme exhibited highest catalytic efficiency (Kcat/Km 3.75 µM(-1) s(-1)) with cinnamyl aldehyde among all the substrates investigated. The pH and temperature optima of the purified CAD were pH 8.8 and 40 °C, respectively. The enzyme activity was enhanced in the presence of 2.0 mM Mg(2+), while Zn(2+) at the same concentration exerted an inhibitory effect. The inclusion of 2.0 mM EDTA in the assay system activated the enzyme. The enzyme was inhibited with caffeic acid and ferulic acid in a concentration-dependent manner, while no inhibition was observed with salicylic acid. Peptide mass analysis of the purified CAD by MALDI-TOF showed a significant homology to alcohol dehydrogenases of MDR superfamily.


Subject(s)
Alcohol Oxidoreductases/chemistry , Alcohol Oxidoreductases/isolation & purification , Fabaceae/enzymology , Plant Proteins/chemistry , Zinc/metabolism , Alcohol Oxidoreductases/metabolism , Enzyme Stability , Fabaceae/chemistry , Hydrogen-Ion Concentration , Kinetics , Plant Proteins/isolation & purification , Plant Proteins/metabolism , Substrate Specificity , Temperature
16.
ACS Chem Biol ; 8(10): 2140-4, 2013 Oct 18.
Article in English | MEDLINE | ID: mdl-23937634

ABSTRACT

N-glycans play important roles in many cellular processes and can increase protein conformational stability in specific structural contexts. Glycosylation (with a single GlcNAc) of the reverse turn sequence Phe-Yyy-Asn-Xxx-Thr at Asn stabilizes the Pin 1 WW domain by -0.85 ± 0.12 kcal mol(-1). Alternative methods exist for attaching carbohydrates to proteins; some occur naturally (e.g., the O-linkage), whereas others use chemoselective ligation reactions to mimic the natural N- or O-linkages. Here, we assess the energetic consequences of replacing the Asn linkage in the glycosylated WW domain with a Gln linkage, with two natural O-linkages, with two unnatural triazole linkages, and with an unnatural α-mercaptoacetamide linkage. Of these alternatives, only glycosylation of the triazole linkages stabilizes WW, and by a smaller amount than N-glycosylation, highlighting the need for caution when using triazole- or α-mercaptoacetamide-linked carbohydrates to mimic native N-glycans, especially where the impact of glycosylation on protein conformational stability is important.


Subject(s)
Asparagine/chemistry , Proteins/chemistry , Circular Dichroism , Cytoplasmic Dyneins/chemistry , Glycosylation , Humans , Models, Molecular , Protein Folding , Protein Stability , Protein Structure, Tertiary , Thermodynamics
17.
Bioconjug Chem ; 24(5): 796-802, 2013 May 15.
Article in English | MEDLINE | ID: mdl-23578107

ABSTRACT

Protein PEGylation is an effective method for reducing the proteolytic susceptibility, aggregation propensity, and immunogenicity of protein drugs. These pharmacokinetic challenges are fundamentally related to protein conformational stability, and become much worse for proteins that populate the unfolded state under ambient conditions. If PEGylation consistently led to increased conformational stability, its beneficial pharmacokinetic effects could be extended and enhanced. However, the impact of PEGylation on protein conformational stability is currently unpredictable. Here we show that appending a short PEG oligomer to a single Asn side chain within a reverse turn in the WW domain of the human protein Pin 1 increases WW conformational stability in a manner that depends strongly on the length of the PEG oligomer: shorter oligomers increase folding rate, whereas longer oligomers increase folding rate and reduce unfolding rate. This strong length dependence is consistent with the possibility that the PEG oligomer stabilizes the transition and folded states of WW relative to the unfolded state by interacting favorably with side-chain or backbone groups on the WW surface.


Subject(s)
Peptidylprolyl Isomerase/chemistry , Polyethylene Glycols/chemistry , Protein Folding , Humans , Models, Molecular , NIMA-Interacting Peptidylprolyl Isomerase , Protein Conformation , Protein Stability , Protein Structure, Tertiary
18.
Protein Expr Purif ; 79(2): 197-203, 2011 Oct.
Article in English | MEDLINE | ID: mdl-21708267

ABSTRACT

A cDNA encoding cinnamyl alcohol dehydrogenase (CAD), catalyzing conversion of cinnamyl aldehydes to corresponding cinnamyl alcohols, was cloned from secondary xylem of Leucaena leucocephala. The cloned cDNA was expressed in Escherichia coli BL21 (DE3) pLysS cells. Temperature and Zn(2+) ion played crucial role in expression and activity of enzyme, such that, at 18°C and at 2 mM Zn(2+) the CAD was maximally expressed as active enzyme in soluble fraction. The expressed protein was purified 14.78-folds to homogeneity on Ni-NTA agarose column with specific activity of 346 nkat/mg protein. The purified enzyme exhibited lowest Km with cinnamyl alcohol (12.2 µM) followed by coniferyl (18.1 µM) and sinapyl alcohol (23.8 µM). Enzyme exhibited high substrate inhibition with cinnamyl (beyond 20 µM) and coniferyl (beyond 100 µM) alcohols. The in silico analysis of CAD protein exhibited four characteristic consensus sequences, GHEXXGXXXXXGXXV; C(100), C(103), C(106), C(114); GXGXXG and C(47), S(49), H(69), L(95), C(163), I(300) involved in catalytic Zn(2+) binding, structural Zn(2+) binding, NADP(+) binding and substrate binding, respectively. Tertiary structure, generated using Modeller 9v5, exhibited a trilobed structure with bulged out structural Zn(2+) binding domain. The catalytic Zn(2+) binding, substrate binding and NADP(+) binding domains formed a pocket protected by two major lobes. The enzyme catalysis, sequence homology and 3-D model, all supported that the cloned CAD belongs to alcohol dehydrogenase family of plants.


Subject(s)
Acacia/enzymology , Alcohol Oxidoreductases/isolation & purification , Phenols/metabolism , Plant Proteins/isolation & purification , Propanols/metabolism , Recombinant Proteins/isolation & purification , Xylem/enzymology , Acacia/chemistry , Alcohol Oxidoreductases/chemistry , Alcohol Oxidoreductases/genetics , Alcohol Oxidoreductases/metabolism , Amino Acid Sequence , Chromatography, Affinity , Cloning, Molecular , Electrophoresis, Polyacrylamide Gel , Escherichia coli , Hydrogen-Ion Concentration , Kinetics , Models, Molecular , Molecular Sequence Data , Plant Proteins/chemistry , Plant Proteins/genetics , Plant Proteins/metabolism , Plasmids , Protein Structure, Tertiary/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Substrate Specificity , Temperature , Transformation, Bacterial , Xylem/chemistry
19.
Biochem J ; 436(3): 609-20, 2011 Jun 15.
Article in English | MEDLINE | ID: mdl-21434868

ABSTRACT

Cytotoxicity, a major obstacle in therapeutic application of antimicrobial peptides, is controlled by leucine-zipper-like sequences in melittin and other naturally occurring antimicrobial peptides. Magainin 2 shows significantly lower cytotoxicity than many naturally occurring antimicrobial peptides and lacks this structural element. To investigate the consequences of introducing a leucine zipper sequence in magainin 2, a novel analogue (Mag-mut) was designed by rearranging only the positions of its hydrophobic amino acids to include this structural element. Both magainin 2 and Mag-mut showed appreciable similarities in their secondary structures in the presence of negatively charged lipid vesicles, in localizing and permeabilizing the selected bacteria and exhibiting bactericidal activities. However, Mag-mut bound and localized strongly on to the mammalian cells tested and exhibited significantly higher cytotoxicity than magainin 2. Only Mag-mut, but not magainin 2, permeabilized human red blood cells and zwitterionic lipid vesicles. In contrast with magainin 2, Mag-mut self-assembled in an aqueous environment and bound co-operatively on to zwitterionic lipid vesicles. The peptides formed pores of different sizes on to a selected mammalian cell. The results of the present study indicate an important role of the leucine zipper sequence in the cytotoxicity of Mag-mut and demonstrate that its introduction into a non-toxic peptide, without altering the amino acid composition, can render cytotoxicity.


Subject(s)
Magainins/chemistry , Xenopus Proteins/chemistry , 3T3 Cells , Animals , CHO Cells , Cricetinae , Cricetulus , Erythrocytes/drug effects , Humans , Leucine Zippers , Magainins/toxicity , Mice , Microbial Sensitivity Tests , Protein Structure, Secondary , Xenopus Proteins/toxicity
20.
Biochemistry ; 49(36): 7920-9, 2010 Sep 14.
Article in English | MEDLINE | ID: mdl-20695504

ABSTRACT

Melittin is a good model antimicrobial peptide to understand the basis of its lytic activities against bacteria and mammalian cells. Novel analogues of melittin were designed by substituting the leucine residue(s) at the "d" and "a" positions of its previously identified leucine zipper motif. A scrambled peptide having the same composition of melittin with altered leucine zipper sequence was also designed. The analogues of melittin including the scrambled peptide showed a drastic reduction in cytotoxicity though they exhibited comparable bactericidal activities. Only melittin but not its analogues localized strongly onto hRBCs and formed pores of approximately 2.2-3.4 nm. However, melittin and its analogues localized similarly onto Escherichia coli and formed pores of varying sizes as tested onto Bacillus megaterium. The data showed that the substitution of hydrophobic leucine residue(s) by lesser hydrophobic alanine residue(s) in the leucine zipper sequence of melittin disturbed its pore-forming activity and mechanism only in hRBCs but not in the tested bacteria.


Subject(s)
Anti-Bacterial Agents/pharmacology , Erythrocytes/drug effects , Escherichia coli/drug effects , Melitten/analogs & derivatives , Melitten/pharmacology , Amino Acid Sequence , Anti-Bacterial Agents/chemistry , Cell Membrane/drug effects , Cell Membrane/metabolism , Erythrocytes/metabolism , Escherichia coli/metabolism , Hemolysis , Humans , Hydrophobic and Hydrophilic Interactions , Leucine Zippers , Microscopy, Confocal , Molecular Sequence Data
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