Ile Mutation Research Articles

Targeted mutagenesis on PDGFRα-Fc identifies amino acid modifications that allow efficient inhibition of HCMV infection while abolishing PDGF sequestration.

Platelet-derived growth factor receptor alpha (PDGFRα) serves as an entry receptor for the human cytomegalovirus (HCMV), and soluble PDGFRα-Fc can neutralize HCMV at a half-maximal effective concentration (EC50) of about 10 ng/ml. While this indicates a potential for usage as an HCMV entry inhibitor PDGFRα-Fc can also bind the physiological ligands of PDGFRα (PDGFs), which likely interferes with the respective signaling pathways and represents a potential source of side effects. Therefore, we tested the hypothesis that interference with PDGF signaling can be prevented by mutations in PDGFRα-Fc or combinations thereof, without losing the inhibitory potential for HCMV. To this aim, a targeted mutagenesis approach was chosen. The mutations were quantitatively tested in biological assays for interference with PDGF-dependent signaling as well as inhibition of HCMV infection and biochemically for reduced affinity to PDGF-BB, facilitating quantification of PDGFRα-Fc selectivity for HCMV inhibition. Mutation of Ile 139 to Glu and Tyr 206 to Ser strongly reduced the affinity for PDGF-BB and hence interference with PDGF-dependent signaling. Inhibition of HCMV infection was less affected, thus increasing the selectivity by factor 4 and 8, respectively. Surprisingly, the combination of these mutations had an additive effect on binding of PDGF-BB but not on inhibition of HCMV, resulting in a synergistic 260fold increase of selectivity. In addition, a recently reported mutation, Val 242 to Lys, was included in the analysis. PDGFRα-Fc with this mutation was fully effective at blocking HCMV entry and had a drastically reduced affinity for PDGF-BB. Combining Val 242 to Lys with Ile 139 to Glu and/or Tyr 206 to Ser further reduced PDGF ligand binding beyond detection. In conclusion, this targeted mutagenesis approach identified combinations of mutations in PDGFRα-Fc that prevent interference with PDGF-BB but maintain inhibition of HCMV, which qualifies such mutants as candidates for the development of HCMV entry inhibitors.

Mutations in the SARS CoV-2 spike protein may cause functional changes in the protein quaternary structure

Abstract Objectives This study aimed to model the changes resulting from mutations in surface (spike/S) glycoproteins, which play a key role in the entry of the severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) into host cells, in a protein quaternary structure and to evaluate their possible effects on the functional structure. Methods Genome sequence information of SARS CoV-2-infected patients located in Turkey was obtained from the GISAID EpiCoV database. Structural analysis of spike proteins was done using bioinformatics tools (MAFFT, PSIPRED, ProMod3, PyMoL and DynOmics). Results We identified 76 Thr>Ile mutations in the N-terminal domain; 468 Ile>Val mutations in the receptor binding site and 614 Asp>Gly, 679 Asn>Lys, 771 Ala>Val and 772 Val>Ile mutations in the S1 subunit. It has been observed that the mutations, except those of residues 771 and 772, may cause significant conformational, topological and electrostatic changes in a protein quaternary structure. It has been determined that the mutations in the receptor binding site transform the protein structure into a formation that can mask the binding site and affect receptor affinity. Conclusions It has been considered that SARS CoV-2 S glycoprotein mutations may cause changes in a protein functional structure that can affect the severity of disease.

The Arabidopsis cryptochrome 2 I404F mutant is hypersensitive and shows flavin reduction even in the absence of light.

The cryptochrome photoreceptor mutant cry2I404F exhibits hyperactivity in the dark, hypersensitivity in different light conditions, and in contrast to the wild-type protein, its flavin chromophore is reducible even in the absence of light. Plant cryptochromes (cry) are blue-light photoreceptors involved in multiple signaling pathways and various photomorphogenic responses. One biologically hyperactive mutant of a plant cryptochrome that was previously characterized is Arabidopsis cry1L407F (Exner et al. in Plant Physiol 154:1633-1645, 2010). Protein sequence alignments of different cryptochromes revealed that L407 in cry1 corresponds to I404 in cry2. Point mutation of Ile to Phe in cry2 in this position created a novel mutant. The present study provided a baseline data on the elucidation of the properties of cry2I404F. This mutant was still able to bind ATP-triggering conformational changes, as confirmed by partial tryptic digestion and thermo-FAD assays. Surprisingly, the FAD cofactor of cry2I404F was reduced by the addition of reductant even in the absence of light. In vivo, cry2I404F exhibited a cop phenotype in the dark and hypersensitivity to various light conditions compared to cry2 wild type. Overall, these data suggest that the hypersensitivity to red and blue light and hyperactivity of this novel mutant in the dark can be mostly accounted to structural alterations brought forth by the Ile to Phe mutation at position 404 that allows reduction of the flavin chromophore even in the absence of light.

Importance of Val567 on heme environment and substrate recognition of neuronal nitric oxide synthase.

Nitric oxide (NO) produced by mammalian nitric oxide synthases (mNOSs) is an important mediator in a variety of physiological functions. Crystal structures of mNOSs have shown strong conservation of the active‐site residue Val567 (numbering for rat neuronal NOS, nNOS). NOS‐like proteins have been identified in several bacterial pathogens, and these display striking sequence identity to the oxygenase domain of mNOS (NOSoxy), with the exception of a Val to Ile mutation at the active site. Preliminary studies have highlighted the importance of this Val residue in NO‐binding, substrate recognition, and oxidation in mNOSs. To further elucidate the role of this valine in substrate and substrate analogue recognition, we generated five Val567 mutants of the oxygenase domain of the neuronal NOS (nNOSoxy) and used UV‐visible and EPR spectroscopy to investigate the effects of these mutations on the heme distal environment, the stability of the heme‐FeII‐CO complexes, and the binding of a series of substrate analogues. Our results are consistent with Val567 playing an important role in preserving the integrity of the active site for substrate binding, stability of heme‐bound gaseous ligands, and potential NO production.

Phe71 in Type III Trypanosomal Protein Arginine Methyltransferase 7 (TbPRMT7) Restricts the Enzyme to Monomethylation.

Protein arginine methyltransferase 7 (PRMT7) is unique within the PRMT family as it is the only isoform known to exclusively make monomethylarginine (MMA). Given its role in epigenetics, the mechanistic basis for the strict monomethylation activity is under investigation. It is thought that PRMT7 enzymes are unable to add a second methyl group because of steric hindrance in the active site that restricts them to monomethylation. To test this, we probed the active site of trypanosomal PRMT7 (TbPRMT7) using accelerated molecular dynamics, site-directed mutagenesis, kinetic, binding, and product analyses. Both the dynamics simulations and experimental results show that the mutation of Phe71 to Ile converts the enzyme from a type III methyltransferase into a mixed type I/II, that is, an enzyme that can now perform dimethylation. In contrast, the serine and alanine mutants of Phe71 preserve the type III behavior of the native enzyme. These results are inconsistent with a sterics-only model to explain product specificity. Instead, molecular dynamics simulations of these variants bound to peptides show hydrogen bonding between would-be substrates and Glu172 of TbPRMT7. Only in the case of the Phe71 to Ile mutation is this interaction between MMA and the enzyme maintained, and the geometry for optimal SN2 methyl transfer is obtained. The results of these studies highlight the benefit of combined computational and experimental methods in providing a better understanding for how product specificity is dictated by PRMTs.

Effects of pyruvate kinase on the growth of Corynebacterium glutamicum and L-serine accumulation

Abstract Pyruvate kinase (PYK) is an important enzyme in the intermediary metabolism and has attracted much attention as a target for metabolic engineering of Corynebacterium glutamicum. Genome sequencing revealed that the 308 residue of PYK was mutated from methionine in model strain C. glutamicum ATCC14067 to isoleucine in L-serine-producing strain C. glutamicum SYPS-062. Consequently, a significantly lower PYK activity (77%) was noted in C. glutamicum SYPS-062, when compared with that in C. glutamicum ATCC14067. To confirm the role of this point mutation, pyk in both C. glutamicum SYPS-062 and C. glutamicum SYPS-062-33aΔSSAA was reversely mutated to restore the PYK enzyme activity, which led to a 33.1% and 28.8% decrease in L-serine titer, respectively. This is the first report to show that the (Met-308→Ile) mutation site of pyk is closely associated with its activity and apparently affected L-serine production. Furthermore, pyk was deleted in strain C. glutamicum SYPS-062-33aΔSSAA, and the resulting strain did not show alteration in growth rate and presented a 12% increase in L-serine production.

Modeling and experimental assessment of a buried Leu–Ile mutation in dengue envelope domain III

Envelope protein domain III (ED3) of the dengue virus is important for both antibody binding and host cell interaction. Here, we focused on how a L387I mutation in the protein core could take place in DEN4 ED3, but cannot be accommodated in DEN3 ED3 without destabilizing its structure. To this end, we modeled a DEN4_L387I structure using the Penultimate Rotamer Library and taking the DEN4 ED3 main-chain as a fixed template. We found that three out of seven Ile387 conformers fit in DEN4 ED3 without introducing the severe atomic clashes that are observed when DEN3 serotype’s ED3 is used as a template. A more extensive search using 273 side-chain rotamers of the residues surrounding Ile387 confirmed this prediction. In order to assess the prediction, we determined the crystal structure of DEN4_L387I at 2 Å resolution. Ile387 indeed adopted one of the three predicted rotamers. Altogether, this study demonstrates that the effects of single mutations are to a large extent successfully predicted by systematically modeling the side-chain structures of the mutated as well as those of its surrounding residues using fixed main-chain structures and assessing inter-atomic steric clashes. More accurate and reliable predictions require considering sub-angstrom main-chain deformation, which remains a challenging task.

Establishment of a mouse-adapted seasonal influenza A H3N2 virus strain and preliminary inquiry its molecular mechanism

Objective To establish adapted strain of seasonal influenza virus influenza A virus[A/Hong Kong/1968(H3N2)] in mice and explore the molecular mechanism of adaption preliminary. Methods The mice model was induced by nose dropping with wild type H3N2 influenza virus, by continuous passage in the lung of mice and detection of the clinical manifestation, viral load, virus titer, pathology, cytokines, to get the adapted strain of seasonal influenza A virus[A/Hong Kong/1968(H3N2)]. Results After 7 times continuous passage in the lung of mice, virulence was increased, viral load and virus titer were increased either. Genome sequencing and alignment indicated that the HA and NA gene was mutated. Conclusion The influenza virus H3N2 of mice lung adaption can be acquired from wild type seasonal H3N2 by continuous passage in the lung tissues of mice. Mutation of Ile to Val at residue 248 of HA and Val to Ile at residue 444of NA protein may be the key virulence determinant. Key words: Influenza A virus; Mice, inbread BALBC; Vircs cultivastion

Osmotic Pressure Effects Reveal a Specific Dehydration-Induced Hydrophobic Electron Transfer Structure Comprising Cytochrome C and Cytochrome C Oxidase

In the mitochondrial respiratory chain, Cytochrome c oxidase (CcO) accepts electrons from Cytochrome c (Cyt c) to reduce molecular oxygen. Previous studies showed that the complex formation of Cyt c with CcO is characterized by the positive entropy change, suggesting the dehydration from hydrophobic residues, but no experimental evidence of such dehydration has been reported. To confirm the dehydration during the complex formation between Cyt c and CcO, we focused on the partial molar volume change of protein (ΔV W) for the complex formation, which reflects the volume of dehydrated water molecules. ΔV W is correlated with the osmotic pressure (π) dependence of the K d. Osmotic pressure was increased by addition of sugars or polyols having no specific interactions with proteins and K d was estimated by the Michaelis-Menten analysis of the steady state kinetics for the electron transfer from Cyt c to CcO. As Figure 1 shows, the K d value is decreased with increasing the osmotic pressure, corresponding to the negative ΔV W of – 300 ± 78 mL mol-1. Assuming that the partial molar volume change of one hydrated water molecule around hydrophobic residues would be－17.5 mL mol-1, the volume change we obtained here corresponds to the dehydration of 17 ± 4 water molecules. Considering that the entropy change from the dehydration (dehydΔS) of one water molecule was estimated to be 5.5 JK-1mol-1, dehydΔS of 17 water molecules corresponds to ~90 JK-1mol-1, which is about 75% of total entropy change for the Cyt c-CcO complex formation. The dehydration is, therefore, one of the major factors to increase the entropy for the complex formation. To identify the dehydration sites from hydrophobic residues in the interaction site for CcO on Cyt c, we mutated Ile11 or Ile81, hydrophobic amino acid residues in the interaction site for CcO [1], to Ala, an amino acid residue having a smaller side chain and less number of the hydrated water molecules. As clearly illustrated in Figure 1, the slope of the osmotic pressure dependence of K d for the Ile mutant is less steep than that for the wild type protein. The estimated numbers of the dehydrated water molecules were reduced to 13 ± 3 and 8 ± 2 for the Ile11 and Ile81 mutants, respectively. The reduced numbers of the dehydrated water molecules in these Ile mutants indicate that the hydrated water molecules around Ile11 and Ile81 were expelled to the solvent in the complex formation between Cyt c and CcO. In conclusion, we successfully identified that about 17 water molecules are dehydrated in the Cyt c-CcO complex formation and the primary dehydration sites are Ile11 and Ile81. Such dehydration from the hydrophobic residues can be a major factor to increase the entropy, facilitating the complex formation and the electron transfer from Cyt c to CcO.

Characterization of antimicrobial resistance and application of RFLP for epidemiological monitoring of thermophilic Campylobacter spp. isolated from dogs and humans in Korea

Abstract : An antimicrobial susceptibility test was conducted to compare the resistance rates among Campylobacterspp. isolates from dogs (n = 50) raised under diverse conditions and humans (n = 50). More than 60% of Campylobacter(C.) jejuni from dogs and humans showed resistance to nalidixic acid, enrofloxacin and ciprofloxacin. C. jejuni isolatesfrom humans showed higher resistance to tetracycline (83.3%) and ampicillin (91.3%) than those from dogs. Noneof the C. jejuni or Campylobacter coli isolates from humans or dogs were resistant to erythromycin. Overall, 85%of Campylobacter spp. isolates showed a multidrug resistant phenotype. Nucleotide sequencing analysis of the gryAgene showed that 100% of NA R /CIP R C. jejuni isolates from dogs and humans had the Thr-86 th -Ile mutation, whichis associated with fluoroquinolone resistance. flaA PCR restriction fragment length polymorphism (RFLP) typing todifferentiate the isolates below the species level revealed 12 different clusters out of 73 strains. The human isolatesbelonged to eight different RFLP clusters, while five clusters contained dog and human isolates.Keywords : antibiotic resistance, Campylobacter spp., DNA gyrase, point mutation, RFLP

Determining the Molecular Mechanisms that Link a Titin Mutation to Cardiomyopathy

A mutation in the giant elastic protein titin has recently been linked to arrhythmogenic cardiomyopathy (AC), a disease primarily characterized by fibrofatty infiltration of the myocardium. Titin is the first sarcomeric protein linked to AC. In addition to largely unstructured segments, the extensible I-band region of titin contains ∼40 immunoglobulin(Ig)-like domains that are natively folded as highly stable beta barrels. One of these domains, Ig10, contains a single Thr→Ile mutation that leads to AC. The first step in determining how this mutation leads to severe cardiac disease was to study the mutation at the single molecule level using atomic force microscopy (AFM) and in vitro degradation assays. With AFM individual proteins are mechanically stretched, and it was found that the mutation significantly reduces the force needed to unfold Ig10. Although no difference in refolding rate was found, by comparing the experimental AFM unfolding forces with computer simulated Ig unfolding, it was found that the mutation increases Ig10's unfolding rate fourfold. This effect predicts increased Ig10 unfolding (i.e. transition into a non-native state) under physiological conditions. It was also found that mutant Ig10 is more prone to protease degradation due to compromised local structure at the point mutation. This suggests that accelerated titin turnover in cardiomyocytes instigates the cardiac remodeling process in patients with titin-linked AC. This is the first time an Ig domain in titin's elastic I-band region has been linked to cardiac disease, and this study proposes a novel disease mechanism contingent on Ig domain unfolding.

H5N1 influenza vaccine quality is affected by hemagglutinin conformational stability

ABSTRACT Since 1997, highly pathogenic H5N1 avian influenza viruses have circulated in wild and domestic birds and sporadically have infected humans. Conventional inactivated vaccines made from these viruses were shown to have decreased HA content and immunogenicity compared to seasonal preparations. We assumed that the high pH threshold (5.6-6.0) known for the HA conformational change (pH of fusion or activation) of avian highly pathogenic influenza viruses was the reason of the low stability of native HA conformation and affected the vaccine quality. The 58Lys→Ile mutation introduced into the HA2 subunit of the HA of A/chicken/Kurgan/5/05 (H5N1) virus decreased the pH threshold of the HA activation. The mutant virus demonstrated increased HA stability toward acidic pH and elevated temperature, decreased binding efficiency to the monoclonal antibody IIF4 that recognizes the HA low pH form, and increased HA resistance to trypsin digestion. Virus with modified HA was less susceptible to freezing stress and showed an increased content of immunocompetent HA in inactivated vaccine preparation compared to the analogous virus with original HA. Therefore, we have shown a way to increase the quality of inactivated vaccines made from highly pathogenic avian influenza viruses.

Влияние конформационной стабильности гемагглютинина вируса гриппа на качество инактивированных вакцин H5N1

Начиная с 1997 года, в популяции диких и домашних птиц наблюдается постоянная циркуляция высокопатогенных вирусов гриппа подтипа H5N1. Периодически эти вирусы инфицируют людей, что создает угрозу возникновения новой пандемии. При производстве инактивированных вакцин из вирусов H5N1 замечено, что содержание главного компонента – антигена гемагглютинина (HA) – гораздо ниже, чем в аналогичных препаратах сезонных вирусов гриппа. Мы предположили, что урожайность НА определяется его стабильностью. Белки HA, входящие в состав вирионов высокопатогеннных вирусов гриппа птиц, отличаются от HA человеческих изолятов вируса гриппа высоким порогом рН-слияния, или рН-активации (5.6–6.0 vs 5.0–5.4), – значение pH, при котором НА изменяет конформацию, переходя в форму, необходимую для проникновения вируса в клетку. Нами получен мутантный вариант НА вируса A/chicken/Kurgan/5/05 (H5N1) с единственной заменой 58Lys→Ile, находящейся в HA2 субъединице белка. По сравнению с НА дикого типа у мутантного варианта порог рН-активации снижен, а стабильность увеличена как в кислой среде, так и при повышенной температуре. Кроме того, вирионы, содержащие мутантный НА, оказались более устойчивы к расщеплению трипсином и при их замораживании/размораживании нативная структура шипов HA сохранялась лучше, чем в родительском вирусе. Повышенная стабильность мутантного НА коррелировала с увеличением его продукции как антигена в вакцинном препарате. Таким образом, высокое значение рН-активации НА высокопатогенных штаммов вируса гриппа H5N1 определяет низкую конформационную стабильность НА и, как следствие, низкую стабильность вирионов, что влияет на качество получаемых из них вакцинных препаратов.

Side-chain hydrophobicity and the stability of Aβ₁₆₋₂₂ aggregates.

Recent mutagenesis studies using the hydrophobic segment of Aβ suggest that aromatic π-stacking interactions may not be critical for fibril formation. We have tested this conjecture by probing the effect of Leu, Ile, and Ala mutation of the aromatic Phe residues at positions 19 and 20, on the double-layer hexametric chains of Aβ fragment Aβ₁₆₋₂₂ using explicit solvent all-atom molecular dynamics. As these simulations rely on the accuracy of the utilized force fields, we first evaluated the dynamic and stability dependence on various force fields of small amyloid aggregates. These initial investigations led us to choose AMBER99SB-ILDN as force field in multiple long molecular dynamics simulations of 100 ns that probe the stability of the wild-type and mutants oligomers. Single-point and double-point mutants confirm that size and hydrophobicity are key for the aggregation and stability of the hydrophobic core region (Aβ₁₆₋₂₂). This suggests as a venue for designing Aβ aggregation inhibitors the substitution of residues (especially, Phe 19 and 20) in the hydrophobic region (Aβ₁₆₋₂₂) with natural and non-natural amino acids of similar size and hydrophobicity.

Molecular cloning, sequence characterization and heterologous expression of buffalo (Bubalus bubalis) oviduct-specific glycoprotein in E. coli

Oviductin is a high molecular weight oviduct-specific glycoprotein secreted by the non-ciliated epithelial cells of oviduct during estrous cycle and early pregnancy. It plays an important role during fertilization and early embryonic development. The oviductin gene from oviductal tissues of buffalo was successfully cloned and sequenced. The sequence analysis revealed that buffalo and cattle oviductin share very high homology between their cDNA sequences. The predicted amino acid sequences of the buffalo oviductin exhibited the highest percent of identity of 97 % with bovine followed by 94 % with goat, 93 % with sheep, 78 % with porcine, 72 % with human, 67 % with hamster and rabbit and 65 % with mouse. Oviductin was also observed to share high similarity with the mammalian chitinase, however oviductins do not show chitinase activity due to Glu→Ile mutation in the active site responsible for chitinase activity. The phylogenetic tree based on amino acid sequences of oviductin indicated that buffalo oviductin was closely related to its cattle counterpart, and this clustering is in accordance with the classic taxonomic relationship. Tissue specific expression of the transcripts for buffalo oviductin revealed a high level expression in oviduct and ovary followed by testis, mammary gland, kidney, while in mammary epithelial cells and liver its expression was very low. The full length matured oviductin and its domains constituting chitinase-like domain and mucin-like domain were cloned into pET and pGEX series of expression vectors and over expressed in E. coli. The soluble recombinant oviductin was successfully purified to homogeneity. Full length recombinant oviductin was expressed partially in soluble form, where as the chitinase-like and mucin-like domains of oviductin were expressed in insoluble form and aggregating to form inclusion bodies at both 37 and 16 °C induction temperatures.

The cysteine 703 to isoleucine or histidine mutation of the oxidosqualene-lanosterol cyclase from Saccharomyces cerevisiae generates an iridal-type triterpenoid

The Cys703 to Ile or His mutation within Saccharomyces cerevisiae oxidosqualene-lanosterol cyclase ERG7 (ERG7(C703I/H)) generates an unusual truncated bicyclic rearranged intermediate, (8R,9R,10R)-polypoda-5,13E,17E,21-tetraen-3β-ol, related to iridal-skeleton triterpenoid. Numerous oxidosqualene-cyclized truncated intermediates, including tricyclic, unrearranged tetracyclic with 17α/β exocyclic hydrocarbon side chain, rearranged tetracyclic, and chair-chair-chair tricyclic intermediates (compounds 3-9), were also isolated from the ERG7(C703X) site-saturated mutations or the ERG7(F699T/C703I) double mutation, indicating the functional role of the Cys703 residue in stabilizing the bicyclic C-8 cation and the rearranged intermediate or interacting with Phe699, and opened a new avenue of engineering ERG7 for producing biological active agents.

Mutation of the Calmodulin Binding Motif IQ of the L-type Cav1.2 Ca2+ Channel to EQ Induces Dilated Cardiomyopathy and Death

Cardiac excitation-contraction coupling (EC coupling) links the electrical excitation of the cell membrane to the mechanical contractile machinery of the heart. Calcium channels are major players of EC coupling and are regulated by voltage and Ca(2+)/calmodulin (CaM). CaM binds to the IQ motif located in the C terminus of the Ca(v)1.2 channel and induces Ca(2+)-dependent inactivation (CDI) and facilitation (CDF). Mutation of Ile to Glu (Ile1624Glu) in the IQ motif abolished regulation of the channel by CDI and CDF. Here, we addressed the physiological consequences of such a mutation in the heart. Murine hearts expressing the Ca(v)1.2(I1624E) mutation were generated in adult heterozygous mice through inactivation of the floxed WT Ca(v)1.2(L2) allele by tamoxifen-induced cardiac-specific activation of the MerCreMer Cre recombinase. Within 10 days after the first tamoxifen injection these mice developed dilated cardiomyopathy (DCM) accompanied by apoptosis of cardiac myocytes (CM) and fibrosis. In Ca(v)1.2(I1624E) hearts, the activity of phospho-CaM kinase II and phospho-MAPK was increased. CMs expressed reduced levels of Ca(v)1.2(I1624E) channel protein and I(Ca). The Ca(v)1.2(I1624E) channel showed "CDI" kinetics. Despite a lower sarcoplasmic reticulum Ca(2+) content, cellular contractility and global Ca(2+) transients remained unchanged because the EC coupling gain was up-regulated by an increased neuroendocrine activity. Treatment of mice with metoprolol and captopril reduced DCM in Ca(v)1.2(I1624E) hearts at day 10. We conclude that mutation of the IQ motif to IE leads to dilated cardiomyopathy and death.

Modifications on the hydrogen bond network by mutations of Escherichia coli copper efflux oxidase affect the process of proton transfer to dioxygen leading to alterations of enzymatic activities

CueO has a branched hydrogen bond network leading from the exterior of the protein molecule to the trinuclear copper center. This network transports protons in the four-electron reduction of dioxygen. We replaced the acidic Glu506 and Asp507 residues with the charged and uncharged amino acid residues. Peculiar changes in the enzyme activity of the mutants relative to the native enzyme indicate that an acidic amino acid residue at position 506 is essential for effective proton transport. The Ala mutation resulted in the formation of a compensatory hydrogen bond network with one or two extra water molecules. On the other hand, the Ile mutation resulted in the complete shutdown of the hydrogen bond network leading to loss of enzymatic activities of CueO. In contrast, the hydrogen bond network without the proton transport function was constructed by the Gln mutation. These results exerted on the hydrogen bond network in CueO are discussed in comparison with proton transfers in cytochrome oxidase.

Kinetics of Doubletime Kinase-dependent Degradation of the Drosophila Period Protein

Robust circadian oscillations of the proteins PERIOD (PER) and TIMELESS (TIM) are hallmarks of a functional clock in the fruit fly Drosophila melanogaster. Early morning phosphorylation of PER by the kinase Doubletime (DBT) and subsequent PER turnover is an essential step in the functioning of the Drosophila circadian clock. Here using time-lapse fluorescence microscopy we study PER stability in the presence of DBT and its short, long, arrhythmic, and inactive mutants in S2 cells. We observe robust PER degradation in a DBT allele-specific manner. With the exception of doubletime-short (DBT(S)), all mutants produce differential PER degradation profiles that show direct correspondence with their respective Drosophila behavioral phenotypes. The kinetics of PER degradation with DBT(S) in cell culture resembles that with wild-type DBT and posits that, in flies DBT(S) likely does not modulate the clock by simply affecting PER degradation kinetics. For all the other tested DBT alleles, the study provides a simple model in which the changes in Drosophila behavioral rhythms can be explained solely by changes in the rate of PER degradation.

The Proximal Hydrogen Bond Network Modulates Bacillus subtilis Nitric-oxide Synthase Electronic and Structural Properties

Bacterial nitric-oxide synthase (NOS)-like proteins are believed to be genuine NOSs. As for cytochromes P450 (CYPs), NOS-proximal ligand is a thiolate that exerts a push effect crucial for the process of dioxygen activation. Unlike CYPs, this catalytic electron donation seems controlled by a hydrogen bond (H-bond) interaction between the thiolate ligand and a vicinal tryptophan. Variations of the strength of this H-bond could provide a direct way to tune the stability along with the electronic and structural properties of NOS. We generated five different mutations of bsNOS Trp66, which can modulate this proximal H-bond. We investigated the effects of these mutations on different NOS complexes (FeIII, FeIICO, and FeIINO), using a combination of UV-visible absorption, EPR, FTIR, and resonance Raman spectroscopies. Our results indicate that (i) the proximal H-bond modulation can selectively decrease or increase the electron donating properties of the proximal thiolate, (ii) this modulation controls the σ-competition between distal and proximal ligands, (iii) this H-bond controls the stability of various NOS intermediates, and (iv) a fine tuning of the electron donation by the proximal ligand is required to allow at the same time oxygen activation and to prevent uncoupling reactions.