Trp Mutants Research Articles

Probing Tertiary Structure of Proteins Using Single Trp Mutations with Circular Dichroism at Low Temperature

Trp is the most spectroscopically informative aromatic amino acid of proteins. However, the near-UV circular dichroism (CD) spectrum of Trp is complicated because the intensity and sign of 1La and 1Lb bands vary independently. To resolve vibronic structure and gain site-specific information from complex spectra, deconvolution was combined with cooling and site-directed tryptophan substitution. Low temperature near-UV CD was used to probe the local tertiary structure of a loop and α-helix in tear lipocalin. Upon cooling, the enhancement of the intensities of the near-UV CD was not uniform, but depends on the position of Trp in the protein structure. The most enhanced 1Lb band was observed for Trp at position 124 in the α-helix segment matching the known increased conformational mobility during ligand binding. Some aspects of the CD spectra of W28 and W130 were successfully linked to specific rotamers of Trp previously obtained from fluorescence lifetime measurements. The discussion was based on a framework that the magnitude of the energy differences in local conformations governs the changes in the CD intensities at low temperature. The Trp CD spectral classification of Strickland was modified to facilitate the recognition of pseudo peaks. Near-UV CD spectra harbor abundant information about the conformation of proteins that site directed Trp CD can report.

Photosensitive TRPs.

The Drosophila "transient receptor potential" channel is the prototypical TRP channel, belonging to and defining the TRPC subfamily. Together with a second TRPC channel, trp-like (TRPL), TRP mediates the transducer current in the fly's photoreceptors. TRP and TRPL are also implicated in olfaction and Malpighian tubule function. In photoreceptors, TRP and TRPL are localised in the ~30,000 packed microvilli that form the photosensitive "rhabdomere"-a light-guiding rod, housing rhodopsin and the rest of the phototransduction machinery. TRP (but not TRPL) is assembled into multimolecular signalling complexes by a PDZ-domain scaffolding protein (INAD). TRPL (but not TRP) undergoes light-regulated translocation between cell body and rhabdomere. TRP and TRPL are also found in photoreceptor synapses where they may play a role in synaptic transmission. Like other TRPC channels, TRP and TRPL are activated by a G protein-coupled phospholipase C (PLCβ4) cascade. Although still debated, recent evidence indicates the channels can be activated by a combination of PIP2 depletion and protons released by the PLC reaction. PIP2 depletion may act mechanically as membrane area is reduced by cleavage of PIP2's bulky inositol headgroup. TRP, which dominates the light-sensitive current, is Ca(2+) selective (P Ca:P Cs >50:1), whilst TRPL has a modest Ca(2+) permeability (P Ca:P Cs ~5:1). Ca(2+) influx via the channels has profound positive and negative feedback roles, required for the rapid response kinetics, with Ca(2+) rapidly facilitating TRP (but not TRPL) and also inhibiting both channels. In trp mutants, stimulation by light results in rapid depletion of microvillar PIP2 due to lack of Ca(2+) influx required to inhibit PLC. This accounts for the "transient receptor potential" phenotype that gives the family its name and, over a period of days, leads to light-dependent retinal degeneration. Gain-of-function trp mutants with uncontrolled Ca(2+) influx also undergo retinal degeneration due to Ca(2+) cytotoxicity. In vertebrate retina, mice knockout studies suggest that TRPC6 and TRPC7 mediate a PLCβ4-activated transducer current in intrinsically photosensitive retinal ganglion cells, expressing melanopsin. TRPA1 has been implicated as a "photo-sensing" TRP channel in human melanocytes and light-sensitive neurons in the body wall of Drosophila.

Modeling the Structural Properties of the Transmembrane Peptide of Influenza Hemagglutinin in a Membrane Bilayer

Like all enveloped viruses, influenza virus enters the host cell by fusing its membrane with the host membrane, in a process mediated by the hemagglutinin (HA) glycoprotein. HA is a homotrimeric protein comprised by a soluble part (which contains the receptor binding site and the fusion peptide) and a transmembrane (TM) peptide. The TM peptide attaches the protein to the viral membrane and is also thought to play a role in the fusion process. Although this peptide has been gaining considerable attention in recent years, its 3D structure and the molecular determinants of membrane insertion remain unknown.To analyze the structural determinants of membrane insertion of the TM peptide, we simulated this peptide in the presence of a DMPC bilayer [1]. We observed that the peptide adopts a mainly helical conformation and inserts in the membrane with a tilt angle of ∼64°. Simulations with mutant forms of the TM peptide revealed that mutations of Trp 24 and Tyr 5 found in the C-terminal and N-terminal regions, respectively, affect the helicity and consequently the peptide arrangement inside the membrane bilayer. Since HA is a trimer, we also performed simulations with three copies of the TM peptide embedded in a membrane. The simulations showed that the three peptides assemble in a triangular arrangement that approximately matches the positions where they should attach to the available crystallographic structure of the soluble part of HA.1. B. L. Victor, A. M. Baptista and C. M. Soares, J Chem Inf Model, 2012, 52, 3001-3012.

Effect of Cation–π Interactions and Steric Bulk on the Catalytic Action of Oxidosqualene Cyclase: A Case Study of Phe728 of β‐Amyrin Synthase from Euphorbia tirucalli L

The function of the active-site residues of oxidosqualene cyclases (OSCs) has been presumed mainly in light of the product distribution; however, not much research has been performed into the enzymatic activity of mutated OSCs. β-Amyrin, which is widely found in the plant kingdom, is classified as an OSC; mutational studies on β-amyrin cyclase are very limited. Six site-specific mutations targeted at the Phe728 residue of Euphorbia tirucalli β-amyrin synthase (EtAS) were constructed to inspect the function of this aromatic residue. We developed a simple method to evaluate the in vivo enzymatic activity; the expression levels of EtASs and the quantities of the cyclic triterpenes produced were determined by use of western blot and GC analyses, respectively. Measurement of the relative in vivo activity of the mutants versus that of the wild-type enzyme showed that the Ala, Met, His, and Trp variants had significantly decreased activity, but that the Tyr mutant had a high activity, which was nearly the same as that of the wild-type enzyme. In contrast to Tyr, Ala and Met possess no π-electrons; thus, the role of Phe728 is to stabilize the cationic intermediates, resulting in facilitation of the ring-expansion processes, especially by stabilizing the secondary cations. The decreased activity of the Trp mutant is ascribed to the introduction of a large steric bulk, leading to looser binding of oxidosqualene in the Trp variant. The His mutant afforded germanicol as the main product, indicating that the Phe residue is located near the D/E-ring-formation site. Changes in the steric bulk gave some cationic intermediates, resulting in the formation of 13 cyclic triterpenes, including an unnatural triterpene, (17E)-dammara-17(20),24-dien-3β-ol, and isoursenol, which has rarely been found in nature. In this study, we provide the first experimental evidence that cation-π interactions play a key role in the catalytic action of OSCs.

Pharmacology of TRP Channels in the Vasculature

The TRP family of cation-permeable channels owes its name to a Drosophila TRP mutant with impaired vision due to transient rather than sustained receptor potential. Mammalian TRP channels can be grouped into 6 subfamilies, including TRPC, TRPM, TRPV, TRPA, TRPP and TRPML and a number of TRP family members have been identified in the vasculature. TRP channels play an important functional role in the vasculature as mediators of cation influx across the plasma membrane, thus contributing to a large number of processes such as vascular smooth muscle contraction and vascular pressure or the responses to oxidative stress, mechanical stimuli, heat and hypoxia-induced vascular remodelling. TRP channelopaties are involved in the pathogenesis of different disorders including hypertension and cardiomyopathy. A number of identified natural compounds and synthetic agents have been reported to modulate TRP function, and are the base for therapeutical strategies.

Trp replacements for tightly interacting Gly–Gly pairs in LacY stabilize an outward-facing conformation

Trp replacements for conserved Gly-Gly pairs between the N- and C-terminal six-helix bundles on the periplasmic side of lactose permease (LacY) cause complete loss of transport activity with little or no effect on sugar binding. Moreover, the detergent-solubilized mutants exhibit much greater thermal stability than WT LacY. A Cys replacement for Asn245, which is inaccessible/unreactive in WT LacY, alkylates readily in the Gly→Trp mutants, indicating that the periplasmic cavity is patent. Stopped-flow kinetic measurements of sugar binding with the Gly→Trp mutants in detergent reveal linear dependence of binding rates on sugar concentration, as observed with WT or the C154G mutant of LacY, and are compatible with free access to the sugar-binding site in the middle of the molecule. Remarkably, after reconstitution of the Gly→Trp mutants into proteoliposomes, the concentration dependence of sugar-binding rates increases sharply with even faster rates than measured in detergent. Such behavior is strikingly different from that observed for reconstituted WT LacY, in which sugar-binding rates are independent of sugar concentration because opening of the periplasmic cavity is limiting for sugar binding. The observations clearly indicate that Gly→Trp replacements, which introduce bulky residues into tight Gly-Gly interdomain interactions on the periplasmic side of LacY, prevent closure of the periplasmic cavity and, as a result, shift the distribution of LacY toward an outward-open conformation.

Primary structural response in tryptophan residues of Anabaena sensory rhodopsin to photochromic reactions of the retinal chromophore

Anabaena sensory rhodopsin (ASR) is a microbial rhodopsin found in eubacteria and functions as a photosensor. The photoreaction of ASR is photochromic between all-trans, 15-anti (ASRAT), and 13-cis, 15-syn (ASR13C) isomers. To understand primary protein dynamics in the photoreaction starting in ASRAT and ASR13C, picosecond time-resolved ultraviolet resonance Raman spectra were obtained. In the intermediate state appearing in the picosecond temporal region, spectral changes of Trp bands were observed. For both ASRAT and ASR13C, the intensities of the Trp bands were bleached within the instrumental response time and recovered with a time constant of 30ps. This suggests that the rates of structural changes in the Trp residue in the vicinity of the chromophore do not depend on the direction of the isomerization of retinal. A comparison between spectra of the wild-type and Trp mutants indicates that the structures of Trp76 and Trp46 change upon the primary photoreaction of retinal.

Depletion of PtdIns(4,5)P2 underlies retinal degeneration in Drosophila trp mutants

The prototypical transient receptor potential (TRP) channel is the major light-sensitive, and Ca(2+)-permeable channel in the microvillar photoreceptors of Drosophila. TRP channels are activated following hydrolysis of phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P₂] by the key effector enzyme phospholipase C (PLC). Mutants lacking TRP channels undergo light-dependent retinal degeneration, as a consequence of the reduced Ca(2+) influx. It has been proposed that degeneration is caused by defects in the Ca(2+)-dependent visual pigment cycle, which result in accumulation of toxic phosphorylated metarhodopsin-arrestin complexes (MPP-Arr2). Here we show that two interventions, which prevent accumulation of MPP-Arr2, namely rearing under red light or eliminating the C-terminal rhodopsin phosphorylation sites, failed to rescue degeneration in trp mutants. Instead, degeneration in trp mutants reared under red light was rescued by mutation of PLC. Degeneration correlated closely with the light-induced depletion of PtdIns(4,5)P₂ that occurs in trp mutants due to failure of Ca(2+)-dependent inhibition of PLC. Severe retinal degeneration was also induced in the dark in otherwise wild-type flies by overexpression of a bacterial PtdInsPn phosphatase (SigD) to deplete PtdIns(4,5)P₂. In degenerating trp photoreceptors, phosphorylated Moesin, a PtdIns(4,5)P₂-regulated membrane-cytoskeleton linker essential for normal microvillar morphology, was found to delocalize from the rhabdomere and there was extensive microvillar actin depolymerisation. The results suggest that compromised light-induced Ca(2+) influx, due to loss of TRP channels, leads to PtdIns(4,5)P₂ depletion, resulting in dephosphorylation of Moesin, actin depolymerisation and disintegration of photoreceptor structure.

Understanding the roles of strictly conserved tryptophan residues in O2producing chlorite dismutases

The chlorite dismutases (Clds) degrade ClO(2)(-) to O(2) and Cl(-) in perchlorate respiring bacteria, and they serve still poorly defined cellular roles in other diverse microbes. These proteins share 3 highly conserved Trp residues, W155, W156, and W227, on the proximal side of the heme. The Cld from Dechloromonas aromatica (DaCld) has been shown to form protein-based radicals in its reactions with ClO(2)(-) and peracetic acid. The roles of the conserved Trp residues in radical generation and in enzymatic function were assessed via spectroscopic and kinetic analysis of their Phe mutants. The W155F mutant was the most dramatically affected, appearing to lose the characteristic pentameric oligomerization state, secondary structure, and heme binding properties of the WT protein. The W156F mutant initially retains many features of the WT protein but over time acquires many of the features of W155F. Conversion to an inactive, heme-free form is accelerated by dilution, suggesting loss of the protein's pentameric state. Hence, both W155 and W156 are important for heme binding and maintenance of the protein's reactive pentameric structure. W227F by contrast retains many properties of the WT protein. Important differences are noted in the transient kinetic reactions with peracetic acid (PAA), where W227F appears to form an [Fe(IV)=O]-containing intermediate, which subsequently converts to an uncoupled [Fe(IV)=O + AA(+)˙] system in a [PAA]-dependent manner. This is in contrast to the peroxidase-like formation of [Fe(IV)=O] coupled to a porphyrin π-cation radical in the WT protein, which decays in a [PAA]-independent manner. These observations and the lack of redox protection for the heme in any of the Trp mutants suggests a tendency for protein radical formation in DaCld that is independent of any of these conserved active site residues.

P-glycoprotein is fully active after multiple tryptophan substitutions

P-glycoprotein (Pgp) is an important contributor to multidrug resistance of cancer. Pgp contains eleven native tryptophans (Trps) that are highly conserved among orthologs. We replaced each Trp by a conservative substitution to determine which Trps are important for function. Individual Trp mutants W44R, W208Y, W132Y, W704Y and W851Y, situated at the membrane surface, revealed significantly reduced Pgp induced drug resistance against one or more fungicides and/or reduced mating efficiencies in Saccharomyces cerevisiae. W158F and W799F, located in the intracellular coupling helices, abolished mating but retained resistance against most drugs. In contrast, W228F and W311Y, located within the membrane, W694L, at the cytoplasmic membrane interface, and W1104Y in NBD2 retained high levels of drug resistance and mating efficiencies similar to wild-type Pgp. Those were combined into pair (W228F/W311Y and W694L/W1104Y) and quadruple (W228F/W311Y/W694L/W1104Y) mutants that were fully active in yeast, and could be purified to homogeneity. Purified pair and quad mutants exhibited drug-stimulated ATPase activity with binding affinities very similar to wild-type Pgp. The combined mutations reduced Trp fluorescence by 35%, but drug induced fluorescence quenching was unchanged from wild-type Pgp suggesting that several membrane-bound Trps are sensitive to drug binding. Overall, we conclude that Trps at the membrane surface are critical for maintaining the integrity of the drug binding sites, while Trps in the coupling helices are important for proper interdomain communication. We also demonstrate that functional single Trp mutants can be combined to form a fully active Pgp that maintains drug polyspecificity, while significantly reducing intrinsic fluorescence.

Structure of the proton-gated urea channel from the gastric pathogen Helicobacter pylori

Half the world's population is chronically infected with Helicobacter pylori1, causing gastritis, ulcers and increased incidence of gastric adenocarcinoma2. Its proton-gated inner-membrane urea channel, HpUreI, is essential for survival in the acidic environment of the stomach3. The channel is closed at neutral pH and opens at acidic pH to allow rapid urea access to cytoplasmic urease4. Urease produces NH3 and CO2 that neutralize entering protons and thus buffer the periplasm to pH ∼6.1 even in gastric juice at pH <2.0. Here we report the structure of HpUreI, revealing six protomers assembled in a hexameric ring surrounding a central bilayer plug of ordered lipids. Each protomer encloses a channel formed by a twisted bundle of six transmembrane helices. The bundle defines a novel fold comprising a two-helix hairpin motif repeated three times around the central axis of the channel, without the inverted repeat of mammalian urea transporters. Both the channel and the protomer interface contain residues conserved in the AmiS/UreI superfamily, suggesting preservation of channel architecture and oligomeric state in this superfamily. Predominantly aromatic or aliphatic side chains line the entire channel and define two consecutive constriction sites in the middle of the channel. Mutation of Trp153 in the cytoplasmic constriction site to Ala or Phe reduces the selectivity for urea compared to thiourea, suggesting that solute interaction with Trp153 contributes specificity. The novel hexameric channel structure described here provides a new paradigm for permeation of urea and other small amide solutes in prokaryotes and archaea.

Tryptophan Rotamer Distribution Revealed for the α-Helix in Tear Lipocalin by Site-Directed Tryptophan Fluorescence

Rotamer libraries are a valuable tool for protein structure determination, modeling, and design. Site-directed tryptophan fluorescence (SDTF) was used in combination with the rotamer model for the fluorescence intensity decays to solve α-helical conformations of proteins in solution. Single Trp mutations located in an α-helical segment of human tear lipocalin were explored for structure assignment. Along with fluorescence λ(max) values, the rotamer model assignment of fluorescence lifetimes fits the backbone conformation. Typically, Trp fluorescence in proteins shows three lifetimes. However, for the α-helix, two lifetimes assigned to t and g(-) rotamers were satisfactory to describe Trp fluorescence intensity decays. The g(+) rotamer is not feasible in the α-helix due to steric restriction. Trp rotamer distributions obtained by fluorescence were compared with the rotamer library derived from X-ray crystallography data of proteins. The Trp rotamer distributions vary for solvent exposed and buried (tertiary interaction) sites. A new strategy using the rotamer distribution with SDTF (RD-SDTF) removes the limitation of regular SDTF and other labeling techniques, in which site-specific differences, e.g., accessibility, are presumed. The RD-SDTF technique does not rely on environmental differences of side chains and is able to detect α-helical structure where all side chains are exposed to solvent. Potentially, this technique is applicable to various proteins including membrane proteins, which are rich in α-helix motif.

Role of the -PEWY-glutamate in catalysis at the Qo-site of the Cyt bc1 complex

We re-examine the pH dependence of partial processes of ubihydroquinone (QH2) turnover in Glu-295 mutants in Rhodobacter sphaeroides to clarify the mechanistic role. In more crippled mutants, the bell-shaped pH profile of wildtype was replaced by dependence on a single pK at ~8.5 favoring electron transfer. Loss of the pK at 6.5 reflects a change in the rate-limiting step from the first to the second electron transfer. Over the range of pH 6–8, no major pH dependence of formation of the initial reaction complex was seen, and the rates of bypass reactions were similar to the wildtype. Occupancy of the Qo-site by semiquinone (SQ) was similar in the wildtype and the Glu→Trp mutant. Since heme bL is initially oxidized in the latter, the bifurcated reaction can still occur, allowing estimation of an empirical rate constant <103s−1 for reduction of heme bL by SQ from the domain distal from heme bL, a value 1000-fold smaller than that expected from distance. If the pK ~8.5 in mutant strains is due to deprotonation of the neutral semiquinone, with Q•− as electron donor to heme bL, then in wildtype this low value would preclude mechanisms for normal flux in which semiquinone is constrained to this domain. A kinetic model in which Glu-295 catalyzes H+ transfer from QH•, and delivery of the H+ to exit channel(s) by rotational displacement, and facilitates rapid electron transfer from SQ to heme bL by allowing Q•− to move closer to the heme, accounts well for the observations.

Regulation of Arrestin Translocation by Ca2+ and Myosin III in Drosophila Photoreceptors

Upon illumination several phototransduction proteins translocate between cell body and photosensory compartments. In Drosophila photoreceptors arrestin (Arr2) translocates from cell body to the microvillar rhabdomere down a diffusion gradient created by binding of Arr2 to photo-isomerized metarhodopsin. Translocation is profoundly slowed in mutants of key phototransduction proteins including phospholipase C (PLC) and the Ca(2+)-permeable transient receptor potential channel (TRP), but how the phototransduction cascade accelerates Arr2 translocation is unknown. Using real-time fluorescent imaging of Arr2-green fluorescent protein translocation in dissociated ommatidia, we show that translocation is profoundly slowed in Ca(2+)-free solutions. Conversely, in a blind PLC mutant with ∼100-fold slower translocation, rapid translocation was rescued by the Ca(2+) ionophore, ionomycin. In mutants lacking NINAC (calmodulin [CaM] binding myosin III) in the cell body, translocation remained rapid even in Ca(2+)-free solutions. Immunolabeling revealed that Arr2 in the cell body colocalized with NINAC in the dark. In intact eyes, the impaired translocation found in trp mutants was rescued in ninaC;trp double mutants. Nevertheless, translocation following prolonged dark adaptation was significantly slower in ninaC mutants, than in wild type: a difference that was reflected in the slow decay of the electroretinogram. The results suggest that cytosolic NINAC is a Ca(2+)-dependent binding target for Arr2, which protects Arr2 from immobilization by a second potential sink that sequesters and releases arrestin on a much slower timescale. We propose that rapid Ca(2+)/CaM-dependent release of Arr2 from NINAC upon Ca(2+) influx accounts for the acceleration of translocation by phototransduction.

한우의 ACADS 유전자내의 SNP 탐색 및 경제형질과의 연관성 분석

The acyl-CoA dehydrogenase, C-2 to C-3 short chain (ACADS) gene is known to be related with fat metabolism, especially coverts the fat to the energy sources in cattle. In human, the mutations in this gene cause SCAD deficiency, which is one of the fatty acid metabolism disorders. The ACADS gene is located on bovine chromosome 17. The objective of this study was to identify SNPs in Hanwoo ACADS gene and identify the relationships with economic traits. In this study, two SNPs, T1570G SNP in exon 2 and G13917A SNP in exon 4, were observed. Moreover, in the coding region, 2 missense mutations, T (Cys) → G (Trp) mutation at 1570 bp and G (Arg) → A (Gln) mutation at 13917 bp, were observed. These mutations were subjected to the PCR-RFLP for typing 198 Hanwoo animals. The observed genotype frequency for T1570G was 0.135 (TT), 0.860 (TG) and 0.005 (GG), respectively. Also, 0.900 (GG) and 0.100 (GA) were observed for the G13917A mutation. The association of these SNPs with four economic traits, CW (Carcass Weight), BF (Backfat Thickness), LMA (Longissimus Muscle Area), MS (Marbling Score), were also observed. The results indicated that no significant results were observed in all four traits (P＞0.05). This might indicate that further studies are ultimately needed to use the SNPs in ACADS gene in lager populations for effectively used for the marker assisted selection.

Manipulation of the Conformation and Enzymatic Properties of T1 Lipase by Site-Directed Mutagenesis of the Protein Core

In silico and experimental investigations were conducted to explore the effects of substituting hydrophobic residues, Val, Met, Leu, Ile, Trp, and Phe into Gln 114 of T1 lipase. The in silico investigations accurately predicted the enzymatic characteristics of the mutants in the experimental studies and provided rationalization for some of the experimental observations. Substitution with Leu successfully improved the conformational stability and enzymatic characteristics of T1 lipase. However, replacement of Gln114 with Trp negatively affected T1 lipase and resulted in the largest disruption of protein stability, diminished lipase activity and inferior enzymatic characteristics. These results suggested that the substitution of a larger residue in a densely packed area of the protein core can have considerable effects on the structure and function of an enzyme. This is especially true when the residue is next to the catalytic serine as demonstrated with the Phe and Trp mutation.

Curcumin Prevents Aggregation in α-Synuclein by Increasing Reconfiguration Rate

α-Synuclein is a protein that is intrinsically disordered in vitro and prone to aggregation, particularly at high temperatures. In this work, we examined the ability of curcumin, a compound found in turmeric, to prevent aggregation of the protein. We found strong binding of curcumin to α-synuclein in the hydrophobic non-amyloid-β component region and complete inhibition of oligomers or fibrils. We also found that the reconfiguration rate within the unfolded protein was significantly increased at high temperatures. We conclude that α-synuclein is prone to aggregation because its reconfiguration rate is slow enough to expose hydrophobic residues on the same time scale that bimolecular association occurs. Curcumin rescues the protein from aggregation by increasing the reconfiguration rate into a faster regime.

Communication Between an Allosteric Inhibitor Binding Site and the Active Site in Beta-Lactamase

Beta-lactamases hydrolyze the beta-lactam ring of antibiotics, rendering them ineffective. Understanding the inhibitor recognition mechanism of beta-lactamases will give important information toward the fight against beta-lactamase mediated antibiotic resistance. Most inhibitors of beta-lactamase bind to the active site and thus inhibit beta-lactamase in a competitive manner. An allosteric inhibitor binding site, near the H10 helix (residues 218-230), has also been discovered in TEM-1 and KPC-2 beta-lactamases. Multiple sequence alignment of beta-lactamases shows that Trp 229, which resides on the H10 helix, is a highly conserved residue within the beta-lactamase family. In this study, computational mutagenesis of Trp 229 on two clinically relevant beta-lactamases, TEM-1 and SHV-1, was performed. Beta-lactamase inhibitor protein (BLIP) is known to bind TEM-1 with 1000 fold higher affinity than it binds to SHV-1. Molecular dynamics simulations were carried out on the unbound and BLIP bound forms of the wild type and W229A mutant beta-lactamases. The simulation trajectories were analyzed to obtain information about the changes in mobility. The binding free energies of the beta-lactamase - BLIP complexes were obtained and the individual energy terms contributing to the difference in affinity in the different mutants were determined. The results were compared for TEM-1 and SHV-1 to elucidate the difference in affinity toward BLIP. The change in binding dynamics upon mutation of Trp 229 was examined.

Effects of Lipids on the Conformation and Aggregation of the Repeat Domain of a Functional Amyloid, Pmel17

Pmel17 is a structural protein involved in melanin synthesis and deposition that forms fibrous striations in melanosomes, acidic organelles where pigmentation occurs. It was recently shown that a fragment of Pmel17 named the repeat domain (RPT, residues 315-444) is responsible for fibril formation in vitro under mildly acidic conditions. (McGlinchey RP. et al., PNAS, 2009; Pfefferkorn CM. et al., PNAS, 2010; McGlinchey RP. et al., JBC, 2010) Moreover, at neutral pH these fibrils disassemble, supporting a highly reversible aggregation/disaggregation process that could be a way for melanosomes to recycle amyloid fibrils. Here, we investigate the conformation and aggregation state of the RPT domain in the presence of membrane mimics, since it is localized in a membranous organelle. Specifically, micelles formed from detergents like sodium dodecyl sulfate or from lipids such as lysolipid as well as phospholipid vesicles were examined. Along with circular dichroism spectroscopy, which reports on the formation of secondary structure, we exploited the sole intrinsic Trp fluorophore (W423) located at the C-terminal region as a site-specific probe of interaction. To determine the specificity of this interaction, we also produced and examined single Trp mutants at the N-terminal region. Because the melanosome is an acidic organelle, we also explored the pH dependence of interaction in detail. Finally, we carried out aggregation experiments in the presence of lipid monomers and micelles in determining their effects on fibril formation.

Functional significance of some particular amino acid residues in Bombyx mori pyridoxal kinase

Pyridoxal kinase (PLK; EC 2.7.1.35) is a key enzyme for vitamin B(6) metabolism in animals. It catalyzes the ATP-dependent phosphorylation of pyridoxal, generating pyridoxal 5'-phosphate, an important cofactor for many enzymatic reactions. Bombyx mori PLK (BmPLK) is 10 or more residues shorter than mammalian PLKs, and some amino acid residues conserved in the PLKs from mammals are not maintained in the protein. Multiple sequence alignment suggested that amino acid residues Thr(47), Ile(54), Arg(88), Asn(121) and Glu(230) might play important roles in BmPLK. In this study, we used a site-directed specific mutagenesis approach to determine the functional significance of these particular amino acid residues in BmPLK. Our results demonstrated that the mutation of Asn(121) to Glu did not affect the catalytic function of BmPLK. The corresponding site-directed mutants of Thr(47) to Asn, Ile(54) to Phe, and Arg(88) to Ile displayed a decreased catalytic efficiency and an elevated Km value for substrate relative to the wild-type value, and no enzyme activity could be detected in mutant of Trp(230) to Glu. Circular dichroism analysis revealed that the mutation of Trp(230) to Glu resulted in mis-folding of the protein. Our results provided direct evidence that residue Trp(230) is crucial to maintain the structural and functional integrity of BmPLK. This study will add to the existing understanding of the characteristic of structure and function of BmPLK.