Identification of Critical Amino Acid Residues for Human iNOS Functional Activity

Nitric oxide (NO) is a short-lived signaling molecule that mediates a variety of biological functions, including vascular homeostasis, neurotransmission, antimicrobial defense and antitumor activities. Three known NOS isoforms (eNOS, nNOS and iNOS) have been cloned and sequenced. Here, we show that upon expression in Escherichia coli using a novel expression vector, an iNOS sequence containing three mutations (A805D, F831S and L832P) within the iNOS reductase domain produced very little functionally active iNOS protein compared to the wild type (wt) iNOS. Each of these point mutations also was individually constructed into the wt iNOS sequence. The activity of the iNOS protein containing the A805D mutation was comparable to wt, while a drastic reduction in iNOS activity was observed for the F831S and L832P mutants. A comparison of the molecular models of the reductase domain of the wt and mutant iNOS revealed a reduced core packing density for the F831S and L832P mutations compared to wt. In addition, the modeling also suggests altered hydrogen bonding, van der Waals and hydrophobic interactions of these mutants.     

Characterization of Colicin Ia and Colicin Ib: Antigenic Homology

Immunological techniques have been employed to determine antigenic homology between colicin Ia and colicin Ib. Results of these experiments demonstrate that the two colicins are antigenically similar.     

Gating Movements of Colicin A and Colicin Ia Are Different

The effect of temperature on fusion of Sendai virus with target membranes and mobility of the viral glycoproteins was studied with fluorescence methods. When intact virus was used, the fusion threshold temperature (20–22°C) was not altered regardless of the different types of target membranes. Viral glycoprotein mobility in the intact virus increased with temperature, particularly sharply at the fusion threshold temperature. This effect was suppressed by the presence of erythrocyte ghosts and/or dextran sulfate in the virus suspension. In these cases also, no change in the fusion threshold temperature was observed. On the other hand, reconstituted viral envelopes (virosomes) bearing viral glycoproteins but lacking matrix proteins were capable of fusing with erythrocyte ghosts even at temperatures lower than the fusion threshold temperature and no fusion threshold temperature was observed over the range of 10–40°C. The mobility of viral glycoproteins on virosomes was much greater and virtually temperature-independent. The intact virus treated with an actin-affector, jasplakinolide, reduced the extent of fusion with erythrocyte ghosts and the mobility of viral glycoproteins, while the treatment of virosomes with the same drug did not affect the extent of fusion of virosomes with erythrocyte ghosts and the mobility of the glycoproteins. These results suggest that viral matrix proteins including actins affect viral glycoprotein mobility and may be responsible for the temperature threshold phenomenon observed in Sendai virus fusion.This revised version was published online in August 2005 with a corrected cover date.     

Transmembrane insertion of the Colicin Ia hydrophobic hairpin

Colicin Ia is a bactericidal protein that forms voltage-dependent, ion-conducting channels, both in the inner membrane of target bacteria and in planar bilayer membranes. Its amino acid sequence is rich in charged residues, except for a hydrophobic segment of 40 residues near the carboxyl terminus. In the crystal structure of colicin Ia and related colicins, this segment forms an α-helical hairpin. The hydrophobic segment is thought to be involved in the initial association of the colicin with the membrane and in the formation of the channel, but various orientations of the hairpin with respect to the membrane have been proposed. To address this issue, we attached biotin to a residue at the tip of the hydrophobic hairpin, and then probed its location with the biotin-binding protein streptavidin, added to one side or the other of a planar bilayer. Streptavidin added to the same side as the colicin prevented channel opening. Prior addition of streptavidin to the opposite side protected channels from this effect, and also increased the rate of channel opening; it produced these effects even before the first opening of the channels. These results suggest a model of membrane association in which the colicin first binds with the hydrophobic hairpin parallel to the membrane; next the hairpin inserts in a transmembrane orientation; and finally the channel opens. We also used streptavidin binding to obtain a stable population of colicin molecules in the membrane, suitable for the quantitative study of voltage-dependent gating. The effective gating charge thus determined is pH-independent and relatively small, compared with previous results for wild-type colicin Ia. Received: 12 November 1996/Revised: 23 January 1997     

Identification of Amino Acid Residues Essential for the Catalytic Reaction of Bacillus kaustophilus Leucine Aminopeptidase

The functional significance of amino acid residues Lys-265, Asp-270, Lys-277, Asp-288, Asp-347, Glu-349, and Arg-351 of Bacillus kaustophilus leucine aminopeptidase was explored by site-directed mutagenesis. Variants with an apparent molecular mass of approximately 54 kDa were overexpressed in Escherichia coli and purified to homogeneity by nickel-chelate chromatography. The purified mutant enzymes had no LAP activity, implying that these residues are important for the catalytic reaction of the enzyme.     

人白细胞介素18突变体的构建及其功能

为研究人白细胞介素 18(hIL 18)结构与功能的关系 ,用PCR定点突变技术分别构建了N末端、C末端缺失突变体(ΔNC)和IL 1特征样序列突变体S154A/Y156F/E157P/C163 T (S)。将突变体cDNA与原核表达载体 pJW 2重组并转化大肠杆菌DH5α ,经热诱导表达蛋白质 ,SDS PAGE证实表达的目的蛋白质以包涵体形式存在。菌体经超声破碎后 ,包涵体以 2mol/L尿素洗涤 ,8mol/L尿素溶解 ,并经SephadexG 75柱纯化 ,纯度可达 95 %以上。突变体蛋白质经逐步稀释复性后 ,以诱导人外周血单个核细胞 (PBMC)产生干扰素 γ(IFN γ)及对核因子 κB(NF κB)的激活能力为指标 ,检测突变体的生物学活性。结果显示ΔNC、S这 2个突变体对IFN γ的诱生能力显著低于野生型hIL 18,分别为野生型hIL 18的 13%和 4 8%。同时 ,ΔNC、S对NF κB的激活能力也低于野生型hIL 18,分别为野生型hIL 18的 6 9.7%和 89.8%。这些结果表明缺失的片段或突变的位点对hIL 18的功能有重要的作用。     

Racemization of Amino Acid Residues in Proteins during Roasting

Formation of N-acetylkanamycin amidohydrolase (NAKA) in a strain of Streptomyces kanamyceticus proceeded in parallel with the increase of both kanamycin (KM) and N-acetylkanamycin (NAK) in the initial period. NAKA formation then suddenly began to decrease in NAK but KM continued to increase before reaching a maximum level. The study on conversion of intracellular NAK into KM using washed cells has shown that the endogenous activity of NAKA is most efficiently induced by acetate together with the activity of isocitrate lyase and N-acetyltyrosine amidohydrolase. Sclerin (SCL) stimulated their induction in the same manner, while N-acetyltyrosine repressed NAKA. Glucose effect was relieved by SCL and some amino acids. From these results, change in the chemical composition of cells in idiophase was well elucidated.     

Understanding the Functional Roles of Amino Acid Residues in Enzyme Catalysis

The MACiE database contains 223 distinct step-wise enzyme reaction mechanisms and holds representatives from each EC sub-subclass where there is a crystal structure and sufficient evidence in the literature to support a mechanism. Each catalytic step of every reaction sequence in MACiE is fully annotated so that it includes the function of the catalytic residues involved in the reaction and the mechanism by which substrates are transformed into products. Using MACiE as a knowledge base, we have seen that the top 10 most catalytic residues are histidine, aspartate, glutamate, lysine, cysteine, arginine, serine, threonine, tyrosine and tryptophan. Of these only seven (cysteine, histidine, aspartate, lysine, serine, threonine and tyrosine) dominate catalysis and provide essentially five functional roles that are essential. Stabilisation is the most common and essential role for all classes of enzyme, followed by general acid/base (proton acceptor and proton donor) functionality, with nucleophilic addition following closely behind (nucleophile and nucleofuge). We investigated the occurrence of these residues in MACiE and the Catalytic Site Atlas and found that, as expected, certain residue types are associated with each functional role, with some residue types able to perform diverse roles. In addition, it was seen that different EC classes of enzyme have a tendency to employ different residues for catalysis. Further, we show that whilst the differences between EC classes in catalytic residue composition are not immediately obvious from the general classes of Ingold mechanisms, there is some weak correlation between the mechanisms involved in a given EC class and the functions that the catalytic amino acid residues are performing. The analysis presented here provides a valuable insight into the functional roles of catalytic amino acid residues, which may have applications in many aspects of enzymology, from the design of novel enzymes to the prediction and validation of enzyme reaction mechanisms.     

Oligomeric Structure of Colicin Ia Channel in Lipid Bilayer Membranes

Colicin Ia is a soluble, harpoon-shaped bacteriocin which translocates across the periplasmic space of sensitive Escherichia coli cell by parasitizing an outer membrane receptor and forms voltage-gated ion channels in the inner membrane. This process leads to cell death, which has been thought to be caused by a single colicin Ia molecule. To directly visualize the three-dimensional structure of the channel, we generated two-dimensional crystals of colicin Ia inserted in lipid-bilayer membranes and determined a ∼17 three-dimensional model by electron crystallography. Supported by velocity sedimentation, chemical cross-linking and single-particle image analysis, the three-dimensional structure is a crown-shaped oligomer enclosing a ∼35 Å-wide extrabilayer vestibule. Our study suggests that lipid insertion instigates a global conformational change in colicin Ia and that more than one molecule participates in the channel architecture with the vestibule, possibly facilitating the known large scale peptide translocation upon channel opening.Colicin Ia is a pore-forming water-soluble bacterial toxin produced by some strains of Escherichia coli to kill other competing bacteria (1, 2). It belongs to a functionally and structurally similar group of proteins that also includes colicins A (3), E1 (4), and N (5). Each of these proteins consist of three domains with distinct properties; the receptor domain (R), which binds a specific outer membrane receptor on the target cell, and the translocation domain (T) at the N terminus, responsible for traversing the outer membrane and the periplasmic space to deliver the channel-forming domain (C) at the C terminus to the bacterial inner membrane. The bundle of 10 α-helices that compose the C domain changes its conformation to form a voltage-gated ion channel in the plasma membrane. Opening of the channel produces an efflux of ions that depletes the cellular energy resources and ultimately leads to cell death.The x-ray structure of full-length, soluble colicin Ia (69 kDa) has been determined (6). The monomeric molecule is mostly α-helical, with the R domain separated from the T and C domains by a pair of unusually long (∼160 Å) α-helices thought possibly to span the periplasmic space during channel formation (6). The C domain is characterized by two hydrophobic helices (VIII and IX; residues Ala-580—Ile-612) that is surrounded by the remaining eight largely amphipathic α-helices. The same structural motif for the C domain is conserved in other members of the colicin family and is also present in the channel-forming domains of diphtheria toxin, exotoxin A, and the Bcl family of pro- and anti-apoptotic proteins (7). This pair of helices, termed the hydrophobic hairpin, is instrumental in driving the initial membrane insertion event (8) that is followed by a series of large scale pH and voltage-dependent conformational changes in the C domain, resulting in the opening of the ion channel in the plasma membrane (9, 10). In the absence of a high resolution membrane-inserted structure of a channel-forming colicin, solid-state NMR (11, 12), streptavidin binding (8) and cross-linking of site-directed cysteine mutants (9) have suggested that the initial membrane-bound intermediate exists as a two-dimensional helical array of the eight amphipathic helices (I-VII and X) spread across the membrane surface, with the hydrophobic helices (VIII and IX) embedded in the bilayer. A recent electron paramagnetic resonance study using preparations of spin-labeled ColA proteoliposomes has supported a similar umbrella model where the eight amphipathic helices reside at the air-water interface for the closed-channel state (13). Biotin-labeled cysteine mutants have also been used to determine how much of the C domain (aside from the hydrophobic hairpin) crosses the plasma membrane (14, 15) for colicin Ia. A large region of the amphipathic sequence (helices II-V; residues Leu-474—Tyr-541) has been found to cross from the cis to the trans side of the membrane in planar lipid bilayer experiments, resulting in a four-transmembrane segment molecule that is thought to form the ion channel.Because the 12–13 residue α-helices of the C domain are well short of the ∼20 residues required to span the plasma membrane, it has been proposed that conformational changes causing helix extension take place during the channel formation process. ¹³C spin diffusion NMR has indicated that whereas the overall secondary structure of the C domain is preserved, most of the helices undergo “opening,” and modulation of the tertiary structure allows for the required extension of the helices to cross the plasma membrane and form the channel (16). The internal structure of the colicin Ia channel has been investigated by examining the effect of different nonelectrolyte molecules on the single-channel conductance in planar lipid bilayer membranes (17). It was determined that the diameter at the cis entrance (equivalent to the outside of the cell) is 18 Å, and the diameter at the trans entrance (inside the membrane) is 10 Å, with a 7 Å diameter constriction located in close proximity to the trans entrance of the channel. More recent studies (18) employing the substituted cysteine accessibility method to determine what residues line the open colicin Ia channel suggest an hourglass-shaped pore with the most constricted part near the cis rather than the trans side, as opposed to the conclusion of Krasilnikov et al. (17). Both studies point to a pore constriction inside the membrane, and as pointed out by Kienker et al. 18), there exist plausible explanations to reconcile some of the differing results. The large diameter of the colicin Ia channel coupled with the studies which indicate that each colicin Ia molecule contributes four transmembrane segments in the membrane integrated state (14) suggests that the ion channel is formed by a multimer of colicin Ia molecules. However, all of the past studies directed at determining the oligomeric state of any of the colicin channels indicate a monomeric structure. The question as to how a four-transmembrane monomeric protein can form an ion channel of sufficient diameter to allow the passage of ions as large as tetraethyl ammonium (19) has remained unanswered.In this work we have subjected colicin Ia incorporated into lipid bilayer membranes to structural and biochemical investigations. We show, based on cross-linking and velocity sedimentation experiments, single-particle analysis of electron micrographs and results from electron crystallographic analysis of two-dimensional crystals of colicin Ia that the protein forms oligomers upon insertion into the bilayer. The suggested architecture of this oligomer based on the ∼17 Å resolution three-dimensional model and the biological implications, are discussed.     

Effects of Hydrophobic Amino Acid Substitutions on Antimicrobial Peptide Behavior

Antimicrobial peptides (AMPs) are naturally occurring components of the immune system that act against bacteria in a variety of organisms throughout the evolutionary hierarchy. There have been many studies focused on the activity of AMPs using biophysical and microbiological techniques; however, a clear and predictive mechanism toward determining if a peptide will exhibit antimicrobial activity is still elusive, in addition to the fact that the mechanism of action of AMPs has been shown to vary between peptides, targets, and experimental conditions. Nonetheless, the majority of AMPs contain hydrophobic amino acids to facilitate partitioning into bacterial membranes and a net cationic charge to promote selective binding to the anionic surfaces of bacteria over the zwitterionic host cell surfaces. This study explores the role of hydrophobic amino acids using the peptide C18G as a model system. These changes were evaluated for the effects on antimicrobial activity, peptide-lipid interactions using Trp fluorescence spectroscopy, peptide secondary structure formation, and bacterial membrane permeabilization. The results show that while secondary structure formation was not significantly impacted by the substitutions, antibacterial activity and binding to model lipid membranes were well correlated. The variants containing Leu or Phe as the sole hydrophobic groups bound bilayers with highest affinity and were most effective at inhibiting bacterial growth. Peptides with Ile exhibited intermediate behavior while those with Val or α-aminoisobutyric acid (Aib) showed poor binding and activity. The Leu, Phe, and Ile peptides demonstrated a clear preference for anionic bilayers, exhibiting significant emission spectrum shifts upon binding. Similarly, the Leu, Phe, and Ile peptides demonstrated greater ability to disrupt lipid vesicles and bacterial membranes. In total, the data indicate that hydrophobic moieties in the AMP sequence play a significant role in the binding and ability of the peptide to exhibit antibacterial activity.     

Phosphate Acceptor Amino Acid Residues in Structural Proteins of Rhabdoviruses

Partial acid hydrolysates of the [(32)P]phosphate- or [(3)H]serine-labeled proteins of purified vesicular stomatitis, rabies, Lagos bat, Mokola, or spring viremia of carp virions and of purified intracellular nucleocapsids of these viruses have been analyzed by paper electrophoresis for the presence of phosphorylated amino acids. Both phosphoserine and phosphothreonine, with the former predominant, were present in virion and nucleocapsid preparations that contained phosphoproteins. An exception was the fish rhabdovirus, which contained only phosphoserine. When vesicular stomatitis or rabies virus proteins were phosphorylated in a cell-free system by the virion-associated protein kinase and analyzed for the presence of phosphorylated amino acid residues, phosphoserine was again found to be more abundant than phosphothreonine. After in vitro protein phosphorylation, another phospho-compound, possibly a third phosphoamino acid, was detected in the partial acid hydrolysates of these viruses.     

Identification of Key Amino Acid Residues Involved in the Localization of Sorting Nexin 10 and Induction of Vacuole Formation

Biochemistry (Moscow) - Sorting nexin 10 (SNX10) induces formation of vacuoles participating in the endosome morphogenesis in mammalian cells, but the key amino acids involved in this function have...     

Identification of Bacillus thuringiensis Delta-Endotoxin Cry1C Domain III Amino Acid Residues Involved in Insect Specificity

Cry1C domain III amino acid residues involved in specificity for beet armyworm (Spodoptera exigua) were identified. For this purpose, intradomain III hybrids between Cry1E (nontoxic) and Cry1E-Cry1C hybrid G27 (toxic) were made. Crossover points of these hybrids defined six sequence blocks containing between 1 and 19 of the amino acid differences between Cry1E and G27. Blocks B, C, D, and E of G27 were shown to be required for optimal activity against S. exigua. Block E was also required for optimal activity against the tobacco hornworm (Manduca sexta), whereas block D had a negative effect on toxicity for this insect. The mutagenesis of individual amino acids in block B identified Trp-476 as the only amino acid in this block essential, although not sufficient by itself, for full S. exigua activity. In block D, we identified a seven-amino-acid insertion in G27 that was not in Cry1E. The deletion of either one of two groups of four consecutive amino acids in this insertion completely abolished activity against S. exigua but resulted in higher activity against M. sexta. Alanine substitutions of the first group had little effect on toxicity, whereas alanine substitutions of the second group had the same effect as its deletion. These results identify groups of amino acids as well as some individual residues in Cry1C domain III, which are strongly involved in S. exigua-specific activity as well as sometimes involved in M. sexta-specific activity.     

Hydrogen Bond Strengths in Phosphorylated and Sulfated Amino Acid Residues

Post-translational modification by the addition of an oxoanion functional group, usually a phosphate group and less commonly a sulfate group, leads to diverse structural and functional consequences in protein systems. Building upon previous studies of the phosphoserine residue (pSer), we address the distinct nature of hydrogen bonding interactions in phosphotyrosine (pTyr) and sulfotyrosine (sTyr) residues. We derive partial charges for these modified residues and then study them in the context of molecular dynamics simulation of model tripeptides and sulfated protein complexes, potentials of mean force for interacting residue pairs, and a survey of the interactions of modified residues among experimental protein structures. Overall, our findings show that for pTyr, bidentate interactions with Arg are particularly dominant, as has been previously demonstrated for pSer. sTyr interactions with Arg are significantly weaker, even as compared to the same interactions made by the Glu residue. Our work sheds light on the distinct nature of these modified tyrosine residues, and provides a physical-chemical foundation for future studies with the goal of understanding their roles in systems of biological interest.     

Identification of Important Amino Acid Residues of the Na+-Ca2+ Exchanger Inhibitory Peptide,XIP

The Na⁺-Ca²⁺ exchanger plays an important role in cardiac contractility by moving Ca²⁺ across the plasma membrane during excitation-contraction coupling. A 20 amino acid peptide, XIP, synthesized to mimic a region of the exchanger, inhibits exchange activity. We identify here amino acid residues important for inhibitory function. Effects of modified peptides on Na⁺-Ca²⁺ exchange activity were determined. Exchange activity was assessed as ⁴⁵Ca²⁺ uptake into Na⁺-loaded cardiac sarcolemmal vesicles. We find that the entire length of XIP is important for maximal potency, though the major inhibitory components are between residues 5 and 16. Basic and aromatic residues are most important for the inhibitory function of XIP. Substitutions of arginine 12 and arginine 14 with alanine or glutamine dramatically decrease the potency of XIP, suggesting that these residues play a key role in possible charge-charge interactions. Substitutions of other basic residues with alanines or glutamines had less effect on the potency of XIP. All aromatic residues participate in binding with the exchanger, probably via hydrophobic interactions as indicated by tryptophan fluorescence. A tyrosine is required at position 6 for maximal inhibition and phenylalanine 5 and tyrosine 8 can only be replaced by other aromatic residues. Tyrosine 10 and tyrosine 13 can be replaced with other bulky residues. A specific conformation of XIP, with structural constrains provided by all parts of the molecule, is required for optimal inhibitory function. Received: 19 September 1996/Revised: 20 November 1996     

Predicting HLA Class I Non-Permissive Amino Acid Residues Substitutions

Prediction of peptide binding to human leukocyte antigen (HLA) molecules is essential to a wide range of clinical entities from vaccine design to stem cell transplant compatibility. Here we present a new structure-based methodology that applies robust computational tools to model peptide-HLA (p-HLA) binding interactions. The method leverages the structural conservation observed in p-HLA complexes to significantly reduce the search space and calculate the system's binding free energy. This approach is benchmarked against existing p-HLA complexes and the prediction performance is measured against a library of experimentally validated peptides. The effect on binding activity across a large set of high-affinity peptides is used to investigate amino acid mismatches reported as high-risk factors in hematopoietic stem cell transplantation.     

A New Spatial Representation of Amino Acid Residues in Globular Proteins

Abstract

For the globular proteins with known three-dimensional structures, an ellipsoid model of each protein was constructed with least volume and its dimensions were derived. The spatial arrangements were made for the C_α and side chain atoms of that protein within that ellipsoid. This new spatial representation shows the residue position from the centroid, as well as the depth from the surface. The average spatial parameters were then calculated. The correlations between these new spatial parameters and the existing parameters of the amino acid residues were then derived.