Residue specific contributions to stability and activity inferred from saturation mutagenesis and deep sequencing

Multiple methods currently exist for rapid construction and screening of single-site saturation mutagenesis (SSM) libraries in which every codon or nucleotide in a DNA fragment is individually randomized. Nucleotide sequences of each library member before and after screening or selection can be obtained through deep sequencing. The relative enrichment of each mutant at each position provides information on its contribution to protein activity or ligand-binding under the conditions of the screen. Such saturation scans have been applied to diverse proteins to delineate hot-spot residues, stability determinants, and for comprehensive fitness estimates. The data have been used to design proteins with enhanced stability, activity and altered specificity relative to wild-type, to test computational predictions of binding affinity, and for protein model discrimination. Future improvements in deep sequencing read lengths and accuracy should allow comprehensive studies of epistatic effects, of combinational variation at multiple sites, and identification of spatially proximate residues.

Sparsely populated residue conformations in protein structures: Revisiting ``experimental'' Ramachandran maps

The Ramachandran map clearly delineates the regions of accessible conformational (phi-) space for amino acid residues in proteins. Experimental distributions of phi, values in high-resolution protein structures, reveal sparsely populated zones within fully allowed regions and distinct clusters in apparently disallowed regions. Conformational space has been divided into 14 distinct bins. Residues adopting these relatively rare conformations are presented and amino acid propensities for these regions are estimated. Inspection of specific examples in a completely arid, fully allowed region in the top left quadrant establishes that side-chain and backbone interactions may provide the energetic compensation necessary for populating this region of phi- space. Asn, Asp, and His residues showed the highest propensities in this region. The two distinct clusters in the bottom right quadrant which are formally disallowed on strict steric considerations correspond to the gamma turn (C7 axial) conformation (Bin 12) and the i + 1 position of Type II turns (Bin 13). Of the 516 non-Gly residues in Bin 13, 384 occupied the i + 1 position of Type II turns. Further examination of these turn segments revealed a high propensity to occur at the N-terminus of helices and as a tight turn in hairpins. The strand-helix motif with the Type II turn as a connecting element was also found in as many as 57 examples. Proteins 2014; 82:1101-1112. (c) 2013 Wiley Periodicals, Inc.

C-11/C-9 Helices in Crystals of alpha beta Hybrid Peptides and Switching Structures between Helix Types by Variation in the alpha-Residue

Close-packed helices with mixed hydrogen bond directionality are unprecedented in the structural chemistry of alpha-polypeptides. While NMR studies in solution state provide strong evidence for the occurrence of mixed helices in (beta beta)(n) and (alpha beta)(n) sequences, limited information is currently available in crystals. The peptide structures presented show the occurrence of C-11/C-9 helices in (alpha beta)(n) peptides. Transitions between C-11 and C-11/C-9 helices are observed upon varying the alpha-amino acid residue.

Influence of crystallographic texture and microstructure on elastic modulus of steels

In this paper the effects of crystallographic texture and microstructure on the elastic modulus of different grades of steel have been collected from the available literature and put in one place. It is expected that this will help researchers in their understanding of both the fundamental and the practical aspects of the different grades of steel used for various purposes.

Directing peptide conformation with centrally positioned pre-organized dipeptide segments: studies of a 12-residue helix and beta-hairpin

Secondary structure formation in oligopeptides can be induced by short nucleating segments with a high propensity to form hydrogen bonded turn conformations. Type I/III turns facilitate helical folding while type II'/I' turns favour hairpin formation. This principle is experimentally verified by studies of two designed dodecapeptides, Boc-Val-Phe-Leu-Phe-Val-Aib-Aib-Val-Phe-Leu-Phe-Val-OMe 1 and Boc-Val-Phe-Leu-Phe-Val- (D) Pro- (L) Pro-Val-Phe-Leu-Phe-Val-OMe 2. The N- and C-terminal flanking pentapeptide sequences in both cases are identical. Peptide 1 adopts a largely alpha-helical conformation in crystals, with a small 3(10) helical segment at the N-terminus. The overall helical fold is maintained in methanol solution as evidenced by NMR studies. Peptide 2 adopts an antiparallel beta-hairpin conformation stabilized by 6 interstrand hydrogen bonds. Key nuclear Overhauser effects (NOEs) provide evidence for the antiparallel beta-hairpin structure. Aromatic proton chemical shifts provide a clear distinction between the conformation of peptides 1 (helical) and 2 (beta-hairpin). The proximity of facing aromatic residues positioned at non-hydrogen bonding positions in the hairpin results in extensively ring current shifted proton resonances in peptide 2.

Effect of grain boundary engineering on the microstructure and mechanical properties of copper containing austenitic stainless steel

The present investigation deals with grain boundary engineering of a modified austenitic stainless steel to obtain a material with enhanced properties. Three types of processing that are generally in agreement with the principles of grain boundary engineering were carried out. The parameters for each of the processing routes were fine-tuned and optimized. The as-processed samples were characterized for microstructure and texture. The influence of processing on properties was estimated by evaluating the room temperature mechanical properties through micro-tensile tests. It was possible to obtain remarkably high fractions of CSL boundaries in certain samples. The results of the micro-tensile tests indicate that the grain boundary engineered samples exhibited higher ductility than the conventionally processed samples. The investigation provides a detailed account of the approach to be adopted for GBE processing of this grade of steel. (C) 2014 Elsevier B.V. All rights reserved.

Discharge Plasma Combined With Bauxite Residue for Biodiesel Exhaust Cleaning: A Case Study on NOx Removal

Experiments were conducted at laboratory level to treat the oxides of nitrogen (NOx) present in raw and dry biodiesel exhaust utilizing a combination of electric discharge plasma and bauxite residue, i. e., red mud, an industrial waste byproduct from the aluminum industry. In this paper, the adsorption and a possible catalytic property of bauxite residue are discussed. Nonthermal plasma was generated using dielectric barrier discharges initiated by ac/repetitive pulse energization. The effect of corona electrodes on the plasma generation was qualitatively studied through NOx cleaning. The plasma reactor and adsorbent reactors were connected in cascade while treating the exhaust. The diesel generator, running on biodiesel fuel, was electrically loaded to study the effectiveness of the cascade system in cleaning the exhaust. Interestingly, under the laboratory conditions studied, plasma-bauxite residue combination has shown good synergistic properties and enhanced the NOx removal up to about 90%. With proper scaling up, the suggested cascade system may become an economically feasible option to treat the exhaust in larger installations. The results were discussed emphasizing the role of bauxite residue as an adsorbent and as a room temperature catalyst.

Synergistic effect of colchicine and iodide ions on the corrosion of mild steel in 0.5 M H2SO4

The inhibition behavior of colchicine (CC) on the corrosion of mild steel in 0.5 M H2SO4 was evaluated by electrochemical methods such as potentiodynamic polarization and electrochemical impedance spectroscopic measurements. The inhibition efficiency increases with increasing concentration of CC. The potentiodynamic polarization results reveal that CC act as a mixed-type inhibitor by retarding both cathodic and anodic corrosion reactions. Additionally, the synergism was carried out between CC and KI to improve the corrosion inhibition behavior of CC on mild steel. The adsorption of both CC alone and the combined inhibitor (CC + KI) on mild steel surface follows Langmuir adsorption isotherm. The synergism parameter (S (theta) ) was calculated to recognize the existence of synergism between CC and iodide ions. Lastly, an adsorption mechanism of CC molecules with iodide ions is discussed.

Damage mechanisms in stainless steel and chromium carbide coatings under controlled environment fretting conditions

Fretting is of a serious concern in many industrial components, specifically, in nuclear industry for the safe and reliable operation of various component and/or system. Under fretting condition small amplitude oscillations induce surface degradation in the form of surface cracks and/or surface wear. Comprehensive experimental studies have been carried out simulating different fretting regimes under ambient and vacuum (10(-9) MPa) conditions and, temperature up to 400 degrees C. Studies have been carried out with stainless steel spheres on stainless steel flats, and stainless steel spheres against chromium carbide, with 25% nickel chrome binder coatings. Mechanical responses are correlated with the damage observed. It has been observed that adhesion plays a vital role in material degradation process, and its effectiveness depends on mechanical variables such as normal load, interfacial tangential displacement, characteristics of the contacting bodies and most importantly on the environment conditions. Material degradation mechanism for ductile materials involved severe plastic deformation, which results in the initiation or nucleation of cracks. Ratcheting has been observed as the governing damage mode for crack nucleation under cyclic tangential loading condition. Further, propagation of the cracks has been observed under fatigue and their orientation has been observed to be governed by the contact conditions prevailing at the contact interface. Coated surfaces show damage in the form of brittle fracture and spalling of the coatings. Existence of stick slip has been observed under high normal load and low displacement amplitude. It has also been observed that adhesion at the contact interface and instantaneous cohesive strength of the contacting bodies dictates the occurrence of material transfer. The paper discusses the mechanics and mechanisms involved in fretting damage under controlled environment conditions. (C) 2015 Elsevier B.V. All rights reserved.

The role of hydrogen in hardening/softening steel: Influence of the charging process

Thermal desorption spectroscopy and nanoindentation techniques were employed to elucidate the key differences in the hydrogen (H) charging methods (electrochemical versus gaseous) and their consequences on the mechanical response of a low carbon steel. While electrochemical charging enhances the hardness, gaseous charging reduces it. This contrasting behavior is rationalized in terms of the dependency of the strength on the absorbed amount of H during charging and the H concentration gradient in the specimen. (C) 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Investigation of the inhibition effect of ibuprofen triazole against mild steel corrosion in an acidic environment

The inhibition performance of ibuprofen triazole (IT) on mild steel (MS) corrosion in 1.0 M HCl and 0.5 M H2SO4 has been investigated by using electrochemical (potentiodynamic polarization and electrochemical impedance spectroscopy), gravimetric, and quantum chemical studies. Electrochemical investigation indicates that IT hampers MS corrosion via adsorption through a mixed inhibition mechanism. The protection ability of IT increases with an increasing concentration of inhibitor and decreases with increasing temperature. The adsorption of IT molecules on MS surface follows the Langmuir adsorption isotherm. Certain quantum chemical parameters were calculated to ascertain the correlation between inhibitive effect and molecular structure of IT.

Ab Initio MD Simulations of the Bronsted Acidity of Glutathione in Aqueous Solutions: Predicting pK(a) Shifts of the Cysteine Residue

The tripeptide glutathione (GSH) is one of the most abundant peptides and the major repository for nonprotein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thiol-disulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influence the redox couple, and hence the pK(a) value of the cysteine residue of GSH is critical to its functioning. Here we report ab initio Car-Parrinello molecular dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. We show that the free-energy landscape for the protonation-deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides shift in the dissociation constant values as compared with the isolated accurate estimates of the pK(a) and correctly predicts the cysteine amino acid.

Luffa acutangula agglutinin: Primary structure determination and identification of a tryptophan residue involved in its carbohydrate-binding activity using mass spectrometry

A lectin from phloem exudates of Luffa acutangula (ridge gourd) was purified on chitin affinity chromatography and characterized for its amino acid sequence and to study the role of tryptophan in its activity. The purified lectin was subjected to various proteolytic digestions, and the resulting peptides were analyzed by liquid chromatography coupled electrospray ionization ion trap mass spectrometer. The peptide precursor ions were fragmented by collision-induced dissociation or electron transfer dissociation experiments, and a manual interpretation of MS/MS was performed to deduce amino acid sequence. This gave rise to almost complete sequence coverage of the lectin which showed high-sequence similarity with deduced sequences of phloem lectins present in the database. Chemical modification of lysine, tyrosine, histidine, arginine, aspartic acid, and glutamic acid residues did not inhibit the hemagglutinating activity. However, the modification of tryptophan residues using N-bromosuccinimide showed the loss of hemagglutinating activity. Additionally, the mapping of tryptophan residues was performed to determine the extent and number of residues modified, which revealed that six residues per molecule were oxidized suggesting their accessibility. The retention of the lectin activity was seen when the modifications were performed in the presence of chitooligosaccharides due to protection of a tryptophan residue (W-102) in the protein. These studies taken together have led to the identification of a particular tryptophan residue (W-102) in the activity of the lectin. (c) 2015 IUBMB Life, 67(12):943-953, 2015

Surface modification of mild steel by a self-assembled cetyl-trimethyl ammonium bromide (CTAB) monolayer: Evaluation of its corrosion protection property

The surface of mild steel was modified by generating cetyl-trimethyl ammonium bromide (CTAB) self-assembled monolayer (SAM) to enhance the corrosion resistance property. The experimental parameters (pH and time) for SAM generation were optimized. The modified surface was characterized by infrared reflection absorption spectroscopy (IRRAS) and contact angle measurements. The SAM generated in 1 mM solution of CTAB at pH 2.5 for 2 h showed a regimented monolayer. Polarization and electrochemical impedance spectroscopic (EIS) studies demonstrated a significant enhancement in the corrosion resistance property of the SAM protected steel in both 1 M HCl and 3.5% NaCl solution. The CTAB SAM surface substantially reduced the corrosion rate by approximately 4 times in 1 M HCl and 1.5 times in 3.5% NaCl media as compared to bare steel. Scanning electron microscopy images confirmed the formation of lesser amounts of corrosion products on the SAM protected surface. (C) 2015 Elsevier B.V. All rights reserved.