Valine Residue Research Articles

How does a valine residue that modulates heme-NO binding kinetics in inducible NO synthase regulate enzyme catalysis?

Nitric oxide (NO) release from nitric oxide synthases (NOSs) depends on the dissociation of a ferric heme-NO product complex (Fe(III)NO) that forms immediately after NO is made in the heme pocket. The NOS-like enzyme of Bacillus subtilis (bsNOS) has 10-20 fold slower Fe(III)NO dissociation rate (k(d)) and NO association rate (k(on)) compared to mammalian NOS counterparts. We previously showed that an Ile for Val substitution at the opening of the heme pocket in bsNOS contributes to these differences. The complementary mutation in mouse inducible NOS oxygenase domain (Val346Ile) decreased the NO k(on) and k(d) by 8 and 3-fold, respectively, compared to wild-type iNOSoxy, and also slowed the reductive processing of the heme-O(2) catalytic intermediate. To investigate how these changes affect steady-state catalytic behaviors, we generated and characterized the V346I mutant of full-length inducible NOS (iNOS). The mutant exhibited a 4-5 fold lower NO synthesis activity, an apparent uncoupled NADPH consumption, and formation of a heme-NO complex during catalysis that was no longer sensitive to solution NO scavenging. We found that these altered catalytic behaviors were not due to changes in the heme reduction rate or in the stability of the enzyme heme-O(2) intermediate, but instead were due to the slower NO k(on) and k(d) and a slower oxidation rate of the enzyme ferrous heme-NO complex. Computer simulations that utilized the measured kinetic values confirmed this interpretation, and revealed that the V346I iNOS has an enhanced NADPH-dependent NO dioxygenase activity that converts almost 1 NO to nitrate for every NO that the enzyme releases into solution. Together, our results highlight the importance of heme pocket geometry in tuning the NO release versus NO dioxygenase activities of iNOS.

Sequence-dependent gelation kinetics of β-hairpin peptide hydrogels.

The gelation kinetics of four β-hairpin oligopeptides that have been designed to exhibit responsive behavior to changes in environmental conditions, such as pH, ionic strength and temperature, are characterized using multiple particle tracking microrheology and circular dichroism (CD) spectroscopy. The peptides, predominantly an alternating sequence of valine and lysine residues, differ by a point substitution of a single amino acid near a type II'β-turn sequence. The rate of gelation becomes faster for point substitutions which reduce the total charge of the peptide. Similarly, increasing the ionic strength reduces or screens intra- and inter-molecular electrostatic repulsions, again leading to faster gelation kinetics. CD measurements show that the concentration of folded peptide at the gel point decreases as the gelation kinetics become slower, possibly indicating a relationship between the assembly rate and the resulting gel microstructure. Finally, a model is developed based on the electrostatic barrier to peptide folding and association which agrees semi-quantitatively with the microrheology results. This represents a first step towards understanding the role of peptide charge and physico-chemical conditions in the self-assembly of these peptide hydrogelators.

A Supramodular FHA/BRCT-Repeat Architecture Mediates Nbs1 Adaptor Function in Response to DNA Damage

The Mre11/Rad50/Nbs1 protein complex plays central enzymatic and signaling roles in the DNA-damage response. Nuclease (Mre11) and scaffolding (Rad50) components of MRN have been extensively characterized, but the molecular basis of Nbs1 function has remained elusive. Here, we present a 2.3A crystal structure of the N-terminal region of fission yeast Nbs1, revealing an unusual but conserved architecture in which the FHA- and BRCT-repeat domains structurally coalesce. We demonstrate that diphosphorylated pSer-Asp-pThr-Asp motifs, recently identified as multicopy docking sites within Mdc1, are evolutionarily conserved Nbs1 binding targets. Furthermore, we show that similar phosphomotifs within Ctp1, the fission yeast ortholog of human CtIP, promote interactions with the Nbs1 FHA domain that are necessary for Ctp1-dependent resistance to DNA damage. Finally, we establish that human Nbs1 interactions with Mdc1 occur through both its FHA- and BRCT-repeat domains, suggesting how their structural and functional interdependence underpins Nbs1 adaptor functions in the DNA-damage response.

Endomannosidase undergoes phosphorylation in the Golgi apparatus

Glucose residues from N-linked oligosaccharides are removed by glucosidases I and II in the endoplasmic reticulum (ER) or by the alternate endomannosidase pathway in the Golgi apparatus. Our morphological analysis demonstrates that recombinant rat endomannosidase exhibited a cis- and medial-Golgi localization alike the endogenous enzyme and its ER to Golgi transport is COP II mediated. Recombinant endomannosidase undergoes a posttranslational modification, which is not related to N-or O-glycosylation. A shift in molecular mass of recombinant endomannosidase was observed upon phosphatase digestion but not for ER-retained CHO cell endomannosidase. Furthermore, immunoprecipitation of (35)S- and (33)P-labeled endomannosidase expressed in CHO-K1 cells suggests that recombinant endomannosidase undergoes phosphorylation. Substitution of the single cytoplasmic threonine residue of rat endomannosidase by either an alanine or valine residue resulted in the same posttranslational modification alike the wild-type enzyme. The subcellular localization and the in vivo activity of the mutant endomannosidase were not affected. Thus, endomannosidase phosphorylation is occurring in luminal sequences. Modification was prevented when endomannosidase was synthesized using reticulocyte lysates in the presence of canine microsomes. Treatment of cells with brefeldin A blocked the posttranslational modification of endomannosidase, suggesting that phosphorylation is occurring in the Golgi apparatus, the residence of endomannosidase.

Molecular cloning of a cDNA encoding for the GLP-1 receptor expressed in rat lung.

Recent data revealed the existence, localization and possible function of specific receptors for glucagon-like peptide 1 (7-36) amide (GLP-1) in rat lung. This receptor has different biochemical features than the GLP-1 receptor in endocrine pancreas. Therefore, we aimed to clone the lung receptor cDNA in order to analyze whether biochemical and functional diversity of the GLP-1 receptors in lung and pancreas is based upon genetic differences. A cDNA library from rat lung in a lambda gt11 vector was screened with a cDNA probe coding for the rat pancreas GLP-1 receptor. Thereby, we found a lung GLP-1 receptor cDNA which shows nearly complete homology to the pancreatic beta-cell receptor cDNA. Only one base exchange occurred at base 1 of a codon at position 977 resulting in a change of valine residue for isoleucine at position 323 of the amino acid sequence within the fifth transmembrane region. Northern blot hybridization identified transcripts at 2.7, 3.4, and 3.6 Kb. Expression of the recombinant lung GLP-1 receptor cDNA in CHO cells displayed a pharmacological profile similar to that seen with cells expressing the beta-cell derived cDNA. Therefore, we conclude that tissue-specificity for GLP-1 receptors is based upon posttranslational modifications of the receptor protein (for example glycosilation) or alternative splicing of primary transcripts and not on variations within the coding sequence of the receptor gene.

Mutations in the TSPYL1 gene associated with 46,XY disorder of sex development and male infertility

We screened 100 individuals with anomalies of testicular development or function for mutations in the TSPYL1 gene. A 46,XY female with complete gonadal dysgenesis carried a p.K320R mutation in the highly conserved NAP domain, and a 46,XY male with idiopathic azoospermia harbored a p.R89H mutation, and this data supports the hypothesis that mutations in TSPYL1 may contribute to anomalies of testicular development/function.

Mechanistic Basis of 5′-3′ Translocation in SF1B Helicases

Superfamily 1B (SF1B) helicases translocate in a 5'-3' direction and are required for a range of cellular activities across all domains of life. However, structural analyses to date have focused on how SF1A helicases achieve 3'-5' movement along nucleic acids. We present crystal structures of the complex between the SF1B helicase RecD2 from Deinococcus radiodurans and ssDNA in the presence and absence of an ATP analog. These snapshots of the reaction pathway reveal a nucleotide binding-induced conformational change of the two motor domains that is broadly reminiscent of changes observed in other SF1 and SF2 helicases. Together with biochemical data, the structures point to a step size for translocation of one base per ATP hydrolyzed. Moreover, the structures also reveal a mechanism for nucleic acid translocation in the 5'-3' direction by SF1B helicases that is surprisingly different from that of 3'-5' translocation by SF1A enzymes, and explains the molecular basis of directionality.

Metal-binding loop length and not sequence dictates structure

The C-terminal copper-binding loop in the β-barrel fold of the cupredoxin azurin has been replaced with a range of sequences containing alanine, glycine, and valine residues to assess the importance of amino acid composition and the length of this region. The introduction of 2 and 4 alanines between the coordinating Cys, His, and Met results in loop structures matching those in naturally occurring proteins with the same loop lengths. A loop with 4 alanines between the Cys and His and 3 between the His and Met ligands has a structure identical to that of the WT protein, whose loop is the same length. Loop structure is dictated by length and not sequence allowing the properties of the main surface patch for interactions with partners, to which the loop is a major contributor, to be optimized. Loops with 2 amino acids between the ligands using glycine, alanine, and valine residues have been compared. An empirical relationship is found between copper site protection by the loop and reduction potential. A loop adorned with 4 methyl groups is sufficient to protect the copper ion, enabling most sequences to adequately perform this task. The mutant with 3 alanine residues between the ligands forms a strand-swapped dimer in the crystal structure, an arrangement that has not, to our knowledge, been seen previously for this family of proteins. Cupredoxins function as redox shuttles and are required to be monomeric; therefore, none have evolved with a metal-binding loop of this length.

Properties of the Thioredoxin Fold Superfamily Are Modulated by a Single Amino Acid Residue

The ubiquitous thioredoxin fold proteins catalyze oxidation, reduction, or disulfide exchange reactions depending on their redox properties. They also play vital roles in protein folding, redox control, and disease. Here, we have shown that a single residue strongly modifies both the redox properties of thioredoxin fold proteins and their ability to interact with substrates. This residue is adjacent in three-dimensional space to the characteristic CXXC active site motif of thioredoxin fold proteins but distant in sequence. This residue is just N-terminal to the conservative cis-proline. It is isoleucine 75 in the case of thioredoxin. Our findings support the conclusion that a very small percentage of the amino acid residues of thioredoxin-related proteins are capable of dictating the functions of these proteins.

Ligand Selectivity and Gene Regulation by the Human Aryl Hydrocarbon Receptor in Transgenic Mice

The aryl hydrocarbon receptor (AHR) is a ligand-inducible transcription factor that displays interspecies differences with the human and mouse AHR C-terminal region sequences sharing only 58% amino acid sequence identity. Compared with the mouse AHR (mAHR), the human AHR (hAHR) displays approximately 10-fold lower relative affinity for prototypical AHR ligands such as 2,3,7,8-tetrachlorodibenzo-p-dioxin, which has been attributed to the amino acid residue valine 381 (alanine 375 in the mAHR) in the ligand binding domain of the hAHR. We investigated whether the 10-fold difference in ligand-binding affinity between the mAHR and hAHR would be observed with a diverse range of AHR ligands. To test this hypothesis, ligand binding assays were performed using the photo-affinity ligand 2-azido-3-[(125)I]iodo-7,8-dibromodibenzo-p-dioxin and liver cytosol isolated from hepatocyte-specific transgenic hAHR mice and C57BL/6J mice. It is noteworthy that competitive ligand-binding assays revealed that, compared with the mAHR, the hAHR has a higher relative affinity for certain compounds, including indirubin [(2Z)-2,3-biindole-2,3 (1'H,1'H)-dione and quercetin (2-(3,4dihydroxyphenyl)-3,5,7-trihydroxy-4H-chromen-4-one]. Electrophoretic mobility shift assays revealed that indirubin was more efficient at transforming the hAHR compared with the mAHR. Indirubin was also a more potent inducer of Cyp1a1 expression in transgenic hAHR mouse hepatocytes compared with C57BL/6J mouse hepatocytes. These observations suggest that indirubin is a potent hAHR ligand that is able to selectively bind to and activate the hAHR. These discoveries imply that there may be a significant degree of structural divergence between mAHR and hAHR ligands and highlights the importance of the hAHR transgenic mouse as a model to study the hAHR in vivo.

Electrochemical characterisation of a conductive polymer molecularly imprinted with an Amadori compound

Type II diabetes is a disease that is often characterised by elevated levels of advanced glycation end-products (AGEs), e.g. glycated haemoglobin (HbA 1c), in a patient's bloodstream. This glycation reaction occurs when the carbonyl group of a circulating sugar (glucose) reacts with the amino group of the terminal valine residue of a haemoglobin chain, to form an unstable imine. This compound then undergoes an Amadori rearrangement to form the stable Amadori compound N-(1-deoxy-β- d-fructopyranose-1-yl)- l-valine (Fru-Val). As an initial approach to fabricating a sensor for the Fru-Val component of HbA 1c, molecular imprints of Fru-Val were made in poly-aminophenylboronic acid (p-APBA), using ammonium persulphate as the initiator, on conductive indium-doped tin oxide (ITO) electrodes (nominal working area 0.5 cm 2). The affinity of the imprints formed in the p-APBA, for fructose and valine as individual molecules, as well as for the complete template used for imprinting (Fru-Val), was assessed electrochemically, by the use of open circuit potential (Δ E oc) measurements. These showed that the imprinted materials when challenged with Fru-Val had an open circuit response of ∼5.0 × 10 −3 V. d-Fructose (10 mM), a component of the template, when introduced into the cell gave a far more significant change in the open circuit potential (Δ E oc = ∼2.9 × 10 −3 V) than did a similar concentration of d-glucose, a non-template carbohydrate (Δ E oc = ∼4.0 × 10 −4 V). Non-template structured p-APBA films, made as controls in the absence of Fru-Val, showed negligible response to either d-fructose or d-glucose. Additionally, we have shown that the imprinted films show a progressive reduction in response to sequential additions of d-fructose, implying the saturation of imprinted sites and a limit to non-specific recognition.

The A563T variation of the renal epithelial calcium channel TRPV5 among African Americans enhances calcium influx

The transient receptor potential cation channel, subfamily V, member 5 (TRPV5) gene, which encodes the Ca(2+) channel in the apical membrane of distal convoluted tubule and connecting tubule of the kidney, exhibits an unusually high frequency of nonsynonymous single nucleotide polymorphisms (SNPs) among African Americans. To assess the functional impacts of the nonsynonymous SNP variations in TRPV5, these variants were analyzed with radiotracer (45)Ca(2+) influx assay and the voltage-clamp technique using Xenopus laevis oocytes. Among the variations tested, including A8V, R154H, A563T, and L712F, the latter two significantly increased TRPV5-mediated Ca(2+) influx. The A563T variant, which exists in African Americans with relative high frequency, exhibited increased Ca(2+) influx at extracellular Ca(2+) from 0.01 to 2 mM despite a lower expression level at the plasma membrane. This variant also exhibited a reduction in Na(+) current as a result of increased sensitivity to extracellular Mg(2+). By substituting threonine-563 (Thr(563)) with serine or valine residue, the bulky side chain of Thr(563) was shown to facilitate Ca(2+) transport, whereas the hydroxyl group of Thr(563) is likely related to Mg(2+) sensitivity. The A563T variant was capable of increasing TRPV5-mediated Ca(2+) influx, even when it was expressed under conditions mimicking heterozygous or compound state with other variants. In conclusion, the A563T variant of TRPV5 significantly increased Ca(2+) influx by affecting the Ca(2+) permeation pathway. Thus the A563T variation in TRPV5 may contribute to the superior ability of renal Ca(2+) conservation in African Americans.

Correction: The Critical Role of Partially Exposed N-Terminal Valine Residue in Stabilizing GH10 Xylanase from Bacillus sp.NG-27 under Poly-Extreme Conditions

Correction: The Critical Role of Partially Exposed N-Terminal Valine Residue in Stabilizing GH10 Xylanase from Bacillus sp.NG-27 under Poly-Extreme Conditions

Isotope-edited Infrared Spectroscopy of 3-10 Helical Peptides

Infrared spectroscopy (IR) is a valuable tool for probing the conformation and dynamics of peptides. The amide I band is particularly sensitive to the strength and position of the hydrogen bonds that define secondary structure. Site-specific structural information can be obtained by sequential, systematic isotope labeling of the backbone (1). In this study, isotope-edited infrared spectroscopy was applied for the elucidation of residue level structural information of model 3-10 hexameric peptides. A series of peptides comprised of four aminoisobutyric acid (Aib) and two α-methyl valine residues were prepared to include two 13C labels at the N-terminus, middle and C-terminus positions (2). The IR spectra were measured in CDCl3 solution. Far-ultraviolet circular dichroism spectra in 2, 2, 2- trifluoroethanol confirmed 3-10 helical structure for all peptides. The spectral features of the 12C and 13C amide I depend on the position of the isotope label and the nature of the buffer. These differences are discussed in terms of the x-ray structure of the peptides and the details of the 3-10 helical conformation.1. Decatur, S.M. (2006) Accounts of Chemical Research 39:169-175.2. Maekawa, H.; Toniolo, C.; Broxterman, Q.B.; Ge, N.H. (2007) J. Phys. Chem B. 111, 3222-3235.

Strategy for Identification by Mass Spectrometry of a New Human Hemoglobin Variant with Two Mutations in Cis in the β-Globin Chain: Hb S-Clichy [β6(A3)Glu→Val; β8(A5)Lys→Thr

Hemoglobinopathies are the most frequent genetic diseases in the world. Among them, the Hb S variant [β6(A3)Glu→Val], which, in the homozygous state, produces a severe disease known as sickle cell anemia with polymerization of Hb S inside red blood cells under hypoxic conditions. Additional mutations, in cis or in trans of the βS-globin chain, may inhibit or enhance the polymerization process. We describe here a new hemoglobin (Hb) variant (Hb S-Clichy) which carries the βS‐globin chain and an additional mutation β8(A5)Lys→Thr. The variant was detected by routine electrophoretic techniques and cation exchange liquid chromatography (CE-LC). Globin chain separation by reversed phase LC (RP-LC) showed normal and abnormal β chains, confirming that the additional abnormality was located in cis to Hb S. Electrospray ionization mass spectrometry (ESI-MS) gave a 57 Da mass decrease for the abnormal globin chain. The abnormal chain was isolated and submitted to trypsin digestion. Normal peptides βT-1 and βT-2 were not observed on the matrix-assisted laser desorption-time of flight (MALDI-TOF) mass spectrum but a new peptide βT-1,2 was detected. Nano LC-ESI-MS/MS of the new peptide showed that the glutamic acid at codon 6 was replaced by a valine residue, and the lysine at codon 8 was replaced by a threonine residue, as confirmed by DNA sequencing. This example demonstrates that in a population where Hb S is present, every unidentified Hb needs to be clearly characterized to prevent major sickle cell syndromes. In addition, the identification of these variants must be considered in newborn screening for sickle cell disease, using either classical biochemical methods or MS techniques.

A novel 9-bp insertion detected in steroid 21-hydroxylase gene (CYP21A2): prediction of its structural and functional implications by computational methods.

BackgroundSteroid 21-hydroxylase deficiency is the most common cause of congenital adrenal hyperplasia (CAH). Detection of underlying mutations in CYP21A2 gene encoding steroid 21-hydroxylase enzyme is helpful both for confirmation of diagnosis and management of CAH patients. Here we report a novel 9-bp insertion in CYP21A2 gene and its structural and functional consequences on P450c21 protein by molecular modeling and molecular dynamics simulations methods.MethodsA 30-day-old child was referred to our laboratory for molecular diagnosis of CAH. Sequencing of the entire CYP21A2 gene revealed a novel insertion (duplication) of 9-bp in exon 2 of one allele and a well-known mutation I172N in exon 4 of other allele. Molecular modeling and simulation studies were carried out to understand the plausible structural and functional implications caused by the novel mutation.ResultsInsertion of the nine bases in exon 2 resulted in addition of three valine residues at codon 71 of the P450c21 protein. Molecular dynamics simulations revealed that the mutant exhibits a faster unfolding kinetics and an overall destabilization of the structure due to the triple valine insertion was also observed.ConclusionThe novel 9-bp insertion in exon 2 of CYP21A2 genesignificantly lowers the structural stability of P450c21 thereby leading to the probable loss of its function.

The Role of Large Gene Deletions and Duplications in Patients with Hypertrophic Cardiomyopathy

Background: Hypertrophic cardiomyopathy (HCM) is a genetically heterogeneous disorder, in which 90% of patients have mutations in the myosin-binding protein C (MYBPC3), myosin heavy chain (MYH7) and cardiac troponin T (TNNT2) genes, when a genetic cause is identified. In up to 50% of cases nomutation is identified.While mutations in other genes could explain such cases, current mutation detection methods overlook large deletions andduplications,whichmaycontribute significantly to the mutational load in known causal genes. Aim: This study sought to investigate the role of large deletions and duplications in the MYBPC3 and TNNT2 genes in HCM. Methods: In 109 patients with HCM, multiple ligationdependent probe amplification (MLPA) DNA analysis of theMYBPC3 gene was performed. A subgroup of patients (n= 96)were also analysed for theTNNT2 gene.MLPAprofiles suggesting a deletion were further investigated with PCR amplification and DNA sequencing to characterise deletion breakpoints and genotype family members. Results: One proband (1%) was found to have a 3 base pair deletion in exon 29 of theMYBPC3 gene, resulting in a deletion of a valine residue. The proband is a 20-year-old female who has severe HCM with a septal wall thickness of 35mm, and has an implantable defibrillator for primary prevention.There isno familyhistoryofHCM.MLPAanalysis did not identify any alterations in the TNNT2 gene. Conclusions: While small gene deletions may account for a proportion of causes of HCM, large deletions and duplications do not appear to play a role in the pathogenesis of HCM.

A One-Residue Switch Reverses the Orientation of a Heme b Cofactor. Investigations of the Ferriheme NO Transporters Nitrophorin 2 and 7 from the Blood-Feeding Insect Rhodnius prolixus

This study represents the identification of a single amino acid residue that has the major responsibility for the isomeric orientation of a heme b cofactor in a ferriheme protein. The insertion of hemin b into the asymmetric environment of a protein pocket facilitates two cofactor orientations, A and B, which is often called "heme rotational disorder". The proteins studied herein are nitrophorins, a class of ferriheme proteins found in the saliva of the blood-sucking insect Rhodnius prolixus, in this case NP2 and NP7. NMR spectroscopy (pH* 5.5) of the imidazole complex of NP7 revealed solely the A orientation, whereas NP2 shows primarily the B orientation ( approximately 1:5 A:B). The glutamate 27 residue in NP7 is an obvious difference in the heme pocket compared to those of NP1-4, all of which present a valine residue [valine 24 (NP2 and NP3) or valine 25 (NP1 and NP4)] at the same position. Consequently, the mutant NP2(V24E) was prepared and shown to reverse the heme orientation to exclusively A, whereas NP7(E27V) revealed an approximately 1:3 A:B ratio. The reversal A <--> B following the change glutamine <--> valine was further indicated in circular dichroism (CD) spectroscopy with a positive (A) or negative (B) Deltaepsilon of the heme Soret band. Moreover, CD spectroscopy was applied to the mutant NP7(E27Q) and indicated mainly the A orientation, which allows us to conclude that the steric hindrance provided by the glutamate residue is responsible for the heme orientation rather then the carboxylate charge.

Intramolecular Charge Interactions as a Tool to Control the Coiled‐Coil‐to‐Amyloid Transformation

Under the influence of a changed environment, amyloid-forming proteins partially unfold and assemble into insoluble beta-sheet rich fibrils. Molecular-level characterization of these assembly processes has been proven to be very challenging, and for this reason several simplified model systems have been developed over recent years. Herein, we present a series of three de novo designed model peptides that adopt different conformations and aggregate morphologies depending on concentration, pH value, and ionic strength. The design strictly follows the characteristic heptad repeat of the alpha-helical coiled-coil structural motif. In all peptides, three valine residues, known to prefer the beta-sheet conformation, have been incorporated at the solvent-exposed b, c, and f positions to make the system prone to amyloid formation. Additionally, pH-controllable intramolecular electrostatic repulsions between equally charged lysine (peptide A) or glutamate (peptide B) residues were introduced along one side of the helical cylinder. The conformational behavior was monitored by circular dichroism spectroscopic analysis and thioflavin T fluorescence, and the resulting aggregates were further characterized by transmission electron microscopy. Whereas uninterrupted alpha-helical aggregates are found at neutral pH, Coulomb repulsions between lysine residues in peptide A destabilize the helical conformation at acidic pH values and trigger an assembly into amyloid-like fibrils. Peptide B features a glutamate-based switch functionality and exhibits opposite pH-dependent folding behavior. In this case, alpha-helical aggregates are found under acidic conditions, whereas amyloids are formed at neutral pH. To further validate the pH switch concept, peptide C was designed by including serine residues, thus resulting in an equal distribution of charged residues. Surprisingly, amyloid formation is observed at all pH values investigated for peptide C. The results of further investigations into the effect of different salts, however, strongly support the crucial role of intramolecular charge repulsions in the model system presented herein.

Molecular Dynamics Study of a Nanotube-Binding Amphiphilic Helical Peptide at Different Water/Hydrophobic Interfaces

Many potential applications of single-walled carbon nanotubes (SWNTs) require that they be isolated from one another. This may be accomplished through covalent or noncovalent SWNT functionalization. The noncovalent approach preserves the intrinsic electrical, optical, and mechanical properties of SWNTs and can be achieved by dispersing SWNTs in aqueous solution using surfactants, polymers, or biomacromolecules like DNA or polypeptides. The designed amphiphilic helical peptide nano-1, which contains hydrophobic valine and aromatic phenylalanine residues for interaction with SWNTs and glutamic acid and lysine residues for water solubility, has been shown to debundle and disperse SWNTs, although the details of the peptide-SWNT interactions await elucidation. Here we use fully atomistic molecular dynamics simulations to investigate the nano-1 peptide at three different water/hydrophobic interfaces: water/oil, water/graphite, and water/SWNT. The amphiphilic nature of the peptide is characterized by its secondary structure, peptide-water hydrogen bonding, and peptide-hydrophobic surface van der Waals energy. We show that nano-1 has reduced amphiphilic character at the water/oil interface because the peptide helix penetrates into the hydrophobic phase. The peptide alpha-helix cannot match its hydrophobic face to the rigid planar graphite surface without partially unfolding. In contrast, nano-1 can curve on the SWNT surface in an alpha-helical conformation to simultaneously maximize its hydrophobic contacts with the SWNT and its hydrogen bonds with water. The molecular insight into the peptide conformation at the various hydrophobic surfaces provides guidelines for future peptide design.