Direct observation of phenylalanine orientations in statherin bound to hydroxyapatite surfaces

Extracellular biomineralization proteins such as salivary statherin control the growth of hydroxyapatite (HAP), the principal component of teeth and bones. Despite the important role that statherin plays in the regulation of hard tissue formation in humans, the surface recognition mechanisms involved are poorly understood. The protein-surface interaction likely involves very specific contacts between the surface atoms and the key protein side chains. This study demonstrates for the first time the power of combining near-edge X-ray absorption fine structure (NEXAFS) spectroscopy with element labeling to quantify the orientation of individual side chains. In this work, the 15 amino acid N-terminal binding domain of statherin has been adsorbed onto HAP surfaces, and the orientations of phenylalanine rings F7 and F14 have been determined using NEXAFS analysis and fluorine labels at individual phenylalanine sites. The NEXAFS-derived phenylalanine tilt angles have been verified with sum frequency generation spectroscopy.     

Homonuclear and heteronuclear NMR studies of a statherin fragment bound to hydroxyapatite crystals

Acidic proteins found in mineralized tissues act as nature's crystal engineers, where they play a key role in promoting or inhibiting the growth of minerals such as hydroxyapatite (HAP), Ca10(PO4)6(OH)2, the main mineral component of bone and teeth. Key to understanding the structural basis of protein-crystal recognition and protein control of hard tissue growth is the nature of interactions between the protein side chains and the crystal surface. In an earlier work we have measured the proximity of the lysine (K6) side chain in an SN-15 peptide fragment of the salivary protein statherin adsorbed to the Phosphorus-rich surface of HAP using solid-state NMR recoupling experiments. 15N{31P} rotational echo double resonance (REDOR) NMR data on the side-chain nitrogen in K6 gave rise to three different models of protein-surface interaction to explain the experimental data acquired. In this work we extend the analysis of the REDOR data by examining the contribution of interactions between surface phosphorus atoms to the observed 15N REDOR decay. We performed 31P-31P recoupling experiments in HAP and (NH4)2HPO4 (DHP) to explore the nature of dipolar coupled 31P spin networks. These studies indicate that extensive networks of dipolar coupled 31P spins can be represented as stronger effective dipolar couplings, the existence of which must be included in the analysis of REDOR data. We carried out 15N{31P} REDOR in the case of DHP to determine how the size of the dephasing spin network influences the interpretation of the REDOR data. Although use of an extended 31P coupled spin network simulates the REDOR data well, a simplified 31P dephasing system composed of two spins with a larger dipolar coupling also simulates the REDOR data and only perturbs the heteronuclear couplings very slightly. The 31P-31P dipolar couplings between phosphorus nuclei in HAP can be replaced by an effective dipolar interaction of 600 Hz between two 31P spins. We incorporated this coupling and applied the above approach to reanalyze the 15N{31P} REDOR of the lysine side chain approaching the HAP surface and have refined the binding models proposed earlier. We obtain 15N-31P distances between 3.3 and 5 A from these models that are indicative of the possibility of a lysine-phosphate hydrogen bond.     

A REDOR NMR study of a phosphorylated statherin fragment bound to hydroxyapatite crystals

Hydroxyapatite (HAP) is the main mineral component of teeth. It is well-known that several salivary proteins and peptides bind strongly to HAP to regulate crystal growth. Interactions between a peptide derived from the N-terminal fragment of the salivary protein statherin and HAP were measured utilizing rotational-echo double-resonance (REDOR) nuclear magnetic resonance (NMR). The REDOR measurement from the side chain of the salivary peptide to the HAP surface is complicated by two effects: a possible additional dipolar coupling to a phosphorylated side chain and the potential proximity of phosphorus atoms to each other, resulting in a homonuclear dipolar interaction. Both of these effects were addressed, and the smallest model applicable to our system includes the nitrogen-15 (15N) spin in the lysine side chain and two phosphorus-31 (31P) spins, at least one of which must be from the surface phosphates of the HAP.     

Adsorption of a statherin peptide fragment on the surface of nanocrystallites of hydroxyapatite

Statherin is an active inhibitor of calcium phosphate precipitation in the oral cavity. For many studies of the interaction between statherin and hydroxyapatite (HAp), the samples are prepared by a direct mixing of statherin or its fragment with well-crystalline HAp crystals. In this work, the HAp sample is precipitated in the presence of peptide fragment derived from the N-terminal 15 amino acids of statherin (SN-15). The in situ prepared HAp crystallites are nanosized, leading to a significant increase of the peptide amount adsorbed on the HAp surface. The enhancement in NMR sensitivity allows, for the first time, the measurement of a two-dimensional 13C-13C correlation spectrum for a 13C uniformly labeled peptide sample adsorbed on mineral surface. The measurement time is about 18.5 h at a field strength of 7.05 T. Preliminary results suggest that there may exist two different mechanisms for the interaction between SN-15 and HAp. In addition to the one which will cause a conformational change near the N-terminal, SN-15 may also be absorbed on the HAp surface by simple electrostatic interaction, without any significant conformational changes of the peptides.     

Adsorption of comb copolymers on weakly attractive solid surfaces

In this work continuum and lattice Monte Carlo simulation methods are used to study the adsorption of linear and comb polymers on flat surfaces. Selected polymer segments, located at the tips of the side chains in comb polymers or equally spaced along the linear polymers, are attracted to each other and to the surface via square-well potentials. The rest of the polymer segments are modeled as tangent hard spheres in the continuum model and as self-avoiding random walks in the lattice model. Results are presented in terms of segment-density profiles, distribution functions, and radii of gyration of the adsorbed polymers. At infinite dilution the presence of short side chains promotes the adsorption of polymers favoring both a decrease in the depletion-layer thickness and a spreading of the polymer molecule on the surface. The presence of long side chains favors the adsorption of polymers on the surface, but does not permit the spreading of the polymers. At finite concentration linear polymers and comb polymers with long side chains readily adsorb on the solid surface, while comb polymers with short side chains are unlikely to adsorb. The simple models of comb copolymers with short side chains used here show properties similar to those of associating polymers and of globular proteins in aqueous solutions, and can be used as a first approximation to investigate the mechanism of adsorption of proteins onto hydrophobic surfaces.     

Effect of n-alkyl and sulfonyl groups on the wetting properties of comblike poly(oxyethylene)s and stick-slip behavior

The influence of side chain length and sulfonyl moiety on the molecular structures and wettability behavior of poly(oxyethylene)s with alkyl sulfonyl side chains (CH(3)-nSE, n = 1, 2, 3, 4, 5, 6, 8, 10), where n is the number of the carbon atom in the n-alkyl side group, was investigated. CH(3)-nSEs having shorter side chains (n < 5) do not have ordered structures, and their surfaces were found to be more polar than those of CH(3)-nSEs having longer side chains (n ≥ 5). The CH(3)-nSEs having longer side chains show double-layered lamellar structures (n ≥ 5) with well-aligned side chains and low surface energies in the range 21.2-25.8 mN/m. Interestingly, stick-slip behavior was observed only on the surfaces of CH(3)-3SE and CH(3)-4SE when water was used as the test liquid. The surface deformation at the three-phase line was generated from interactions between water and sulfonyl groups, and the optimum side chain lengths were believed to cause the stick-slip behavior.     

Relay stations for electron hole migration in peptides: possibility for formation of three-electron bonds along peptide chains

Our calculations found that the O thereforeO three-electron (3e) bonds (2.16 approximately 2.27 A) can be formed not only between two neighboring peptide units in a main chain but also between two adjacent peptide units in two different main chains in proteins. This finding may address electron hole migration from one peptide unit to the next in proteins. Evidently, stability of the O thereforeO 3e bonded species is strongly dependent on the component of the oligopeptides and is reduced owing to the steric hindrance of the side chains when the big chains present in oligopeptides. Besides, formation of the O thereforeO 3e bonds competes with the formation of the other forms of three-electron bonds depending on the component of the polypeptides. Formation of the O thereforeS 3e bond is thermodynamically more favorable than that of the O thereforeO 3e bond for the oligopeptides containing sulfur atom in their side chains. Similarly, formation of the O thereforepi 3e bond between aromatic ring of the side chain and the neighboring peptide unit is more stable than that of the O thereforeO 3e bond when the aromatic amino acids present in the oligopeptides. We infer that a series of three-electron bonds may be formed during the electron hole migration along the peptide backbone in proteins and assist electron hole transport as relay stations, supporting the peptide chain as a conduction wire. The ab initio molecular dynamics simulations of the polypeptides also support this conclusion.     

THE RHEO-OPTICAL FTIR STUDY OF POLYESTERPOLYETHER SEGMENTED COPOLYMER

The polyester-polyetber segmented copolymer has been investigated by rheo-optical FTIR during stretehing for the informastion on strain induced crystallizatinn of soft segment chains, hard and soft chain orientation.At room temperature 15℃, the soft segment chains of polyester-polyether being to crystallize at 220% strain and the degree of crystallixation increa(?)e with draw ratio, but there will not be any soft segment chains crystallization above 21℃even at bigber strain. The average orientation of hard segment chains are higher than that of the soft chain at high strain level, both are positive oriented into the stretching direction at allover strain level. This indicates that the b(?)d (?)ent ch(?)ins are dispersed into the elastomeric phase and without forming spherulite.     

取代烷基侧链长度对二维纳米结构的影响

合成了一系列烷基取代的间苯三酚衍生物,并在大气条件下用扫描隧道显微镜研究了它们在高定向裂解石墨表面的吸附和组装行为.实验结果表明,这些自组装分子具有条状结构特征.在链长较短的分子图像中,两条平行的烷氧基链肩并肩地排列在苯环的一侧,另一条烷氧基链则排列在苯环的另一侧,链与链之间彼此相互交错排列形成均一的烷基条带.当链长增加时,这种高稳定性和密排结构遭到破坏,出现单个分子和分子对共存的组装结构.这是由于烷基链与烷基链之间以及烷基链与基底之间的作用力共同决定的.通过调控分子烷基链的长度可以得到不同的表面二维纳米结构.     

Hydroxyapatite surface-induced peptide folding

Herein, we describe the design and surface-binding characterization of a de novo designed peptide, JAK1, which undergoes surface-induced folding at the hydroxyapatite (HA)-solution interface. JAK1 is designed to be unstructured in buffered saline solution, yet undergo HA-induced folding that is largely governed by the periodic positioning of gamma-carboxyglutamic acid (Gla) residues within the primary sequence of the peptide. Circular dichroism (CD) spectroscopy and analytical ultracentrifugation indicate that the peptide remains unfolded and monomeric in solution under normal physiological conditions; however, CD spectroscopy indicates that in the presence of hydroxyapatite, the peptide avidly binds to the mineral surface adopting a helical structure. Adsorption isotherms indicate nearly quantitative surface coverage and Kd = 310 nM for the peptide-surface binding event. X-ray photoelectron spectroscopy (XPS) coupled with the adsorption isotherm data suggests that JAK1 binds to HA, forming a self-limiting monolayer. This study demonstrates the feasibility of using HA surfaces to trigger the intramolecular folding of designed peptides and represents the initial stages of defining the design rules that allow HA-induced peptide folding.     

Prediction of calcite morphology from computational and experimental studies of mutations of a de novo-designed peptide

Many organisms use macromolecules, often proteins or peptides, to control the growth of inorganic crystals into complex materials. The ability to model peptide-mineral interactions accurately could allow for the design of novel peptides to produce materials with desired properties. Here, we tested a computational algorithm developed to predict the structure of peptides on mineral surfaces. Using this algorithm, we analyzed energetic and structural differences between a 16-residue peptide (bap4) designed to interact with a calcite growth plane and single- and double-point mutations of the charged residues. Currently, no experimental method is available to resolve the structures of proteins on solid surfaces, which precludes benchmarking for computational models. Therefore, to test the models, we chemically synthesized each peptide and analyzed its effects on calcite crystal growth. Whereas bap4 affected the crystal growth by producing heavily stepped corners and edges, point mutants had variable influences on morphology. Calculated residue-specific binding energies correlated with experimental observations; point mutations of residues predicted to be crucial to surface interactions produced morphologies most similar to unmodified calcite. These results suggest that peptide conformation plays a role in mineral interactions and that the computational model supplies valid energetic and structural data that can provide information about expected crystal morphology.     

Biaryl-bridged macrocyclic peptides: conformational constraint via carbogenic fusion of natural amino acid side chains

A general method for constraining peptide conformations via linkage of aromatic sidechains has been developed. Macrocyclization of suitably functionalized tri-, tetra- and pentapeptides via Suzuki-Miyaura cross-coupling has been used to generate side chain to side chain, biaryl-bridged 14- to 21-membered macrocyclic peptides. Biaryl bridges possessing three different configurations, meta-meta, meta-ortho, and ortho-meta, were systematically explored through regiochemical variation of the aryl halide and aryl boronate coupling partners, allowing fine-tuning of the resultant macrocycle conformation. Suzuki-Miyaura macrocyclizations were successfully achieved both in solution and on solid phase for all three sizes of peptide. This approach constitutes a means of constraining peptide conformation via direct carbogenic fusion of side chains of naturally occurring amino acids such as phenylalanine and tyrosine, and so is complementary to strategies involving non-natural, for example, hydrocarbon, bridges.     

Immobilization of amphiphilic polycations by catechol functionality for antimicrobial coatings

A new strategy for preparing antimicrobial surfaces by a simple dip-coating procedure is reported. Amphiphilic polycations with different mole ratios of monomers containing dodecyl quaternary ammonium, methoxyethyl, and catechol groups were synthesized by free-radical polymerization. The polymer coatings were prepared by immersing glass slides into a polymer solution and subsequent drying and heating. The quaternary ammonium side chains endow the coatings with potent antibacterial activity, the methoxyethyl side chains enable tuning the hydrophobic/hydrophilic balance, and the catachol groups promote immobilization of the polymers into films. The polymer-coated surfaces displayed bactericidal activity against Escherichia coli and Staphylococcus aureus in a dynamic contact assay and prevented the accumulation of viable E. coli, S. aureus, and Acinetobacter baumannii for up to 96 h. Atomic force microscopy (AFM) images of coating surfaces indicated that the surfaces exhibit virtually the same smoothness for all polymers except the most hydrophobic. The hydrophobic polymer without methoxyethyl side chains showed clear structuring into polymer domains, causing high surface roughness. Sum-frequency generation (SFG) vibrational spectroscopy characterization of the surface structures demonstrated that the dodecyl chains are predominantly localized at the surface-air interface of the coatings. SFG also showed that the phenyl groups of the catechols are oriented on the substrate surface. These results support our hypothesis that the adhesive or cross-linking functionality of catechol groups discourages polymer leaching, allowing the tuning of the amphiphilic balance by incorporating hydrophilic components into the polymer chains to gain potent biocidal activity.     

Surface morphology at nanometer level and optical phase retardation of rubbed alignment films

The surface morphology of rubbed polyimide LC aligning films has been studied by scanning force microscopy. We examined three types of alignment film: HT-210, AL-1051 (main chain type) and AL-8044 (side chain type) polyimide surfaces. The rubbed polyimide surfaces show anisotropic alignment of the polymer chain cluster, and a microgroove between the ripple pattern streaks. Also, they are periodically oriented along the rubbing direction. The optical phase retardation of the rubbed surface does not increase with increased cumulative time of rubbing, On the other hand, it increases monotonically with increasing rubbing depth.     

Transitions of tethered polymer chains: a simulation study with the bond fluctuation lattice model

A polymer chain tethered to a surface may be compact or extended, adsorbed or desorbed, depending on interactions with the surface and the surrounding solvent. This leads to a rich phase diagram with a variety of transitions. To investigate these transitions we have performed Monte Carlo simulations of a bond fluctuation model with Wang-Landau and umbrella sampling algorithms in a two-dimensional state space. The simulations' density-of-states results have been evaluated for interaction parameters spanning the range from good- to poor-solvent conditions and from repulsive to strongly attractive surfaces. In this work, we describe the simulation method and present results for the overall phase behavior and for some of the transitions. For adsorption in good solvent, we compare with Metropolis Monte Carlo data for the same model and find good agreement between the results. For the collapse transition, which occurs when the solvent quality changes from good to poor, we consider two situations corresponding to three-dimensional (hard surface) and two-dimensional (very attractive surface) chain conformations, respectively. For the hard surface, we compare tethered chains with free chains and find very similar behavior for both types of chains. For the very attractive surface, we find the two-dimensional chain collapse to be a two-step transition with the same sequence of transitions that is observed for three-dimensional chains: a coil-globule transition that changes the overall chain size is followed by a local rearrangement of chain segments.     

Surface morphology at nanometer level and optical phase retardation of rubbed alignment films

The surface morphology of rubbed polyimide LC aligning films has been studied by scanning force microscopy. We examined three types of alignment film: HT-210, AL-1051 (main chain type) and AL-8044 (side chain type) polyimide surfaces. The rubbed polyimide surfaces show anisotropic alignment of the polymer chain cluster, and a microgroove between the ripple pattern streaks. Also, they are periodically oriented along the rubbing direction. The optical phase retardation of the rubbed surface does not increase with increased cumulative time of rubbing, On the other hand, it increases monotonically with increasing rubbing depth.     

Structure of gramicidin a in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data

Two different high-resolution structures recently have been proposed for the membrane-spanning gramicidin A channel: one based on solid-state NMR experiments in oriented phospholipid bilayers (Ketchem, R. R.; Roux, B.; Cross, T. A. Structure 1997, 5, 1655-1669; Protein Data Bank, PDB:1MAG); and one based on two-dimensional NMR in detergent micelles (Townsley, L. E.; Tucker, W. A.; Sham, S.; Hinton, J. F. Biochemistry 2001, 40, 11676-11686; PDB:1JNO). Despite overall agreement, the two structures differ in peptide backbone pitch and the orientation of several side chains; in particular that of the Trp at position 9. Given the importance of the peptide backbone and Trp side chains for ion permeation, we undertook an investigation of the two structures using molecular dynamics simulation with an explicit lipid bilayer membrane, similar to the system used for the solid-state NMR experiments. Based on 0.1 micros of simulation, both backbone structures converge to a structure with 6.25 residues per turn, in agreement with X-ray scattering, and broad agreement with SS backbone NMR observables. The side chain of Trp 9 is mobile, more so than Trp 11, 13, and 15, and undergoes spontaneous transitions between the orientations in 1JNO and 1MAG. Based on empirical fitting to the NMR results, and umbrella sampling calculations, we conclude that Trp 9 spends 80% of the time in the 1JNO orientation and 20% in the 1MAG orientation. These results underscore the utility of molecular dynamics simulations in the analysis and interpretation of structural information from solid-state NMR.     

Nisin antimicrobial activity and structural characteristics at hydrophobic surfaces coated with the PEO-PPO-PEO triblock surfactant Pluronic F108

The antimicrobial peptide nisin has been observed to preferentially locate at surfaces coated with the poly[ethylene oxide]-poly[propylene oxide]-poly[ethylene oxide] (PEO-PPO-PEO) surfactant Pluronic F108, to an extent similar to its adsorption at uncoated, hydrophobic surfaces. In order to evaluate nisin function following its adsorption to surfaces presenting pendant PEO chains, the antimicrobial activity of nisin-loaded, F108-coated polystyrene microspheres and F108-coated polyurethane catheter segments was evaluated against the Gram-positive indicator strain, Pediococcus pentosaceus. The retained biological activity of these nisin-loaded layers was evaluated after incubation in the presence and absence of blood proteins, for contact periods up to one week. While an increase in serum protein concentration reduced the retained activity on both bare hydrophobic and F108-coated materials, F108-coated surfaces retained more antimicrobial activity than the uncoated surfaces. Circular dichroism spectroscopy experiments conducted with nisin in the presence of F108-coated and uncoated, silanized silica nanoparticles suggested that nisin experienced conformational rearrangement at a greater rate and to a greater extent on bare hydrophobic surfaces relative to F108-coated surfaces. These results support the notion that immobilized, pendant PEO chains confer some degree of conformational stability to nisin while also inhibiting its exchange by blood proteins.     

The gas-phase dipeptide analogue acetyl-phenylalanyl-amide: a model for the study of side chain/backbone interactions in proteins

The issue of the influence of the side chain/backbone interaction on the local conformational preferences of a phenylalanine residue in a peptide chain is addressed. A synergetic approach is used, which combines gas-phase UV spectroscopy as well as gas-phase IR/UV double-resonance experiments with DFT and post Hartree-Fock calculations. N-Acetyl-Phe-amide was chosen as a model system for which three different conformers were observed. The most stable conformer has been identified as an extended beta(L) conformation of the peptide backbone. It is stabilized by a weak but significant NH-pi interaction bridging the aromatic ring on the residue (i) with the NH group on residue (i+1), with the aromatic side chain being in an anti conformation. This stable conformation corresponds to the common NH(i+1)-aromatic(i) interaction encountered in proteins for the three aromatic residues (phenylalanine, tyrosine, and tryptophan), which illustrates the relevance of gas-phase investigations to structural biology issues. The two other less abundant conformers have been assigned to two gamma-folded backbone conformations that differ by the orientation of the side chain. In all cases, the IR data provided spectroscopic fingerprints of these interactions. Finally, the strong conformational dependence of the fluorescence yield found for N-acetyl-Phe-amide illustrates the role of the environment on the excited-state dynamics of these species, which is often exploited by biochemists to monitor protein structural changes from tryptophan lifetime measurements.     

The organization of aromatic side groups in an amyloid fibril probed by solid-state 2H and 19F NMR spectroscopy

Some 25 diseases are associated with proteins and peptides that assemble into amyloid fibrils composed of beta-strands connected by hydrogen bonds oriented parallel to the fiber long axis. There is mounting evidence that amyloid formation involves specific interactions between amino acid side groups, which bring together beta-sheets to form layers with buried and exposed faces. This work demonstrates how a combination of solid-state 2H and 19F NMR experiments can provide constraints on fibril architecture by probing the environment and spatial organisation of aromatic side groups. It is shown that phenylalanine rings within fibrils formed by a decapeptide fragment of the islet amyloid polypeptide, amylin, are highly motionally restrained and are situated within 6.5 A of one another. Taken together with existing structural constraints for this peptide, these results are consistent with a fibril architecture that comprises layers of two or more beta-sheets, with the aromatic residues facing into the inter-sheet space and possibly engaged in pi-pi interactions. The methods presented will be of general utility in exploring the architecture of fibrils of larger, full-length peptides and proteins, including amylin itself.