Molecular dynamics simulations of a protein on hydrophobic and hydrophilic surfaces

Enzyme immobilization studied through molecular dynamic simulations

In recent years, simulations have been used to great advantage to understand the structural and dynamic aspects of distinct enzyme immobilization strategies, as experimental techniques have limitations in establishing their impact at the molecular level. In this review, we discuss how molecular dynamic simulations have been employed to characterize the surface phenomenon in the enzyme immobilization procedure, in an attempt to decipher its impact on the enzyme features, such as activity and stability. In particular, computational studies on the immobilization of enzymes using i) nanoparticles, ii) self-assembled monolayers, iii) graphene and carbon nanotubes, and iv) other surfaces are covered. Importantly, this thorough literature survey reveals that, while simulations have been primarily performed to rationalize the molecular aspects of the immobilization event, their use to predict adequate protocols that can control its impact on the enzyme properties is, up to date, mostly missing.

Ionogel-Electrode for the Study of Protein Tunnel Junctions under Physiologically Relevant Conditions

The study of charge transport through proteins is essential for understanding complicated electrochemical processes in biological activities while the reasons for the coexistence of tunneling and hopping phenomena in protein junctions still remain unclear. In this work, a flexible and conductive ionogel electrode is synthesized and is used as a top contact to form highly reproducible protein junctions. The junctions of proteins, including human serum albumin, cytochrome C and hemoglobin, show temperature-independent electron tunneling characteristics when the junctions are in solid states while with a different mechanism of temperature-dependent electron hopping when junctions are hydrated under physiologically relevant conditions. It is demonstrated that the solvent reorganization energy plays an important role in the electron-hopping process and experimentally shown that it requires ≈100 meV for electron hopping through one heme group inside a hydrated protein molecule connected between two electrodes.

Adsorption characteristics of peptides on ω-functionalized self-assembled monolayers: a molecular dynamics study

Molecular dynamics simulations were employed to investigate the adsorption behavior of a variety of amino-acid side-chain analogs (SCAs) and a β-hairpin (HP7) peptide on a series of liquid-like self-assembled monolayers (SAMs) with terminal functional groups of -OH, -OCH₃, -CH₃, and -CF₃. The relationships between the adsorption free energy of the SCAs and the interfacial properties of water on the SAMs were examined to determine the acute predictors of protein adsorption on the SAM surfaces. The structural changes of HP7 on the SAM surfaces were also investigated to understand the relationship between the surface nature and protein denaturation. It was found that the adsorption free energy of the SCAs was linearly related to the surface hydrophobicity, which was computed as the free energy of cavity formation near the SAM-water interfaces. In addition, the hydrophobic -CH₃ and -CF₃ SAMs produced substantial conformational changes in HP7 because of the strong hydrophobic attractions to the nonpolar side chains. The hydrophilic surface terminated by -OH also promoted structural changes in HP7 resulting from the formation of hydrogen bonds between the hydrophilic tail and HP7. Consequently, the moderate amphiphilic surface terminated by -OCH₃ avoided the denaturation of HP7 most efficiently, thus improving the biocompatibility of the surface. In conclusion, these results provide a deep understanding of protein adsorption for a wide range of polymeric surfaces, and they can potentially aid the design of appropriate biocompatible coatings for medical applications.

Impact of Silane Monolayers on the Adsorption of Streptavidin on Silica and Its Subsequent Interactions with Biotin: Molecular Dynamics and Steered Molecular Dynamics Simulations

Protein adsorption on surfaces is used in analytical tools as an immobilization mean to trap the analyte to be detected. However, protein adsorption can lead to a conformational change in the protein structure, resulting in a loss of bioactivity. Here, we study adsorption of a streptavidin-biotin complex on amorphous SiO₂ surfaces functionalized with five different silane self-assembled monolayers by all-atom molecular dynamics simulations. We find that the streptavidin global conformational change, as well as the nature of residues with high mobility, depends on the alkyl chain length and head-group charge of silane molecules. Effects on interactions with biotin are further investigated by steered molecular dynamics (SMD) simulations, which mimics atomic force microscopy (AFM) with the biotin attached on the tip. We show the combined effects of adsorption-induced global conformational changes and of the position of residues with high mobility on the streptavidin-biotin rupture force. By comparing our results to experimental and SMD rupture forces obtained in water, without any surface, we conclude that silane with uncharged and short alkyl chains allows streptavidin immobilization, while keeping biotin interactions better than silanes with long alkyl chains or charged head groups.

Force Field Parameter Development for the Thiolate/Defective Au(111) Interface

A molecular-level understanding of the interplay between self-assembled monolayers (SAMs) of thiolates and gold surface is of great importance to a wide range of applications in surface science and nanotechnology. Despite theoretical research progress of the past decade, an atomistic model, capable of describing key features of SAMs at reconstructed gold surfaces, is still missing. In this work, periodic ab initio density functional theory (DFT) calculations were utilized to develop a new atomistic force field model for alkanethiolate (AT) SAMs on a reconstructed Au(111) surface. The new force field parameters were carefully trained to reproduce the key features, including vibrational spectra and torsion energy profiles of ethylthiolate (C₂S) in the bridge or staple motif model on the Au(111) surface, wherein, the force constants of the bond and angle terms were trained by matching the vibrational spectra, while the torsion parameters of the dihedral angles were trained via fitting the torsion energy profiles from DFT calculations. To validate the developed force field parameters, we performed classical molecular dynamics (MD) simulations for both pristine and reconstructed Au-S interface models with a (2√3 × 3) unit cell, which includes four dodecanethiolate (C₁₀S) molecules on the Au(111) surface. The simulation results showed that the geometrical features of the investigated Au-S interface models and structural properties of the C₁₀S SAMs are in good agreement with the ab initio MD studies. The newly developed atomistic force field model provides new fundamental insights into AT SAMs on the reconstructed Au(111) surface and adds advancement to the existing interface research knowledge.

Influence of Structured Water Layers on Protein Adsorption Process: A Case Study of Cytochrome c and Carbon Nanotube Interactions and Its Implications

Cytochrome c, an essential protein of the electron transport chain, is known to be capable of amplifying the toxicity of carbon nanomaterials via free-radical generation. To understand their interaction, as well as the more general protein-nanoparticle interaction at molecular levels, we investigate the adsorptions between cytochrome c and carbon nanotubes (CNTs) in dynamic and thermodynamic ways using molecular dynamics simulations. The results reveal a well-defined three-phase process separated by two transition points: the diffusion phase where the protein diffuses in the water box, the lockdown phase I where the protein inserts into the surface-bound water layers and rearranges its conformation to fit to the surface of the CNT, and the lockdown phase II where cytochrome c repels the water molecules standing in its way to the surface of CNT and reaches stable adsorption states. The structured water layers affect the movement of atoms by electrostatic forces. In lockdown phase I, the conformation adjustment of the protein dominates the adsorption process. The most thermally favorable adsorption conformation is determined. It shows that except for the deformation of short β sheets and some portions of α helixes, most of the secondary structures of cytochrome c remain unchanged, implying that most of the functions of cytochrome c are preserved. During these processes, the energy contributions of the hydrophilic residues of cytochrome c are much larger than those of hydrophobic residues. Interestingly, the structured water layers at the CNT surface allow more hydrophilic residues such as Lys to get into close contact with the CNT, which plays a significant role during the anchoring process of adsorption. Our results demonstrate that the heme group is in close contact with the CNT in some of the adsorbed states, which hence provides a way for electron transfer from cytochrome c to the CNT surface.

SmoPSI: Analysis and Prediction of Small Molecule Binding Sites Based on Protein Sequence Information

The analysis and prediction of small molecule binding sites is very important for drug discovery and drug design. The traditional experimental methods for detecting small molecule binding sites are usually expensive and time consuming, and the tools for single species small molecule research are equally inefficient. In recent years, some algorithms for predicting binding sites of protein-small molecules have been developed based on the geometric and sequence characteristics of proteins. In this paper, we have proposed SmoPSI, a classification model based on the XGBoost algorithm for predicting the binding sites of small molecules, using protein sequence information. The model achieved better results with an AUC of 0.918 and an ACC of 0.913. The experimental results demonstrate that our method achieves high performances and outperforms many existing predictors. In addition, we also analyzed the binding residues and nonbinding residues and finally found the PSSM; hydrophilicity, hydrophobicity, charge, and hydrogen bonding have obviously different effects on the binding-site predictions.

Comparison between empirical protein force fields for the simulation of the adsorption behavior of structured LK peptides on functionalized surfaces

All-atom empirical molecular mechanics protein force fields, which have been developed to represent the energetics of peptide folding behavior in aqueous solution, have not been parameterized for protein interactions with solid material surfaces. As a result, their applicability for representing the adsorption behavior of proteins with functionalized material surfaces should not be assumed. To address this issue, we conducted replica-exchange molecular dynamics simulations of the adsorption behavior of structured peptides to functionalized surfaces using three protein force fields that are widely used for the simulation of peptide adsorption behavior: CHARMM22, AMBER94, and OPLS-AA. Simulation results for peptide structure both in solution and when adsorbed to the surfaces were compared to experimental results for similar peptide-surface systems to provide a means of evaluating and comparing the performance of these three force fields for this type of application. Substantial differences in both solution and adsorbed peptide conformations were found amongst these three force fields, with the CHARMM22 force field found to most closely match experimental results.

Molecular understanding of conformational dynamics of a fibronectin module on rutile (110) surface

The conformational dynamics of the 10th type-III module of fibronectin (FN-III(10)) adsorbed on the perfect and three reduced rutile TiO(2)(110) surfaces with different types of defects was investigated by molecular dynamics (MD) simulations. Stable protein-surface complexes were presented in the four simulated models and were derived from the contributions of direct and indirect interactions of various functional groups in FN-III(10) with the metal oxide layers. A detailed analysis to characterize the overall structural stability of the adsorbed FN-III(10) molecule suggests that the bonding strength and the loss of protein secondary structure vary widely, depending on the topology of the substrate surface. The additional adsorption sites exhibiting higher activity, provided by the reduced surfaces, are responsible for the stronger FN-III(10)-TiO(2) interactions, but too high an interaction energy will cause a severe conformational deformation and therefore a significant loss of bioactivity of the adsorbed protein.

Quantitative studies of the interactions of metalloproteins with gold nanoparticles: identification of dominant properties of the protein that underlies the spectral changes

The interaction of cytochrome C and a number of its components such as the apo protein, heme and a coordinated iron with gold nanospheres, has been investigated. The role of the heme group and its effect on the observed spectroscopic properties following binding of cytochrome C to the gold surface has been evaluated. Binding of the heme group directly to the gold is not observed, but the presence of the heme group and its effect on the interaction with the metal surface is shown to be influential. Other factors such as the metal oxidation state and the metal-free heme are also studied. A comparison to serum albumin binding as a nonmetallic protein provides further insight into the interaction characteristics.

Bayesian analysis of heterogeneity in the distribution of binding properties of immobilized surface sites

Once a homogeneous ensemble of a protein ligand is taken from solution and immobilized to a surface, for many reasons the resulting ensemble of surface binding sites to soluble analytes may be heterogeneous. For example, this can be due to the intrinsic surface roughness causing variations in the local microenvironment, nonuniform density distribution of polymeric linkers, or nonuniform chemical attachment producing different protein orientations and conformations. We previously described a computational method for determining the distribution of affinity and rate constants of surface sites from analysis of experimental surface binding data. It fully exploits the high signal/noise ratio and reproducibility provided by optical biosensor technology, such as surface plasmon resonance. Since the computational analysis is ill conditioned, the previous approach used a regularization strategy assuming a priori all binding parameters to be equally likely, resulting in the broadest possible parameter distribution consistent with the experimental data. We now extended this method in a Bayesian approach to incorporate the opposite assumption, i.e., that the surface sites a priori are expected to be uniform (as one would expect in free solution). This results in a distribution of binding parameters as close to monodispersity as possible given the experimental data. Using several model protein systems immobilized on a carboxymethyl dextran surface and probed with surface plasmon resonance, we show microheterogeneity of the surface sites in addition to broad populations of significantly altered affinity. The distributions obtained are highly reproducible. Immobilization conditions and the total surface density of immobilized sites can have a substantial impact on the functional distribution of the binding sites.

Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface

In this study we investigated the interaction behavior between thirteen different small peptides and a hydrophobic surface using three progressively more complex methods of representing solvation effects: a united-atom implicit solvation method [CHARMM 19 force field (C19) with Analytical Continuum Electrostatics (ACE)], an all-atom implicit solvation method (C22 with GBMV), and an all-atom explicit solvation method (C22 with TIP3P). The adsorption behavior of each peptide was characterized by the calculation of the potential of mean force as a function of peptide-surface separation distance. The results from the C22/TIP3P model suggest that hydrophobic peptides exhibit relatively strong adsorption behavior, polar and positively-charged peptides exhibit negligible to relatively weak favorable interactions with the surface, and negatively-charged peptides strongly resist adsorption. Compared to the TIP3P model, the ACE and GBMV implicit solvent models predict much stronger attractions for the hydrophobic peptides as well as stronger repulsions for the negatively-charged peptides on the CH(3)-SAM surface. These comparisons provide a basis from which each of these implicit solvation methods may be reparameterized to provide closer agreement with explicitly represented solvation in simulations of peptide and protein adsorption to functionalized surfaces.

Monte Carlo simulations of antibody adsorption and orientation on charged surfaces

Monte Carlo simulations were performed to study the adsorption and orientation of antibodies on charged surfaces based on both colloidal and all-atom models. The colloidal model antibody consists of 12 connected beads representing the 12 domains of an antibody molecule. The structure of the all-atom antibody model was taken from the protein databank. The effects of the surface charge sign and density, the solution pH and ionic strength on the adsorption and orientation of different colloidal model antibodies with different dipole moments were examined. Simulation results show that both the 12-bead and the all-atom models of the antibody, for which the dipole moment points from the Fc to (Fab)2 fragments, tend to have the desired "end-on" orientation on positively charged surfaces and undesired "head-on" orientation on negatively charged surfaces at high surface charge density and low solution ionic strength where electrostatic interactions dominate. At low surface charge density and high solution ionic strength where van der Waals interactions dominate, 12-bead model antibodies tend to have "lying-flat" orientation on surfaces. The orientation of adsorbed antibodies results from the compromise between electrostatic and van der Waals interactions. The dipole moment of an antibody is an important factor for antibody orientation on charged surfaces when electrostatic interactions dominate. This charge-driven protein orientation hypothesis was verified by our simulations results in this work. It was further confirmed by surface plasmon resonance biosensor and time-of-flight secondary ion mass spectrometry experiments reported elsewhere.

Comparison of implicit solvent models for the simulation of protein–surface interactions

Empirical force field-based molecular simulations can provide valuable atomistic-level insights into protein-surface interactions in aqueous solution. While the implicit treatment of solvation effects is desired as a means of improving simulation efficiency, existing implicit solvent models were primarily developed for the simulation of peptide or protein behavior in solution alone, and thus may not be appropriate for protein interactions with synthetic material surfaces. The objective of this research was to calculate the change in free energy as a function of surface-separation distance for peptide-surface interactions using different empirical force field-based implicit solvation models (ACE, ASP, EEF1, and RDIE with the CHARMM 19 force field), and to compare these results with the same calculations conducted using density functional theory (DFT) combined with the self-consistent reaction field (SCRF) implicit solvation model. These comparisons show that distinctly different types of behavior are predicted with each implicit solvation method, with ACE providing the best overall agreement with DFT/SCRF calculations. These results also identify areas where ACE is in need of improvement for this application and provide a basis for subsequent parameter refinement.

Effect of mono-CDNP substitution of lysine residues on the redox reaction of cytochrome c electrostatically adsorbed on a mercaptoheptanoic acid modified Au(111) surface

The effect of charge-inverting modification of single surface lysine residue on the electron transfer (ET) reaction of horse heart cytochrome c (cyt c) is examined for 12 different types of mono-4-chloro-2,5-dinitrobenzoic acid substituted cyt c (mCDNPc) adsorbed on a Au(111) electrode modified with a self-assembled monolayer (SAM) of 7-mercapto-heptanoic acid (MHA). A negative shift in the redox potential by 10-35 mV as compared to that of native cyt c and a monolayer coverage in the range of 13-17 pmol cm(-2) are observed for electroactive mCDNPc's. The magnitude of the decrease in the ET rate constant (k(et)) of mCDNPc's compared with that of native cyt c depends on the position of the CDNP substitution. For mCDNPc's in which the modified lysine residue is outside of the interaction domain of cyt c with the SAM, the ratio of the k(et) of mCDNPc to that of native cyt c is correlated to the change in the dipole moment vector of cyt c due to the CDNP modification. This correlation suggests that the dipole moment of cyt c determines its orientation of adsorption on the SAM of MHA and significantly affects the rate of the ET. The CDNP modification of lysine residues at the interaction domain significantly decreases the rate, demonstrating the importance of the local charge environment in determining the rate of ET.

Electric-field-induced redox potential shifts of tetraheme cytochromes c3 immobilized on self-assembled monolayers: surface-enhanced resonance Raman spectroscopy and simulation studies

The tetraheme protein cytochrome c(3) (Cyt-c(3)) from Desulfovibrio gigas, immobilized on a self-assembled monolayer (SAM) of 11-mercaptoundecanoic acid, is studied by theoretical and spectroscopic methods. Molecular dynamics simulations indicate that the protein docks to the negatively charged SAM via its lysine-rich domain around the exposed heme IV. Complex formation is associated with only little protein structural perturbations. This finding is in line with the resonance Raman and surface-enhanced resonance Raman (SERR) spectroscopic results that indicate essentially the same heme pocket structures for the protein in solution and adsorbed on SAM-coated Ag electrodes. Electron- and proton-binding equilibrium calculations reveal substantial negative shifts of the redox potentials compared to the protein in solution. The magnitude of these shifts decreases in the order heme IV (-161 mV) > heme III (-73 mV) > heme II (-57 mV) > heme I (-26 mV), resulting in a change of the order of reduction. These shifts originate from the distance-dependent electrostatic interactions between the SAM headgroups and the individual hemes, leading to a stabilization of the oxidized forms. The results of the potential-dependent SERR spectroscopic analyses are consistent with the theoretical predictions and afford redox potential shifts of -160 mV (heme IV), -90 mV (heme III), -70 mV (heme II), and +20 mV (heme I) relative to the experimental redox potentials for Cyt-c(3) in solution. SERR spectroscopic experiments reveal electric-field-induced changes of the redox potentials also for the structurally very similar Cyt-c(3) from Desulfovibrio vulgaris, although the shifts are somewhat smaller compared to Cyt-c(3) from D. gigas. This study suggests that electric-field-induced redox potential shifts may also occur upon binding to biomembranes or partner proteins and thus may affect biological electron transfer processes.

Electrostatic Contributions to Protein Retention in Ion-Exchange Chromatography. 2. Proteins with Various Degrees of Structural Differences

The relation of protein structure to retention provides a framework within which to investigate chromatographic adsorption mechanisms. Protein sets with varying degrees of structural differences were studied to relate variations in protein properties to retention behavior. To explore molecular contributions to protein adsorption in ion-exchange chromatography, protein-adsorbent electrostatic interactions were modeled using a continuum approach. The calculations qualitatively capture the chromatographic differentiation of closely related subtilisin variants. Descriptions of the electrostatic interactions of FGF-1 vs FGF-2 with cation exchangers were obtained, and aid in rationalizing differences in experimental retention trends across a set of adsorbents based on different adsorption mechanisms linked to the adsorbent structure. Comparative calculations for proteins with differences in local or overall arginine-lysine composition, including subtilisin variants G166R/G166K and lysozyme/cytochrome c, suggest that continuum electrostatics is not adequate to capture the full quantitative characteristics of the chromatographic retention of proteins. To allow more accurate description of retention, additional molecular interactions, specifically hydration effects, must be incorporated in the model.

A molecular modeling study of the effect of surface chemistry on the adsorption of a fibronectin fragment spanning the 7-10th type III repeats

Although it is well documented that proteins adsorb onto biomaterial surfaces, relatively little is quantitatively understood about the effects of adsorption on protein orientation and conformation. Because this is the primary determining factor of protein bioactivity, the ability to accurately predict a protein's orientation and conformation following adsorption will be essential for the rational design of biomaterial surfaces to control biological responses. Force field-based computational chemistry methods provide an excellent means to theoretically address this issue, with the nontrivial requirement that the force field must be tailored to appropriately represent protein adsorption behavior. Accordingly, we have modified an existing force field (CHARMm) based on semiempirical quantum-mechanical peptide adsorption data to enable it to simulate protein adsorption behavior in an implicit aqueous environment. This modified force field was then applied to predict the adsorption behavior of the 7-10 type III repeats of fibronectin on functionalized surfaces. Predicted changes in adsorption energy and adsorption-induced conformation as a function of surface chemistry were found to correlate well with experimentally observed trends for these same systems. This work represents a first attempt towards the development of a molecular mechanics force field that is specifically parameterized to accurately simulate protein adsorption to biomaterial surfaces.

EPR spectroscopy of protein microcrystals oriented in a liquid crystalline polymer medium

Correlation of the g-tensor of a paramagnetic active center of a protein with its structure provides a unique experimental information on the electronic structure of the metal site. To address this problem, we made solid films containing metalloprotein (Desulfovibrio gigas cytochrome c(3)) microcrystals. The microcrystals in a liquid crystalline polymer medium (water/hydroxypropylcellulose) were partially aligned by a shear flow. A strong orientation effect of the metalloprotein was observed by EPR spectroscopy and polarizing optical microscopy. The EPR spectra of partially oriented samples were simulated, allowing for molecular orientation distribution function determination. The observed effect results in enhanced sensitivity and resolution of the EPR spectra and provides a new approach towards the correlation of spectroscopic data, obtained by EPR or some other technique, with the three-dimensional structure of a protein or a model compound.

Molecular simulation study of water interactions with oligo (ethylene glycol)-terminated alkanethiol self-assembled monolayers

Molecular simulations were performed to study a system consisting of protein (e.g., lysozyme) and self-assembled monolayers (SAMs) terminating with different chemical groups in the presence of explicit water molecules and ions. Mixed SAMs of oligo (ethylene glycol) [S(CH2)4(OCH2CH2)4OH, (OEG)] and hydroxyl-terminated SAMs [S(CH2)4OH] with a mole fraction of OEG at chiOEG = 0.2, 0.5, 0.8, and 1.0 were used in this study. In addition, methyl-terminated SAMs [S(CH2)11CH3] were also studied for comparison. The structural and dynamic behavior of hydration water, the flexibility and conformation state of SAMs, and the orientation and conformation of protein were examined. Simulation results were compared with those of experiments. It appears that there is a correlation between OEG surface resistance to protein adsorption and the surface density of OEG chains, which leads to a large number of tightly bound water molecules around OEG chains and the rapid mobility of hydrated SAM chains.

Exploring the electronic and mechanical properties of protein using conducting atomic force microscopy

In interfacing man-made electronic components with specifically folded biomacromolecules, the perturbative effects of junction structure on any signal generated should be considered. We report herein on the electron-transfer characteristics of the blue copper metalloprotein, azurin, as characterized at a refined level by conducting atomic force microscopy (C-AFM). Specifically, the modulation of current-voltage (I-V) behavior with compressional force has been examined. In the absence of assignable resonant electron tunneling within the confined bias region, from -1 to 1 V, the I-V behavior was analyzed with a modified Simmons formula. To interpret the variation of tunneling barrier height and barrier length obtained by fitting with the modified Simmons formula, an atom packing density model associated with protein mechanical deformation was proposed and simulated by molecular dynamics. The barrier heights determined at the minimum forces necessary for stable electrical contact correlate reasonably well with those estimated from bulk biophysical (electroanalytical and photochemical) experiments previously reported. At higher forces, the tunnel barrier decreases to fall within the range observed with saturated organic systems. Molecular dynamics simulations revealed changes in secondary structure and atomic density of the protein with respect to compression. At low compression, where transport measurements are made, secondary structure is retained, and atomic packing density is observed to increase linearly with force. These predictions, and those made at higher compression, are consistent with both experimentally observed modulations of tunneling barrier height with applied force and the applicability of the atom packing density model of electron tunneling in proteins to molecular-level analyses.

Theoretical analysis of adsorption thermodynamics for charged peptide residues on SAM surfaces of varying functionality

Cellular response to an implant is largely controlled by protein adsorption because cells directly interact with the adsorbed protein rather than the implant surface. Protein adsorption will occur when the change in Gibbs free energy (Delta G) of the system decreases during the adsorption process. Electrostatic interactions between charged peptide residues presented by a protein's surface and surface functional groups greatly contribute to the Delta G of protein adsorption. In this study, semiempirical molecular orbital calculations were used to theoretically determine the adsorption enthalpy between charged peptide residues [aspartic acid (-1), glutamic acid (-1), and arginine (+1)] and functionalized SAM surfaces [methyl, hydroxyl, amine (+1), and carboxylic acid (-1)]. Additional enthalpic and entropic contributions attributed to water restructuring effects were then approximated based on literature values for functional group solvation and considered along with the calculated enthalpy values to estimate the change in Delta G for each residue/surface system as a function of surface separation distance. The results predict long-range attraction and repulsion to the opposite and same-charge residue/surface systems, respectively, followed by strong short-range repulsion caused by functional group dehydration. Short-range repulsion alone was predicted for the charged residues on the methyl and hydroxyl surfaces. These results provide a theoretical quantitative description of fundamental mechanisms governing protein adsorption behavior and provide a basis for the development of a knowledge-based surface design approach to control biological response.

Molecular dynamics simulations of a hydrated protein vectorially oriented on polar and nonpolar soft surfaces

We present a collection of molecular dynamics computer simulation studies on a model protein-membrane system, namely a cytochrome c monolayer attached to an organic self-assembled monolayer (SAM). Modifications of the system are explored, including the polarity of the SAM endgroups, the amount of water present for hydration, and the coordination number of the heme iron atom. Various structural parameters are measured, e.g., the protein radius of gyration and eccentricity, the deviation of the protein backbone from the x-ray crystal structure, the orientation of the protein relative to the SAM surface, and the profile structures of the SAM, protein, and water. The polar SAM appears to interact more strongly with the protein than does the nonpolar SAM. Increased hydration of the system tends to reduce the effects of other parameters. The choice of iron coordination model has a significant effect on the protein structure and the heme orientation. The overall protein structure is largely conserved, except at each end of the sequence and in one loop region. The SAM structure is only perturbed in the region of its direct contact with the protein. Our calculations are in reasonably good agreement with experimental measurements (polarized optical absorption/emission spectroscopy, x-ray interferometry, and neutron interferometry).

Orientation distributions for cytochrome c on polar and nonpolar interfaces by total internal reflection fluorescence

The formation of chemisorbed monolayers of yeast cytochrome c on both uncharged polar and nonpolar soft surfaces of organic self-assembled monolayers (SAM) on solid inorganic substrates was followed in situ by polarized total internal reflection fluorescence. Two types of nonpolar surfaces and one type of uncharged polar surface were used. The first type of nonpolar surface contained only thiol endgroups, while the other was composed of a mixture of thiol and methyl endgroups. The uncharged polar surface was provided by the mixture of thiol and hydroxyl endgroups. The thiol endgroups were used to form a covalent disulfide bond with the unique surface-exposed cysteine residue 102 of the protein. The mean tilt angle of the protein's zinc-substituted porphyrin was found to be 41 degrees and 50 degrees for the adsorption onto the nonpolar and uncharged polar surfaces, respectively. The distribution widths for the pure thiol and the thiol/methyl and thiol/hydroxyl mixtures were 9 degrees, 1 degrees, and 18 degrees, respectively. The high degree of the orientational order and good stability achieved for the protein monolayer on the mixed thiol/methyl endgroup SAM makes this system very attractive for studies of both intramolecular and intermolecular electron transfer processes.

Does the redox status of cytochrome C act as a fail-safe mechanism in the regulation of programmed cell death?

It has now become recognized that one of the key events in the induction of apoptosis, or programmed cell death, in both plants and animals is the release of cytochrome c from mitochondria. It is also known that oxidative stress imposed on cells can have a profound effect on the onset or progression of apoptosis. Here, we discuss how the redox status of cytochrome c, and thus its structure, can be altered by the presence of reactive oxygen species (ROS) and reduced glutathione (GSH). We suggest that cytochrome c will only induce programmed cell death if present in the cytoplasm in the oxidized state, and that the presence of high levels of cytoplasmic GSH maintain cytochrome c in an inactive (reduced) state, thus behaving as a fail-safe mechanism if cytochrome c is released by mitochondria when programmed cell death is not the required outcome. If the redox status of the cell is disturbed however, perhaps in the presence of hydrogen peroxide, GSH concentrations will drop, the cellular E(h) will rise, and cytochrome c will tend towards the oxidized state, allowing programmed cell death to proceed. Therefore, we propose that the redox state of cytoplasmic cytochrome c may be a key regulator of programmed cell death.

Molecular dynamics study of substance P peptides in a biphasic membrane mimic

Two neuropeptides, substance P (SP) and SP-tyrosine-8 (SP-Y8), have been studied by molecular dynamics (MD) simulation in a TIP3P water/CCl4 biphasic solvent system as a mimic for the water-membrane system. Initially, distance restraints derived from NMR nuclear Overhauser enhancements (NOE) were incorporated in the restrained MD (RMD) in the equilibration stage of the simulation. The starting orientation/position of the peptides for the MD simulation was either parallel to the water/CCl4 interface or in a perpendicular/insertion mode. In both cases the peptides equilibrated and adopted a near-parallel orientation within approximately 250 ps. After equilibration, the conformation and orientation of the peptides, the solvation of both the backbone and the side chain of the residues, hydrogen bonding, and the dynamics of the peptides were analyzed from trajectories obtained in the RMD or the subsequent free MD (where the NOE restraints were removed). These analyses showed that the peptide backbone of nearly all residues are either solvated by water or are hydrogen-bonded. This is seen to be an important factor against the insertion mode of interaction. Most of the interactions with the hydrophobic phase come from the hydrophobic interactions of the side chains of Pro-4, Phe-7, Phe-8, Leu-10, and Met-11 for SP, and Phe-7, Leu-10, Met-11 and, to a lesser extent, Tyr-8 in SP-Y8. Concerted conformational transitions took place in the time frame of hundreds of picoseconds. The concertedness of the transition was due to the tendency of the peptide to maintain the necessary secondary structure to position the peptide properly with respect to the water/CCl4 interface.

Vectorially oriented monolayers of the cytochrome c/cytochrome oxidase bimolecular complex

Vectorially oriented monolayers of yeast cytochrome c and its bimolecular complex with bovine heart cytochrome c oxidase have been formed by self-assembly from solution. Both quartz and Ge/Si multilayer substrates were chemical vapor deposited with an amine-terminated alkylsiloxane monolayer that was then reacted with a hetero-bifunctional cross-linking reagent, and the resulting maleimide endgroup surface then provided for covalent interactions with the naturally occurring single surface cysteine 102 of the yeast cytochrome c. The bimolecular complex was formed by further incubating these cytochrome c monolayers in detergent-solubilized cytochrome oxidase. The sequential formation of such monolayers and the vectorially oriented nature of the cytochrome oxidase was studied via meridional x-ray diffraction, which directly provided electron density profiles of the protein(s) along the axis normal to the substrate plane. The nature of these profiles is consistent with previous work performed on vectorially oriented monolayers of either cytochrome c or cytochrome oxidase alone. Furthermore, optical spectroscopy has indicated that the rate of binding of cytochrome oxidase to the cytochrome c monolayer is an order of magnitude faster than the binding of cytochrome oxidase to an amine-terminated surface that was meant to mimic the ring of lysine residues around the heme edge of cytochrome c, which are known to be involved in the binding of this protein to cytochrome oxidase.

Small-scale lipid-membrane structure: simulation versus experiment

Recently, it has become obvious that the conventional picture of the fluid lipid-bilayer component of biological membranes being a fairly structureless 'fluid mosaic' solvent is far from correct. The lipid bilayer displays distinct static and dynamic structural organization on a small scale, for example in terms of differentiated lipid domains, and evidence is accumulating that these structures are of importance for the functioning of biological membranes, including the activity of membrane-bound enzymes and receptors and morphological changes at the cell surface. Insight into the relationship between this small-scale structure and biological functioning holds promise for a more rational approach to modulate function via manipulation of the lipid microenvironment and the lipid/protein interface in particular. Computer simulation has proved to be a useful tool in investigating membrane structure on a small scale-specifically the nanometer scale (1-100 nm), which is in between the molecular scale accessible by various spectroscopic techniques and molecular dynamics calculations, and the micrometer scale accessible by scattering and microscopy techniques.