Structure, dynamics, and energetics of water at the surface of a small globular protein: a molecular dynamics simulation

Solvent Structure and Dynamics near the Surfaces of β-Hematin Crystals

Hematin crystallization, which is an essential component of the physiology of malaria parasites and the most successful target for antimalarial drugs, proceeds in mixed organic-aqueous solvents both in vivo and in vitro. Here we employ molecular dynamics simulations to examine the structuring and dynamics of a water-normal octanol mixture (a solvent that mimics the environment hosting hematin crystallization in vivo) in the vicinity of the typical faces in the habit of a hematin crystal. The simulations reveal that the properties of the solvent in the layer adjacent to the crystal are strongly impacted by the distinct chemical and topological features presented by each crystal face. The solvent organizes into at least three distinct layers. We also show that structuring of the solvent near the different faces of β-hematin strongly impacts the interfacial dynamics. The relaxation time of n-octanol molecules is longest in the contact layers and correlates with the degree of structural ordering at the respective face. We show that the macroscopically homogeneous water-octanol solution holds clusters of water and n-octanol connected by hydrogen bonds that entrap the majority of the water but are mostly smaller than 30 water molecules. Near the crystal surface the clusters anchor on hematin carboxyl groups. These results provide a direct example that solvent structuring is not restricted to aqueous and other hydrogen-bonded solutions. Our findings illuminate two fundamental features of the mechanisms of hematin crystallization: the elongated shapes of natural and synthetic hematin crystals and the stabilization of charged groups of hematin and antimalarials by encasing in water clusters. In addition, these findings suggest that hematin crystallization may be controlled by additives that disrupt or reinforce solvent structuring.

Dynamics of TMAO and urea in the hydration shell of the protein SNase

Using all-atom molecular dynamics simulations of aqueous solutions of the globular protein SNase, the dynamic behavior of water molecules and cosolvents (trimethylamine-N-oxide (TMAO) and urea) in the hydration shell of the protein was studied for different solvent compositions. TMAO is a potent protein-stabilizing osmolyte, whereas urea is known to destabilize proteins. For molecules that are initially located in successive narrow layers at a given distance from the protein, the mean displacements and the distribution of displacements for short time intervals are calculated. For molecules that are initially located in solvation shells of a given thickness around the protein, the characteristic residence times in these shells are determined to characterize the dynamic behavior of the solvent molecules as a function of the distance to the protein. A combined consideration of these characteristics allows to reveal additional features of the dynamics of the cosolvents. It is shown that TMAO molecules leave the nearest vicinity of the protein faster than urea molecules, despite the fact that the mobility of TMAO molecules, measured by their mean displacements, is lower than that of urea. Moreover, we show that the rate of release of TMAO molecules from the hydration shell is lower in ternary (TMAO + urea + H₂O) solvent mixtures than in the binary ones. This is consistent with a recent observation that the fraction of TMAO near the protein decreases in the presence of urea. From the analysis of the decay of the number of particles initially located in the region of the first peak of the distribution function of solvent molecules around the protein, we estimated that about 20 water molecules and 6-7 urea molecules stay near the protein for more than 1000 ps.

Direct Evidence for the Effect of Glycerol on Protein Hydration and Thermal Structural Transition

The mechanisms of protein stabilization by uncharged solutes, such as polyols and sugars, have been intensively studied with respect to the chemical thermodynamics of molecular crowding. In particular, many experimental and theoretical studies have been conducted to explain the mechanism of the protective action on protein structures by glycerol through the relationship between hydration and glycerol solvation on protein surfaces. We used wide-angle x-ray scattering (WAXS), small-angle neutron scattering, and theoretical scattering function simulation to quantitatively characterize the hydration and/or solvation shell of myoglobin in aqueous solutions of up to 75% v/v glycerol. At glycerol concentrations below ∼40% v/v, the preservation of the hydration shell was dominant, which was reasonably explained by the preferential exclusion of glycerol from the protein surface (preferential hydration). In contrast, at concentrations above 50% v/v, the partial penetration or replacement of glycerol into or with hydration-shell water (neutral solvation by glycerol) was gradually promoted. WAXS results quantitatively demonstrated the neutral solvation, in which the replacement of hydrated water by glycerol was proportional to the volume fraction of glycerol in the solvent multiplied by an exchange rate (β ≤ 1). These phenomena were confirmed by small-angle neutron scattering measurements. The observed WAXS data covered the entire hierarchical structure of myoglobin, ranging from tertiary to secondary structures. We separately analyzed the effect of glycerol on the thermal stability of myoglobin at each hierarchical structural level. The thermal transition midpoint temperature at each hierarchical structural level was raised depending on the glycerol concentration, with enhanced transition cooperativeness between different hierarchical structural levels. The onset temperature of the helix-to-cross β-sheet transition (the initial process of amyloid formation) was evidently elevated. However, oligomerization connected to fibril formation was suppressed, even at a low glycerol concentration.

Conformational States of E7010 Is Complemented by Microclusters of Water Inside the α,β-Tubulin Core

The α,β-tubulin is the building block of microtubules, which is associated with and dissociated from the microtubular architecture complying with the dynamic instability of the microtubules. This dynamic instability has a direct relation with the spindle formation by the microtubules and cell division kinetics. E7010 is one of the promising ligands of an α,β-tubulin protein that binds at the core of this protein and can diminish the protein's ability to fit to a growing microtubule, thus frustrating cell division. Although X-ray crystallography has reported a specific binding conformation of E7010 in PDB, molecular dynamics (MD) simulations have revealed two other conformational states of the ligand capable of binding to tubulin with stabilities close to that state reported in PDB. To rationalize this quasidegeneracy of ligand binding modes, MD simulations have further revealed that the understanding of the mechanism of E7010-tubulin binding remains incomplete unless the role of water molecules to bridge this interaction is taken into consideration, a very critical insight that was not visible from the PDB structure. Further, these water molecules differ from the standard examples of "bridging" waters which generally exist as isolated water molecules between the receptor and the ligand. In the present case, the water molecules sandwiched between ligand and protein, sequestered from the bulk solvent, integrate with each other by an H-bonds network forming a group, which appear as microclusters of water. The structural packing with the ligand binding pocket and the bridging interactions between protein and ligand take place through such clusters. The presence of this microcluster of water is not just cosmetic, instead they have a crucial impact on the ligand binding thermodynamics. Only with the explicit consideration of these water clusters in the binding energy calculations (MMGBSA) is the stability of the native mode of ligand binding reported in PDB rationalized. At the same time, two other binding modes are elucidated to be quasi-degenerate with the native state and that indicates the further possibility in gaining more entropic stabilization of the complex. The role of such "bridging" water clusters to enhance the protein-ligand interaction will be insightful for designing the next generation prospective compounds in the field of cancer therapeutics.

Investigating cyclic peptides inhibiting CD2-CD58 interactions through molecular dynamics and molecular docking methods

The CD2-CD58 protein-protein interaction is known to favor the recognition of antigen presenting cells by T cells. The structural, energetics, and dynamical properties of three known cyclic CD58 ligands, named P6, P7, and RTD-c, are studied through molecular dynamics (MD) simulations and molecular docking calculations. The ligands are built so as to mimic the C and F β-strands of protein CD2, connected via turn inducers. The MD analyses focus on the location of the ligands with respect to the experimental binding site and on the direct and water-mediated hydrogen bonds (H bonds) they form with CD58. Ligand P6, with a sequence close to the experimental β-strands of CD2, presents characteristics that explain its higher experimental affinity, e.g., the lower mobility and flexibility at the CD58 surface, and the larger number and occurrence frequency of ligand-CD58 H bonds. For the two other ligands, the structural modifications lead to changes in the binding pattern with CD58 and its dynamics. In parallel, a large set of molecular docking calculations, carried out with various search spaces and docking algorithms, are compared to provide a consensus view of the preferred ligand binding modes. The analysis of the ligand side chain locations yields results that are consistent with the CD2-CD58 crystal structure and suggests various binding modes of the experimentally identified hot spot of the ligands, i.e., Tyr86. P6 is shown to form a number of contacts that are also present in the experimental CD2-CD58 structure.

Deciphering complex dynamics of water counteraction around secondary structural elements of allosteric protein complex: Case study of SAP-SLAM system in signal transduction cascade

The first hydration shell of a protein exhibits heterogeneous behavior owing to several attributes, majorly local polarity and structural flexibility as revealed by solvation dynamics of secondary structural elements. We attempt to recognize the change in complex water counteraction generated due to substantial alteration in flexibility during protein complex formation. The investigation is carried out with the signaling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, and interacting with SLAM-associated protein (SAP), composed of one SH2 domain. All atom molecular dynamics simulations are employed to the aqueous solutions of free SAP and SLAM-peptide bound SAP. We observed that water dynamics around different secondary structural elements became highly affected as well as nicely correlated with the SLAM-peptide induced change in structural rigidity obtained by thermodynamic quantification. A few instances of contradictory dynamic features of water to the change in structural flexibility are explained by means of occluded polar residues by the peptide. For βD, EFloop, and BGloop, both structural flexibility and solvent accessibility of the residues confirm the obvious contribution. Most importantly, we have quantified enhanced restriction in water dynamics around the second Fyn-binding site of the SAP due to SAP-SLAM complexation, even prior to the presence of Fyn. This observation leads to a novel argument that SLAM induced more restricted water molecules could offer more water entropic contribution during the subsequent Fyn binding and provide enhanced stability to the SAP-Fyn complex in the signaling cascade. Finally, SLAM induced water counteraction around the second binding site of the SAP sheds light on the allosteric property of the SAP, which becomes an integral part of the underlying signal transduction mechanism.

Effect of temperature on the structure and hydration layer of TATA-box DNA: A molecular dynamics simulation study

DNA within the living cells experiences a diverse range of temperature, ranging from freezing condition to hot spring water. How the structure, the mechanical properties of DNA, and the solvation dynamics around DNA changes with the temperature is important to understand the functionality of DNA under those acute temperature conditions. In that notion, we have carried out molecular dynamics simulations of a DNA oligomer, containing TATA-box sequence for three different temperatures (250K, 300K and 350K). We observed that the structure of the DNA, in terms of backbone torsion angles, sugar pucker, base pair parameters, and base pair step parameters, did not show any unusual properties within the studied range of temperatures, but significant structural alteration was noticed between BI and BII forms at higher temperature. As expected, the flexibility of the DNA, in terms of the torsional rigidity and the bending rigidity is highly temperature dependent, confirming that flexibility increases with increase in temperature. Additionally, the groove widths of the studied DNA showed temperature sensitivity, specifically, the major groove width decreases and the minor groove width increases, respectively, with the increase in temperature. We observed that at higher temperature, water around both the major and the minor groove of the DNA is less structured. However, the water dynamics around the minor groove of the DNA is more restricted as compared to the water around the major groove throughout the studied range of temperatures, without any anomalous behavior.

C-terminal tail insertion of Bcl-xL in membrane occurs via partial unfolding and refolding cycle associating microsolvation

Insertion of the Bcl-x_L C-terminal into the mitochondrial outer membrane is found to be guided by the partial unfolding–refolding cycle, assisted by micro-solvation.

Diffusion of Hydration Water around Intrinsically Disordered Proteins

Hydration water dynamics around globular proteins have attracted considerable attention in the past decades. This work investigates the hydration water dynamics around partially/fully intrinsically disordered proteins and compares it to that of the globular proteins via molecular dynamics simulations. The translational diffusion of the hydration water is examined by evaluating the mean-square displacement and the velocity autocorrelation function, while the rotational diffusion is probed through the dipole-dipole time correlation function. The results reveal that the translational and rotational motions of water molecules at the surface of intrinsically disordered proteins/regions are less restricted as compared to those around globular proteins/ordered regions, which is reflected in their higher diffusion coefficient and lower orientational relaxation time. The restricted mobility of hydration water in the vicinity of the protein leads to a sublinear diffusion in a heterogeneous interface. A positive correlation between the mean number of hydrogen bonds and the diffusion coefficient of hydration water implies higher mobility of water molecules at the surface of disordered proteins, which is due to their higher number of hydrogen bonds. Enhanced hydration water mobility around disordered proteins/regions is also related to their higher hydration capacity, low hydrophobicity, and increased internal protein motions. Thus, we generalize that the intrinsically disordered proteins/regions are associated with higher hydration water mobility as compared to globular protein/ordered regions, which may help to elucidate their varied functional specificity.

A bicyclic peptide scaffold promotes phosphotyrosine mimicry and cellular uptake

While peptides are promising as probes and therapeutics, targeting intracellular proteins will require greater understanding of highly structured, cell-internalized scaffolds. We recently reported BC1, an 11-residue bicyclic peptide that inhibits the Src homology 2 (SH2) domain of growth factor receptor-bound protein 2 (Grb2). In this work, we describe the unique structural and cell uptake properties of BC1 and similar cyclic and bicyclic scaffolds. These constrained scaffolds are taken up by mammalian cells despite their net neutral or negative charges, while unconstrained analogs are not. The mechanism of uptake is shown to be energy-dependent and endocytic, but distinct from that of Tat. The solution structure of BC1 was investigated by NMR and MD simulations, which revealed discrete water-binding sites on BC1 that reduce exposure of backbone amides to bulk water. This represents an original and potentially general strategy for promoting cell uptake.

Searching for protein binding sites from Molecular Dynamics simulations and paramagnetic fragment-based NMR studies

Hotspot delineation on protein surfaces represents a fundamental step for targeting protein-protein interfaces. Disruptors of protein-protein interactions can be designed provided that the sterical features of binding pockets, including the transient ones, can be defined. Molecular Dynamics, MD, simulations have been used as a reliable framework for identifying transient pocket openings on the protein surface. Accessible surface area and intramolecular H-bond involvement of protein backbone amides are proposed as descriptors for characterizing binding pocket occurrence and evolution along MD trajectories. TEMPOL induced paramagnetic perturbations on (1)H-(15)N HSQC signals of protein backbone amides have been analyzed as a fragment-based search for surface hotspots, in order to validate MD predicted pockets. This procedure has been applied to CXCL12, a small chemokine responsible for tumor progression and proliferation. From combined analysis of MD data and paramagnetic profiles, two CXCL12 sites suitable for the binding of small molecules were identified. One of these sites is the already well characterized CXCL12 region involved in the binding to CXCR4 receptor. The other one is a transient pocket predicted by Molecular Dynamics simulations, which could not be observed from static analysis of CXCL12 PDB structures. The present results indicate how TEMPOL, instrumental in identifying this transient pocket, can be a powerful tool to delineate minor conformations which can be highly relevant in dynamic discovery of antitumoral drugs.

Concentration-dependent like-charge pairing of guanidinium ions and effect of guanidinium chloride on the structure and dynamics of water from all-atom molecular dynamics simulation

An all-atom molecular dynamics simulation shows concentration-dependent like-charge ion pairing of the guanidinium ion in an aqueous solution of guanidinium chloride. We have observed two types of like-charge ion pairing for guanidinium ions, namely, stacked ion pairs and solvent-separated ion pairs. Interestingly, both of these like-charge ion-pair formations are dependent on the concentration of guanidinium chloride in water. The probability of stacked like-charge ion-pair formation decreases, whereas, the probability of solvent-separated like-charge pairing increases as the concentration of guanidinium chloride increases, which is shown from radial distribution functions and is confirmed from the energy calculations. Besides like-charge ion-pair formation, we also investigated guanidinium chloride induced changes in water structure. Hydrogen-bond analysis indicates that guanidinium chloride does not alter the strict-hydrogen-bonding patterns of water, whereas, it breaks the bend-hydrogen bond and the non-hydrogen-bonding patterns. Tetrahedral order, nearest neighbor orientation, and distance distribution of water molecules around a probe water molecule show the extent of water structure distortion.

Discrimination of ligands with different flexibilities resulting from the plasticity of the binding site in tubulin

Tubulin, an α,β heterodimer, has four distinct ligand binding sites (for paclitaxel, peloruside/laulimalide, vinca, and colchicine). The site where colchicine binds is a promising drug target for arresting cell division and has been observed to accommodate compounds that are structurally diverse but possess comparable affinity. This investigation, using two such structurally different ligands as probes (one being colchicine itself and another, TN16), aims to provide insight into the origin of this diverse acceptability to provide a better perspective for the design of novel therapeutic molecules. Thermodynamic measurements reveal interesting interplay between entropy and enthalpy. Although both these parameters are favourable for TN16 binding (ΔH < 0, ΔS > 0), but the magnitude of entropy has the determining role for colchicine binding as its enthalpic component is destabilizing (ΔH > 0, ΔS > 0). Molecular dynamics simulation provides atomistic insight into the mechanism, pointing to the inherent flexibility of the binding pocket that can drastically change its shape depending on the ligand that it accepts. Simulation shows that in the complexed states both the ligands have freedom to move within the binding pocket; colchicine can switch its interactions like a "flying trapeze", whereas TN16 rocks like a "swing cradle", both benefiting entropically, although in two different ways. Additionally, the experimental results with respect to the role of solvation entropy correlate well with the computed difference in the hydration: water molecules associated with the ligands are released upon complexation. The complementary role of van der Waals packing versus flexibility controls the entropy-enthalpy modulations. This analysis provides lessons for the design of new ligands that should balance between the "better fit" and "flexibility"', instead of focusing only on the receptor-ligand interactions.

NMR studies on structure and dynamics of the monomeric derivative of BS-RNase: new insights for 3D domain swapping

Three-dimensional domain swapping is a common phenomenon in pancreatic-like ribonucleases. In the aggregated state, these proteins acquire new biological functions, including selective cytotoxicity against tumour cells. RNase A is able to dislocate both N- and C-termini, but usually this process requires denaturing conditions. In contrast, bovine seminal ribonuclease (BS-RNase), which is a homo-dimeric protein sharing 80% of sequence identity with RNase A, occurs natively as a mixture of swapped and unswapped isoforms. The presence of two disulfides bridging the subunits, indeed, ensures a dimeric structure also to the unswapped molecule. In vitro, the two BS-RNase isoforms interconvert under physiological conditions. Since the tendency to swap is often related to the instability of the monomeric proteins, in these paper we have analysed in detail the stability in solution of the monomeric derivative of BS-RNase (mBS) by a combination of NMR studies and Molecular Dynamics Simulations. The refinement of NMR structure and relaxation data indicate a close similarity with RNase A, without any evidence of aggregation or partial opening. The high compactness of mBS structure is confirmed also by H/D exchange, urea denaturation, and TEMPOL mapping of the protein surface. The present extensive structural and dynamic investigation of (monomeric) mBS did not show any experimental evidence that could explain the known differences in swapping between BS-RNase and RNase A. Hence, we conclude that the swapping in BS-RNase must be influenced by the distinct features of the dimers, suggesting a prominent role for the interchain disulfide bridges.

Water and backbone dynamics in a hydrated protein

Rotational immobilization of proteins permits characterization of the internal peptide and water molecule dynamics by magnetic relaxation dispersion spectroscopy. Using different experimental approaches, we have extended measurements of the magnetic field dependence of the proton-spin-lattice-relaxation rate by one decade from 0.01 to 300 MHz for (1)H and showed that the underlying dynamics driving the protein (1)H spin-lattice relaxation is preserved over 4.5 decades in frequency. This extension is critical to understanding the role of (1)H(2)O in the total proton-spin-relaxation process. The fact that the protein-proton-relaxation-dispersion profile is a power law in frequency with constant coefficient and exponent over nearly 5 decades indicates that the characteristics of the native protein structural fluctuations that cause proton nuclear spin-lattice relaxation are remarkably constant over this wide frequency and length-scale interval. Comparison of protein-proton-spin-lattice-relaxation rate constants in protein gels equilibrated with (2)H(2)O rather than (1)H(2)O shows that water protons make an important contribution to the total spin-lattice relaxation in the middle of this frequency range for hydrated proteins because of water molecule dynamics in the time range of tens of ns. This water contribution is with the motion of relatively rare, long-lived, and perhaps buried water molecules constrained by the confinement. The presence of water molecule reorientational dynamics in the tens of ns range that are sufficient to affect the spin-lattice relaxation driven by (1)H dipole-dipole fluctuations should make the local dielectric properties in the protein frequency dependent in a regime relevant to catalytically important kinetic barriers to conformational rearrangements.

Dimensionality of diffusive exploration at the protein interface in solution

The dynamics of water are critically important to the energies of interaction between proteins and substrates and determine the efficiency of transport at the interface. The magnetic field dependence of the nuclear spin-lattice relaxation rate constant 1/T(1) of water protons provides a direct characterization of water diffusional dynamics at the protein interface. We find that the surface-average translational correlation time is 30-40 ps and the magnetic field dependence of the water proton 1/T(1) is characteristic of two-dimensional diffusion of water in the protein interfacial region. The reduced dimensionality substantially increases the intermolecular re-encounter probability and the efficiency of the surface exploration by the small molecule, water in this case. We propose a comprehensive theory of the translational effects of a small diffusing particle confined in the vicinity of a spherical macromolecule as a function of the relative size of the two particles. We show that the change in the apparent dimensionality of the diffusive exploration is a general result of the small diffusing particle encountering a much larger particle that presents a diffusion barrier. Examination of the effects of the size of the confinement relative to the macromolecule size reveals that the reduced dimensionality characterizing the small-molecule diffusion persists to remarkably small radius ratios. The experimental results on several different proteins in solution support the proposed theoretical model, which may be generalized to other small-particle-large-body systems like vesicles and micelles.

Transport properties of water at functionalized molecular interfaces

Understanding transport properties of solvent such as diffusion and viscosity at interfaces with biomacromolecules and hard materials is of fundamental importance to both biology and biotechnology. Our study utilizes equilibrium molecular dynamics simulations to calculate solvent transport properties at a model peptide and microarray surface. Both diffusion and selected components of viscosity are considered. Solvent diffusion is found to be affected near the peptide and surface. The stress-stress correlation function of solvent near the hard surface exhibits long time memory. Both diffusion and viscosity are shown to be closely correlated with the density distribution function of water along the microarray surface.

Molecular simulation studies of protein interactions with zwitterionic phosphorylcholine self-assembled monolayers in the presence of water

Molecular simulations were performed to study the interactions between a protein (lysozyme, LYZ) and phosphorylcholine-terminated self-assembled monolayers (PC-SAMs) in the presence of explicit water molecules and ions. The results show that the water molecules above the PC-SAM surface create a strong repulsive force on the protein as it approaches the surface. The structural and dynamic properties of the water molecules above the PC-SAM surface were analyzed to provide information regarding the role of hydration in surface resistance to protein adsorption. It can be seen from residence time dynamics that the water molecules immediately above the PC-SAM surface are significantly slowed down as compared to bulk water, suggesting that the PC-SAM surface generates a tightly bound, structured water layer around its head groups. Moreover, the orientational distribution and reorientational dynamics of the interfacial water molecules near the PC-SAM surface were found to have the ionic solvation nature of the PC head groups. These properties were also compared to those obtained previously for an oligo(ethylene glycol) (OEG) SAM system and bulk water.

Effects of dimerization of Serratia marcescens endonuclease on water dynamics

The dynamics and structure of Serratia marcescens endonuclease and its neighboring solvent are investigated by molecular dynamics (MD). Comparisons are made with structural and biochemical experiments. The dimer form is physiologic and functions more processively than the monomer. We previously found a channel formed by connected clusters of waters from the active site to the dimer interface. Here, we show that dimerization clearly changes correlations in the water structure and dynamics in the active site not seen in the monomer. Our results indicate that water at the active sites of the dimer is less affected compared with bulk solvent than in the monomer where it has much slower characteristic relaxation times. Given that water is a required participant in the reaction, this gives a clear advantage to dimerization in the absence of an apparent ability to use both active sites simultaneously.

How a vicinal layer of solvent modulates the dynamics of proteins

The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk solvent at low temperatures, and communicates with it through a vicinal layer at physiological temperatures. A linear viscoelastic model elucidates the less-than-expected increase in the relaxation times observed in the backbone dynamics of the protein. The model further explains the increase in the flexibility of the protein once the transition takes place and the differences in the flexibility under the different solvent environments. Coupling between the vicinal layer and the protein fluctuations is necessary to interpret these observations. The vicinal layer is postulated to form once a threshold for the volumetric fluctuations in the protein to accommodate solvents of different sizes is reached. Compensation of entropic-energetic contributions from the protein-coupled vicinal layer quantifies the scaling of the dynamical transition temperatures in various solvents. The protein adapts different conformational routes for organizing the required coupling to a specific solvent, which is achieved by adjusting the amount of conformational jumps in the surface-group dihedrals.

Understanding the nonfouling mechanism of surfaces through molecular simulations of sugar-based self-assembled monolayers

This paper presents a molecular simulation study of the interactions of a protein (lysozyme) with self-assembled monolayers (SAMs) of mannitol and sorbitol terminated alkanethiols in the presence of explicit water molecules and ions. The all-atom simulations were performed to calculate the force generated on the protein as a function of its distance above the SAM surfaces. The structural and dynamic properties of water molecules both above the SAM surfaces and around the SAM head groups were analyzed to provide a better understanding of the nonfouling behavior of the sugar-based SAM surfaces. Results from this work suggest that both mannitol and sorbitol SAMs generate a tightly bound, structured water layer around the SAM chains. This hydration layer creates a repulsive force on the protein when it approaches the surface, resulting in a nonfouling surface despite the presence of hydrogen-bond donor groups. This work demonstrates the importance of strong surface-water interactions for surface resistance to nonspecific protein adsorption.

Transfer of structural elements from compact to extended states in unsolvated ubiquitin

Multidimensional ion mobility spectrometry techniques (IMS-IMS and IMS-IMS-IMS) combined with mass spectrometry are used to study structural transitions of ubiquitin ions in the gas phase. It is possible to select and activate narrow distributions of compact and partially folded conformation types and examine new distributions of structures that are formed. Different compact conformations unfold, producing a range of new partially folded states and three resolvable peaks associated with elongated conformers. Under gentle activation conditions, the final populations of the three elongated forms depend on the initial structures of the selected ions. This requires that some memory of the compact state (most likely secondary structure) is preserved along the unfolding pathway. Activation of selected, partially folded intermediates (formed from specific compact states) leads to elongated state populations that are consistent with the initial selected compact form-evidence that intermediates not only retain elements of initial structure but also are capable of transmitting structure to final states.

Do we underestimate the importance of water in cell biology?

Liquid water is a highly versatile material. Although it is formed from the tiniest of molecules, it can shape and control biomolecules. The hydrogen-bonding properties of water are crucial to this versatility, as they allow water to execute an intricate three-dimensional 'ballet', exchanging partners while retaining complex order and enduring effects. Water can generate small active clusters and macroscopic assemblies, which can both transmit information on different scales.

Unfolding dynamics of the protein ubiquitin: insight from simulation

The temperature-induced unfolding pathway of ubiquitin has been investigated by molecular dynamics simulation at four different temperatures. It has been observed that the sequences of the unfolding events are same at all the temperatures. However, the time scale of the dynamics at different temperatures are different. The transition states at various temperatures also possess similar secondary structural elements. The intermediate conformations visited by the protein at different temperatures can help determination of the transition states. The well known " state" of ubiquitin, hitherto found to be stable only in methanol water mixture, have been observed to be a common transient intermediate conformation in the unfolding path of the protein in water. Our observation about the similarities of the unfolding process at different temperatures strongly recommend for a defined pathway for the unfolding process.

Diffusion of water in confined geometry: the case of a multilamellar bilayer

The diffusion of water confined in a stack of GM3 ganglioside bilayers is studied by computer simulation. A theoretical analysis of the behavior of the mean square displacement parallel and perpendicular to the bilayer surface is also provided in terms of diffusion equations in a very long time interval, between 2 ps and 2 ns. Such an analysis has allowed us to identify two different time regimes, to clarify the nature of nonlinear time dependence of the mean square displacement, and to give an interpretation to the origin of the often used time dependent diffusion coefficient. Both the effects of spatial inhomogeneities and boundary conditions are demonstrated to be the key points for the interpretation of all these results within a consistent theoretical framework.

Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties

Long dynamics simulations were carried out on the B1 immunoglobulin-binding domain of streptococcal protein G (ProtG) and bovine pancreatic trypsin inhibitor (BPTI) using atomistic descriptions of the proteins and a continuum representation of solvent effects. To mimic frictional and random collision effects, Langevin dynamics (LD) were used. The main goal of the calculations was to explore the stability of tens-of-nanosecond trajectories as generated by this molecular mechanics approximation and to analyze in detail structural and dynamical properties. Conformational fluctuations, order parameters, cross correlation matrices, residue solvent accessibilities, pKa values of titratable groups, and hydrogen-bonding (HB) patterns were calculated from all of the trajectories and compared with available experimental data. The simulations comprised over 40 ns per trajectory for ProtG and over 30 ns per trajectory for BPTI. For comparison, explicit water molecular dynamics simulations (EW/MD) of 3 ns and 4 ns, respectively, were also carried out. Two continuum simulations were performed on each protein using the CHARMM program, one with the all-atom PAR22 representation of the protein force field (here referred to as PAR22/LD simulations) and the other with the modifications introduced by the recently developed CMAP potential (CMAP/LD simulations). The explicit solvent simulations were performed with PAR22 only. Solvent effects are described by a continuum model based on screened Coulomb potentials (SCP) reported earlier, i.e., the SCP-based implicit solvent model (SCP-ISM). For ProtG, both the PAR22/LD and the CMAP/LD 40-ns trajectories were stable, yielding C(alpha) root mean square deviations (RMSD) of about 1.0 and 0.8 A respectively along the entire simulation time, compared to 0.8 A for the EW/MD simulation. For BPTI, only the CMAP/LD trajectory was stable for the entire 30-ns simulation, with a C(alpha) RMSD of approximately 1.4 A, while the PAR22/LD trajectory became unstable early in the simulation, reaching a C(alpha) RMSD of about 2.7 A and remaining at this value until the end of the simulation; the C(alpha) RMSD of the EW/MD simulation was about 1.5 A. The source of the instabilities of the BPTI trajectories in the PAR22/LD simulations was explored by an analysis of the backbone torsion angles. To further validate the findings from this analysis of BPTI, a 35-ns SCP-ISM simulation of Ubiquitin (Ubq) was carried out. For this protein, the CMAP/LD simulation was stable for the entire simulation time (C(alpha) RMSD of approximately 1.0 A), while the PAR22/LD trajectory showed a trend similar to that in BPTI, reaching a C(alpha) RMSD of approximately 1.5 A at 7 ns. All the calculated properties were found to be in agreement with the corresponding experimental values, although local deviations were also observed. HB patterns were also well reproduced by all the continuum solvent simulations with the exception of solvent-exposed side chain-side chain (sc-sc) HB in ProtG, where several of the HB interactions observed in the crystal structure and in the EW/MD simulation were lost. The overall analysis reported in this work suggests that the combination of an atomistic representation of a protein with a CMAP/CHARMM force field and a continuum representation of solvent effects such as the SCP-ISM provides a good description of structural and dynamic properties obtained from long computer simulations. Although the SCP-ISM simulations (CMAP/LD) reported here were shown to be stable and the properties well reproduced, further refinement is needed to attain a level of accuracy suitable for more challenging biological applications, particularly the study of protein-protein interactions.

Molecular dynamics of a protein surface: ion-residues interactions

Time-resolved measurements indicated that protons could propagate on the surface of a protein or a membrane by a special mechanism that enhanced the shuttle of the proton toward a specific site. It was proposed that a suitable location of residues on the surface contributes to the proton shuttling function. In this study, this notion was further investigated by the use of molecular dynamics simulations, where Na(+) and Cl(-) are the ions under study, thus avoiding the necessity for quantum mechanical calculations. Molecular dynamics simulations were carried out using as a model a few Na(+) and Cl(-) ions enclosed in a fully hydrated simulation box with a small globular protein (the S6 of the bacterial ribosome). Three independent 10-ns-long simulations indicated that the ions and the protein's surface were in equilibrium, with rapid passage of the ions between the protein's surface and the bulk. However, it was noted that close to some domains the ions extended their duration near the surface, thus suggesting that the local electrostatic potential hindered their diffusion to the bulk. During the time frame in which the ions were detained next to the surface, they could rapidly shuttle between various attractor sites located under the electrostatic umbrella. Statistical analysis of the molecular dynamics and electrostatic potential/entropy consideration indicated that the detainment state is an energetic compromise between attractive forces and entropy of dilution. The similarity between the motion of free ions next to a protein and the proton transfer on the protein's surface are discussed.

Hydration and Dewetting near Graphite−CH3 and Graphite−COOH Plates

The dynamics of water near the nanoscale hydrophobic (graphite-CH(3)) and hydrophilic (graphite-COOH) plates has been studied in detail with molecular dynamics simulations in this paper. It is shown that these designed surfaces (by growing a layer of methyl or carboxyl groups on top of graphite) can have a significant impact on the neighboring water dynamics, with the hydrophilic carboxyl surface having even more profound effects. The water hydrogen bond lifetime is much longer near both types of surfaces than that in the bulk, while on the other hand the water diffusion constant is much smaller than that in the bulk. The difference in the diffusion constant can be as large as a factor of 8 and the difference in the hydrogen bond lifetime can be as large as a factor of 2, depending on the distance from the surface. Furthermore, the water molecules in the first solvation shell of surface atoms show a strong bias in hydroxyl group orientation near the surface, confirming some of the previous findings. Finally, the possible water dewetting transition between two graphite-CH(3) plates and the effect of the strength of the solute-solvent attractions on the water drying transition are investigated. The relationship among the dewetting transition critical distance, van der Waals potential well depth, and water contact angle on the graphite-CH(3) surface is also analyzed on the basis of a simple macroscopic theory, which can be used to predict the dewetting transition critical distance.

Hydration Layer of a Cationic Micelle, C10TAB: Structure, Rigidity, Slow Reorientation, Hydrogen Bond Lifetime, and Solvation Dynamics

We report a theoretical study of the structure and dynamics of the water layer (the hydration layer) present at the surface of the cationic micelle decyltrimethylammonium bromide (DeTAB) by using atomistic molecular dynamics simulations. The simulated micelle consisted of 47 surfactant molecules (and an equal number of bromide ions), in good agreement with the pioneering light scattering experiments by Debye which found an aggregation number of 50. In this micelle, three partially positively charged methyl groups of each surfactant headgroup face the surrounding water. The nature of the cationic micellar surface is found to play an important role in determining the arrangement of water which is quite different from that in the bulk or on the surface of an anionic micelle, like cesium perfluorooctanoate. Water molecules present in the hydration layer are found to be preferentially distributed in the region between the three partially charged methyl headgroups. It is found that both the translational and rotational motions of water exhibit appreciably slower dynamics in the layer than those in the bulk. The solvation time correlation function (TCF) of bromide ions exhibits a long time component which is found to originate primarily from the interaction of the probe with the micellar headgroups. Thus, the decay of the solvation TCF is controlled largely by the residence time of the probe in the surface. The residence time distribution of the water molecules also exhibits a slow time component. We also calculate the collective number density fluctuation in the layer and find a prominent slow component compared to the similar quantity in the bulk. This slow component demonstrates that water structure in the hydration layer is more rigid than that in the bulk. These results demonstrate that the slow dynamics of hydration layer water is generic to macromolecular surfaces of either polarity.

Dynamics and Thermodynamics of Water in PAMAM Dendrimers at Subnanosecond Time Scales

Atomistic molecular dynamics simulations are used to study generation 5 polyamidoamine (PAMAM) dendrimers immersed in a bath of water. We interpret the results in terms of three classes of water: buried water well inside of the dendrimer surface, surface water associated with the dendrimer-water interface, and bulk water well outside of the dendrimer. We studied the dynamic and thermodynamic properties of the water at three pH values: high pH with none of the primary or tertiary amines protonated, intermediate pH with only the primary amines protonated, and low pH with all amines protonated. For all pH values we find that both buried and surface water exhibit two relaxation times: a fast relaxation ( approximately 1 ps) corresponding to the libration motion of the water and a slow ( approximately 20 ps) diffusional component related to the escaping of water from one domain to another. In contrast for bulk water the fast relaxation is approximately 0.4 ps while the slow relaxation is approximately 14 ps. These results are similar to those found in biological systems, where the fast relaxation is found to be approximately 1 ps while the slow relaxation ranges from 20 to 1000 ps. We used the 2PT MD method to extract the vibrational (power) spectrum and found substantial differences for the three classes of water. The translational diffusion coefficient for buried water is 11-33% (depending on pH) of the bulk value while the surface water is about 80%. The change in rotational diffusion is quite similar: 21-45% of the bulk value for buried water and 80% for surface water. This shows that translational and rotational dynamics of water are affected by the PAMAM-water interactions as well as due to the confinement in the interior of the dendrimer. We find that the reduction of translational or rotational diffusion is accompanied by a blue shift of the corresponding libration motions ( approximately 10 cm(-1) for translation, approximately 35 cm(-1) for rotation), indicating higher local force constants for these motions. These effects are most pronounced for the lowest pH, probably because of the increased rigidity caused by the internal charges. From the vibrational density of states we also calculate the enthalpies and entropies of the various waters. We find that water molecules are enthalpically favored near the PAMAM dendrimer: energy for surface water is approximately 0.1 kcal/mol lower to that in the bulk, and approximately 0.5-0.9 kcal/mol lower for buried water. In contrast, we find that both the buried and surface water are entropically unfavored: buried water is 0.9-2.2 kcal/mol lower than the bulk while the surface water is 0.1-0.2 kcal/mol lower. The net result is a thermodynamically unfavored state of the water surrounding the PAMAM dendrimer: 0.4-1.3 kcal/mol higher for buried water and 0.1-0.2 kcal/mol for surface water. This excess free energy of the surface and buried waters is released when the PAMAM dendrimer binds to DNA or metal ions, providing an extra driving force.

Dynamics of Water Trapped between Hydrophobic Solutes

We describe the model dynamical behavior of the solvent between two nanoscopic hydrophobic solutes. The dynamics of the vicinal water in various sized traps is found to be significantly different from bulk behavior. We consider the dynamics at normal temperature and pressure at three intersolute distances corresponding to the three solvent separated minima in the free energy profile between the solutes with attractions. These three states correspond to one, two, and three intervening layers of water molecules. Results are obtained from a molecular dynamics simulation at constant temperature and pressure (NPT) ensemble. Translational diffusion of water molecules trapped between the two solutes has been analyzed from the velocity correlation function as well as from the mean square displacement of the water molecules. The rotational behavior has been analyzed through the reorientational dynamics of the dipole moment vector of the water molecule by calculating both first and second rank dipole-dipole correlation functions. Both the translational and reorientational mobilities of water are found to be much slower at the smaller separation and increases as the separation between solutes becomes larger. The occupation time distribution functions calculated from the trajectories also show that the relaxation is much slower for the smallest intersolute separation as compared to other wider separations. The sublinear trend in mean square displacement and the stretched exponential decay of the relaxation of dipolar correlation and occupation distribution function indicate that the dynamical behavior of water in the confined region between two large hydrophobic solutes departs from usual Brownian behavior. This behavior is reminiscent of the behavior of water in the vicinity of protein surface clefts or trapped between two domains of a protein.

Relaxation kinetics and the glassiness of native proteins: coupling of timescales

We provide evidence that the onset of functional dynamics of folded proteins with elevated temperatures is associated with the effective sampling of its energy landscape under physiological conditions. The analysis is based on data describing the relaxation phenomena governing the backbone dynamics of bovine pancreatic trypsin inhibitor derived from molecular dynamics simulations, previously reported by us. By representing the backbone dynamics of the folded protein by three distinct regimes, it is possible to decompose its seemingly complex dynamics, described by a stretch exponential decay of the backbone motions. Of these three regimes, one is associated with the slow timescales due to the activity along the envelope of the energy surface defining the folded protein. Another, with fast timescales, is due to the activity along the pockets decorating the folded-state envelope. The intermediate regime emerges at temperatures where jumps between the pockets become possible. It is at the temperature window where motions corresponding to all three timescales become operative that the protein becomes active.

Anomalous behavior of water around sodium dodecyl sulphate micelles

The dynamics, structural properties, and energetics of hydration water around a sodium dodecyl sulphate micelle have been investigated using molecular dynamics simulation. A clear revelation of the slow dynamics of the hydration water has been made by separate measurements of the rotational and translational properties. Calculated diffusion coefficients fall within the range of experimentally observed quantities. The water-micelle head group (MHG) hydrogen bond is more stable (by an amount approximately 7.0 kcal/mol) compared to the water-water hydrogen bond. The difference in stability of the water monomers forming different numbers of hydrogen bonds (n=0,1,2) with the MHG has clearly been shown from the analyses of their rotational relaxation, residence times, as well as the energy of interaction with different components of the system. The singly hydrogen-bonded water species is the most abundant and stable. The entropy plays the key role in controlling the relative abundance of the different species.