Amino acid side chain interactions in the presence of salts

Molecular Crowding Alters the Interactions of Polymyxin Lipopeptides within the Periplasm of E. coli: Insights from Molecular Dynamics

The cell envelope of Gram-negative bacteria is a crowded tripartite architecture that separates the cell interior from the external environment. Two membranes encapsulate the aqueous periplasm, which contains the cell wall. Little is known about the mechanisms via which antimicrobial peptides move through the periplasm from the outer membrane to their site of action, the inner membrane. We utilize all-atom molecular dynamics to study two antimicrobial peptides, polymyxins B1 and E, within models of the E. coli periplasm crowded to different extents. In a simple chemical environment, both PMB1 and PME bind irreversibly to the cell wall. The presence of specific macromolecules leads to competition with the polymyxins for cell wall interaction sites, resulting in polymyxin dissociation from the cell wall. Chemical complexity also impacts interactions between polymyxins and Braun's lipoprotein; thus, the interaction modes of lipoprotein antibiotics within the periplasm are dependent upon the nature of the other species present.

Toward Sustainable and Healthy Fish Products-The Role of Feeding and Preservation Techniques

Fish is a fundamental component of the human diet, and in the near future the proportion of aquatic foods originating from aquaculture production is expected to increase to over 56%. The sustainable growth of the aquaculture sector involves the use of new sustainable raw materials as substitutes for traditional fishmeal and fish oil ingredients, but it is crucial that the substitution maintains the nutritional value of the fish meat. In addition, the preservation of the nutritional value should be a mandatory requirement of new technologies that extend the shelf life of fish. In this context, we evaluated the impact of a newly formulated feed and three preservation treatments (brine, pulsed electric field (PEF), and PEF plus brine) on the fatty acid composition and protein and lipid digestibility of sea bass fillets. In non-digested fillets, although slightly reduced by the newly formulated feed (standard = 2.49 ± 0.14; newly formulated = 2.03 ± 0.10) the n-3/n-6 PUFA ratio indicated good nutritional value. The preservation treatments did not modify the fatty acid content and profile of non-digested fillets. Conversely, protein and lipid digestibility were not affected by the different diets but were significantly reduced by brine, with or without PEF, while PEF alone had no effect. Overall, our results indicated that the newly formulated feed containing 50% less fishmeal is a good compromise between the sustainability and nutritional value of cultivated seabass, and PEF is a promising preservation technology deserving of further study.

A conserved oligomerization domain in the disordered linker of coronavirus nucleocapsid proteins

The nucleocapsid (N-)protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a key role in viral assembly and scaffolding of the viral RNA. It promotes liquid-liquid phase separation (LLPS), forming dense droplets that support the assembly of ribonucleoprotein particles with as-of-yet unknown macromolecular architecture. Combining biophysical experiments, molecular dynamics simulations, and analysis of the mutational landscape, we describe a heretofore unknown oligomerization site that contributes to LLPS, is required for the assembly of higher-order protein-nucleic acid complexes, and is coupled to large-scale conformational changes of N-protein upon nucleic acid binding. The self-association interface is located in a leucine-rich sequence of the intrinsically disordered linker between N-protein folded domains and formed by transient helices assembling into trimeric coiled-coils. Critical residues stabilizing hydrophobic and electrostatic interactions between adjacent helices are highly protected against mutations in viable SARS-CoV-2 genomes, and the oligomerization motif is conserved across related coronaviruses, thus presenting a target for antiviral therapeutics.

Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions

The interactions of amino acid side-chains confer diverse energetic contributions and physical properties to a protein's stability and function. Various computational tools estimate the effect of changing a given amino acid on the protein's stability based on parametrized (free) energy functions. When parametrized for the prediction of protein stability in water, such energy functions can lead to suboptimal results for other solvents, such as ionic liquids (IL), aqueous ionic liquids (aIL), or salt solutions. However, to our knowledge, no comprehensive data are available describing the energetic effects of aIL on intramolecular protein interactions. Here, we present the most comprehensive set of potential of mean force (PMF) profiles of pairwise protein-residue interactions to date, covering 50 relevant interactions in water, the two biotechnologically relevant aIL [BMIM/Cl] and [BMIM/TfO], and [Na/Cl]. These results are based on a cumulated simulation time of >1 ms. aIL and salt ions can weaken, but also strengthen, specific residue interactions by more than 3 kcal mol^-1, depending on the residue pair, residue-residue configuration, participating ions, and concentration, necessitating considering such interactions specifically. These changes originate from a complex interplay of competitive or cooperative noncovalent ion-residue interactions, changes in solvent structural dynamics, or unspecific charge screening effects and occur at the contact distance but also at larger, solvent-separated distances. This data provide explanations at the atomistic and energetic levels for complex IL effects on protein stability and should help improve the prediction accuracies of computational tools that estimate protein stability based on (free) energy functions.

Biomolecular interactions of ultrasmall metallic nanoparticles and nanoclusters

The use of nanoparticles (NPs) in biomedicine has made a gradual transition from proof-of-concept to clinical applications, with several NP types meeting regulatory approval or undergoing clinical trials. A new type of metallic nanostructures called ultrasmall nanoparticles (usNPs) and nanoclusters (NCs), while retaining essential properties of the larger (classical) NPs, have features common to bioactive proteins. This combination expands the potential use of usNPs and NCs to areas of diagnosis and therapy traditionally reserved for small-molecule medicine. Their distinctive physicochemical properties can lead to unique in vivo behaviors, including improved renal clearance and tumor distribution. Both the beneficial and potentially deleterious outcomes (cytotoxicity, inflammation) can, in principle, be controlled through a judicious choice of the nanocore shape and size, as well as the chemical ligands attached to the surface. At present, the ability to control the behavior of usNPs is limited, partly because advances are still needed in nanoengineering and chemical synthesis to manufacture and characterize ultrasmall nanostructures and partly because our understanding of their interactions in biological environments is incomplete. This review addresses the second limitation. We review experimental and computational methods currently available to understand molecular mechanisms, with particular attention to usNP-protein complexation, and highlight areas where further progress is needed. We discuss approaches that we find most promising to provide relevant molecular-level insight for designing usNPs with specific behaviors and pave the way to translational applications.

Characterization of the Phosphorylation Site of GRTH/DDX25 and Protein Kinase A Binding Interface Provides Structural Basis for the Design of a Non-Hormonal Male Contraceptive

Gonadotropin Regulated Testicular Helicase (GRTH/DDX25), expressed in the male gonad, is essential for the completion of spermatogenesis. Our early studies revealed a missense mutation (R242H) of GRTH in 5.8% of Japanese patient population with azoospermia. Transfection of the mutant GRTH construct in COS-1 cells leads to loss of the 61 kDa cytoplasmic phospho-species. Mice with knock-in of the human GRTH mutation are sterile and lack sperm with normal androgen and mating behavior. These findings provide an avenue for the development of a non-hormonal male contraceptive. Using site directed mutagenesis and a site-specific phospho-antibody, we have identified T239, structurally adjacent to the patient’s mutant site as the GRTH phospho-site. Molecular modelling provided structural basis for the role of R242 and other critical solvent-exposed residues at the GRTH/PKA interface (E165/K240/D237), on the control of GRTH phosphorylation at T239. Single or double mutations of these residues caused marked reduction or abolition of the phospho-form. These effects can be ascribed to critical disruptions of intramolecular H-bonds at the GRTH/PKA interface, which leads to modest but consequential structural changes that can affect PKA catalytic efficiency. Inhibition of phosphorylation may be achieved by small, drug-like molecules that bind to GRTH and reconfigure the GRTH/PKA interface.

Theoretical Insights into the Role of Water Molecules in the Guanidinium-Based Protein Denaturation Process in Specific to Aromatic Amino Acids

Noncovalent interactions between the guanidinium cation (Gdm⁺) and aromatic amino acids (AAs) in the water molecules have been studied using quantum chemical calculation and molecular dynamics (MD) simulations. Our studies show that there are two different modes of interactions between Gdm⁺ and AAs with and without water molecules. It is observed that nonhydrated Gdm⁺ interacts with AAs through N-H···π interactions, whereas hydrated clusters of Gdm⁺ are stabilized by stacking interactions with the help of the water-mediated hydrogen bond. Thus, different hydration patterns have significant effects on the predominant cation···π interactions in AAs-Gdm⁺ complexes. Findings from MD simulation elicit that the interaction pattern of Gdm⁺ with AAs varies as Phe < Tyr < Trp. Both the QM and MD calculations show a similar trend in the interaction of AAs with Gdm⁺. Moreover, the interaction of AAs with Gdm⁺ depends on the spatial orientation of AAs in the protein and the concomitant local structure, that is, the AAs present in the unstructured region of protein such as coils and bends exhibit higher binding for Gdm⁺ when compared to the AAs present in the structured region of the protein such as the α-helix and the β-sheet. Our study clearly reveals that H-bonded water molecules and the hydration pattern of Gdm⁺ as well as the positional presence of these AAs in the protein structure context play determining roles in the denaturation of protein by the Gdm⁺ cation.

Water in the human body: An anesthesiologist's perspective on the connection between physicochemical properties of water and physiologic relevance

The unique structure and multifaceted physicochemical properties of the water molecule, in addition to its universal presence in body compartments, make water a key player in multiple biological processes in human physiology. Since anesthesiologists deal with physiologic processes where water molecules are critical at different levels, and administer medications whose pharmacokinetics and pharmacodynamics depend on interaction with water molecules, we consider that exploration of basic science aspects related to water and its role in physiology and pharmacology is relevant to the practice of anesthesiology. The purpose of this paper is to delineate the physicochemical basis of water that are critical in enabling it to support various homeostatic processes. The role of water in the formation of solutions, modulation of surface tension and in homeostasis of body temperature, acid-base status and osmolarity, is analyzed. Relevance of molecular water interactions to the anesthesiologist is not limited to the realm of physiology and pathophysiology. Deep knowledge of the importance of water in volatile anesthetic effects on neurons opens a window to a new comprehensive understanding of complex cellular mechanisms underlying the practice of anesthesiology.

Computational Study of the Forces Driving Aggregation of Ultrasmall Nanoparticles in Biological Fluids

Nanoparticle (NP) aggregation can lead to prolonged retention in tissues or embolism, among other adverse effects. Successful use in biomedicine thus requires the capability to make NPs with limited aggregative potential. Rational design is presently a challenge due to incomplete knowledge of their interactions in biofluids. Recently, ultrasmall gold NPs passivated with endogenous antioxidant glutathione have shown promise for use in vivo. Computer simulations are here conducted to identify the forces underlying aggregation (or lack thereof) of these NPs in a cell culture. Electrostatic interactions are insufficient to induce association, but the van der Waals forces exerted by cations, anions, and net-neutral polar species can promote the formation of stable dimers. The entropic effects of depletion are negligible, but the combined effect of depletion and macromolecular crowding at physiological concentrations can stabilize aggregates containing just a few NPs. Interparticle interactions are controlled by modest changes in both the structure and dynamic of the interfacial liquid. The molecular origin of these effects and their dependence on NP size are described. The liquid is shown to be highly structured, with large and long-lived hydrogen-bonded water clusters developing often in the interparticle space; their potential role as transient, long-range proton wires connecting and enveloping neighboring NPs is discussed. The basis for a parsimonious theory of ultrasmall NPs in complex fluids is established.

Biointeractions of ultrasmall glutathione-coated gold nanoparticles: effect of small size variations

Recent in vivo studies have established ultrasmall (<3 nm) gold nanoparticles coated with glutathione (AuGSH) as a promising platform for applications in nanomedicine. However, systematic in vitro investigations to gain a more fundamental understanding of the particles' biointeractions are still lacking. Herein we examined the behavior of ultrasmall AuGSH in vitro, focusing on their ability to resist aggregation and adsorption from serum proteins. Despite having net negative charge, AuGSH particles were colloidally stable in biological media and able to resist binding from serum proteins, in agreement with the favorable bioresponses reported for AuGSH in vivo. However, our results revealed disparate behaviors depending on nanoparticle size: particles between 2 and 3 nm in core diameter were found to readily aggregate in biological media, whereas those strictly under 2 nm were exceptionally stable. Molecular dynamics simulations provided microscopic insight into interparticle interactions leading to aggregation and their sensitivity to the solution composition and particle size. These results have important implications, in that seemingly small variations in size can impact the biointeractions of ultrasmall AuGSH, and potentially of other ultrasmall nanoparticles as well.

Detection and characterization of nonspecific, sparsely populated binding modes in the early stages of complexation

A method is proposed to study protein-ligand binding in a system governed by specific and nonspecific interactions. Strong associations lead to narrow distributions in the proteins configuration space; weak and ultraweak associations lead instead to broader distributions, a manifestation of nonspecific, sparsely populated binding modes with multiple interfaces. The method is based on the notion that a discrete set of preferential first-encounter modes are metastable states from which stable (prerelaxation) complexes at equilibrium evolve. The method can be used to explore alternative pathways of complexation with statistical significance and can be integrated into a general algorithm to study protein interaction networks. The method is applied to a peptide-protein complex. The peptide adopts several low-population conformers and binds in a variety of modes with a broad range of affinities. The system is thus well suited to analyze general features of binding, including conformational selection, multiplicity of binding modes, and nonspecific interactions, and to illustrate how the method can be applied to study these problems systematically. The equilibrium distributions can be used to generate biasing functions for simulations of multiprotein systems from which bulk thermodynamic quantities can be calculated.

β-Defensin 1 plays a role in acute mucosal defense against Candida albicans

Candida is an opportunistic fungal pathogen that colonizes the mucosal tract of humans. Pathogenic infection occurs in the presence of conditions causing perturbations to the commensal microbiota or host immunity. Early innate immune responses by the epithelium, including antimicrobial peptides (AMPs) and cytokines, are critical for protection against overgrowth. Reduced salivary AMP levels are associated with oral Candida infection, and certain AMPs, including human β-defensins 1-3, have direct fungicidal activity. In this study, we demonstrate that murine β-defensin 1 (mBD1) is important for control of early mucosal Candida infection and plays a critical role in the induction of innate inflammatory mediators. Mice deficient in mBD1, as compared with wild-type mice, exhibit elevated oral and systemic fungal burdens. Neutrophil infiltration to the sites of mucosal Candida invasion, an important step in limiting fungal infection, is significantly reduced in mBD1-deficient mice. These mice also exhibit defects in the expression of other AMPs, including mBD2 and mBD4, which may have direct anti-Candida activity. We also show that mBD1 deficiency impacts the production of important antifungal inflammatory mediators, including IL-1β, IL-6, KC, and IL-17. Collectively, these studies demonstrate a role for the mBD1 peptide in early control of Candida infection in a murine model of mucosal candidiasis, as well as in the modulation of host immunity through augmentation of leukocyte infiltration and inflammatory gene regulation.

Structural conservation of the short α-helix in modified higher and lower polarity water solutions

Which conformation is preferred when the polarity of water molecules is scaled byE_P=E_LJ+S²E_C?

Implicit treatment of solvent dispersion forces in protein simulations

A model is proposed for the evaluation of dispersive forces in a continuum solvent representation for use in large-scale computer simulations. The model captures the short- and long-range effects of water-exclusion in conditions of partial and anisotropic hydration. The model introduces three parameters, one of which represents the degree of hydration (water occupancy) at any point in the system, which depends on the solute conformation, and two that represent the strength of water-water and water-solute dispersive interactions. The model is optimized for proteins, using hydration data of a suboptimally hydrated binding site and results from dynamics simulations in explicit water. The model is applied to a series of aliphatic-alcohol/protein complexes and a set of binary and ternary complexes of various sizes. Implications for weak and ultra-weak protein-protein association and for simulation in crowded media are discussed.

Electric field effects on alanine tripeptide in sodium halide solutions

The electric field effects on conformational properties of trialanine in different halide solutions were explored with long-scale molecular dynamics simulations. NaF, NaCl, NaBr and NaI solutions of low (0.2 M) and high (2 M) concentrations were exposed to a constant electric field of 1000 V/m. Generally, the electric field does not disturb trialanine's structure. Large structural changes appear only in the case of the supersaturated 2.0 M NaF solution containing NaF crystals. Although the electric field affects in a complex way, all the ions-water-peptide interactions, it predominantly affects the electroselectivity effect, which describes specific interactions such as the ion-pair formation.

Mixed-salt effects on the conformation of a short salt-bridge-forming α helix: a simulation study

The structure of a single alanine-based ACE-AEAAAKEAAAKA-NH2 peptide in explicit aqueous solutions with mixed inorganic salts (NaCl and KCl) is investigated by using molecular simulations. The concentration of Na(+), c(Na(+)), varies from 0.0M to 1.0M, whereas the concentration of K(+) is 1-c(Na(+)). The simulated peptide is very sensitive to the change of concentration ratio between Na(+) and K(+). When the concentration ratio between Na^{+} and K^{+} is changed from 0.5/0.5, the structure of the peptide becomes loose or disordered. This specific phenomenon is confirmed via checking the changes of helix parameters and mapping the free energy along different coordinates. The higher normalized probability of forming direct and indirect salt bridges between residues Glu7(+) and Lys11(+) and the smallest probability of forming ringlike structures should be responsible for the stabilized helix structure in the 0.5 Na(+)/0.5 K(+) solution. Furthermore, a noticeable conformational transition from an extended helix to an α helix is found in the 0.5 Na(+)/0.5 K(+) solution, where a local ion cloud shows that some Na(+) ions in the inner shells are still directly binding with the peptide, while K(+) in the outer shells are moving into the inner shells, keeping the peptide in the collapsed state.

Specific and non-specific protein association in solution: computation of solvent effects and prediction of first-encounter modes for efficient configurational bias Monte Carlo simulations

Weak and ultraweak protein-protein association play a role in molecular recognition and can drive spontaneous self-assembly and aggregation. Such interactions are difficult to detect experimentally, and are a challenge to the force field and sampling technique. A method is proposed to identify low-population protein-protein binding modes in aqueous solution. The method is designed to identify preferential first-encounter complexes from which the final complex(es) at equilibrium evolve. A continuum model is used to represent the effects of the solvent, which accounts for short- and long-range effects of water exclusion and for liquid-structure forces at protein/liquid interfaces. These effects control the behavior of proteins in close proximity and are optimized on the basis of binding enthalpy data and simulations. An algorithm is described to construct a biasing function for self-adaptive configurational-bias Monte Carlo of a set of interacting proteins. The function allows mixing large and local changes in the spatial distribution of proteins, thereby enhancing sampling of relevant microstates. The method is applied to three binary systems. Generalization to multiprotein complexes is discussed.

Self-consistent treatment of the local dielectric permittivity and electrostatic potential in solution for polarizable macromolecular force fields

A self-consistent method is presented for the calculation of the local dielectric permittivity and electrostatic potential generated by a solute of arbitrary shape and charge distribution in a polar and polarizable liquid. The structure and dynamics behavior of the liquid at the solute/liquid interface determine the spatial variations of the density and the dielectric response. Emphasis here is on the treatment of the interface. The method is an extension of conventional methods used in continuum protein electrostatics, and can be used to estimate changes in the static dielectric response of the liquid as it adapts to charge redistribution within the solute. This is most relevant in the context of polarizable force fields, during electron structure optimization in quantum chemical calculations, or upon charge transfer. The method is computationally efficient and well suited for code parallelization, and can be used for on-the-fly calculations of the local permittivity in dynamics simulations of systems with large and heterogeneous charge distributions, such as proteins, nucleic acids, and polyelectrolytes. Numerical calculation of the system free energy is discussed for the general case of a liquid with field-dependent dielectric response.

Water-exclusion and liquid-structure forces in implicit solvation

A continuum model of solvation is proposed to describe (i) long-range electrostatic effects of water exclusion resulting from incomplete and anisotropic hydration in crowded environments and (ii) short-range effects of liquid-structure forces on the hydrogen-bond interactions at solute/water interfaces. The model is an extension of the phenomenological screened coulomb potential-based implicit model of solvation. The developments reported here allow a more realistic representation of highly crowded and spatially heterogeneous environments, such as those in the interior of a living cell. Only the solvent is treated as a continuum medium. It is shown that the electrostatic effects of long-range water-exclusion can strongly affect protein-protein binding energies and are then related to the thermodynamics of complex formation. Hydrogen-bond interactions modulated by the liquid structure at interfaces are calibrated based on systematic calculations of potentials of mean force in explicit water. The electrostatic component of the model is parametrized for monovalent, divalent and trivalent ions. The conceptual and practical aspects of the model are discussed based on simulations of protein complexation and peptide folding. The current implementation is ~1.5 times slower than the gas-phase force field and exhibits good parallel performance.

Interactions between ionizable amino acid side chains at a lipid bilayer-water interface

Potentials of mean force (PMF) between ionizable amino acid side chains (Arg, Lys, His, Glu) in the headgroup area of a palmitoyl oleoyl phosphatidylcholine lipid bilayer were obtained from all-atom molecular dynamics simulations and the adaptive biasing force method. Simulations in bulk water were also performed for comparison. Side chains were constrained in collinear, stacking, and orthogonal (T-shaped) orientations. The most structured and attractive PMFs were observed for hydrogen-bonded side chains. Contact minima occurred at a distance of 2.6-3.1 Å between selected atoms or centers of mass with the most attractive interaction (-9.6 kcal/mol) observed between Arg(+) and Glu(-). Hydrogen bonds play a significant role in stabilizing these interactions. Interactions between like charged side chains can also be very attractive if the charges are screened by surrounding molecules or groups (e.g., the PMF value at the contact minimum for Arg(+)···Arg(+) is -7.6 kcal/mol). Like charged side chains can have contact minima as close as 3.6 Å. The PMFs depend strongly on the relative orientation of the side chains. In agreement with experimental studies and other simulations, we found the stacking arrangement of like charged side chains to be the most favorable orientation. Interaction energies and Lennard-Jones energies between side chains, headgroups, and water molecules were analyzed in order to rationalize the observed PMFs and their dependence on orientation. In general, the results cannot be explained by simple dielectric arguments.

Computer simulation of ion cluster speciation in concentrated aqueous solutions at ambient conditions

Dynamic simulations are used to investigate ion cluster formation in unsaturated aqueous NaCl at 25 degrees C. Statistical, structural, and dynamic properties are reported. An effort is made to identify general behaviors that are expected to hold beyond the limitations of the force field. Above approximately 1 M, clusters with more than ten ions begin to form after approximately 10-20 ns of simulation time, but no evidence of irreversible ion aggregation is observed. Cluster survival times are estimated, showing that the kinetics become increasingly complex as salt is added, leading to multiple decay rates. Cluster dipole moment distributions show characteristic peaks that reflect the preferred conformations of clusters in solution. These are modulated by electrostatic and liquid-structure forces and are described in detail for clusters of up to five ions. For a given size and charge, the cluster morphology is independent of salt concentration. Below approximately 2 M, clusters affect the structure of water in their first hydration shells, so dipole moments parallel to the cluster macrodipoles are induced. These effects show a weak dependence with concentration below approximately 2 M, but vanish in the 2-3 M range. A possible connection with the structural transition recently suggested by NMR data in concentrated electrolytes is discussed. The effects of electrostatics on cluster speciation and morphology are discussed based on results from a set of simulations carried out with the ionic charges removed.

Morphology of ion clusters in aqueous electrolytes

Formation of ion clusters in aqueous NaCl solutions at 25 degrees C is investigated with dynamics simulations in the 0.1-3M concentration range. The medium is found to be highly structured even at moderate concentrations, and clusters of over 20 ions are observed above approximately 2M . The medium can be viewed as a multicomponent fluid, composed of reacting particles with well-defined average populations, shapes, sizes, and charge distributions. Clusters show substantial morphological variations that are here characterized by their hydrodynamic radii and internal charge distributions. Clusters can be described as prolate spheroids in the subnanometer length scale. The hydrodynamic radius and the radius of gyration follow simple power laws with the number of ions in the cluster. Dipole moment distributions show characteristic peaks in the approximately 10-60 debye range that reflect conformational preferences modulated by electrostatic and liquid-structure forces.

Salt-Induced Vesicle to Micelle Transition in Aqueous Solution of Sodium N-(4-n-Octyloxybenzoyl)-l-valinate

The self-organization of a single-tailed amino acid based chiral surfactant sodium N-(4-n-octyloxybenzoyl)-L-valinate (SOBV) has been studied in water. A number of techniques like surface tension, fluorescence probe, dynamic light scattering (DLS), transmission electron microscopy (TEM), and atomic force microscopy (AFM) have been utilized for characterization of the self-assemblies. The amphiphile forms large spherical vesicles of 400-600 nm diameters in dilute aqueous solution. However, the vesicles get transformed into spherical micelles with increase of surfactant concentration or upon addition of relatively low amount (20 mM) of NaCl or KCl. This is the first example of salt-induced vesicle to micelle transition (VMT) in a single surfactant system. The vesicles are stable in the temperature range of 30-70 degrees C. Cleavage of intermolecular hydrogen bonds among the amide groups in the presence of salt appears to be the plausible cause for the VMT.

Liquid-structure forces and electrostatic modulation of biomolecular interactions in solution

Molecular interactions in solution are controlled by the bulk medium and by the forces originating in the structured region of the solvent close to the solutes. In this paper, a model of electrostatic and liquid-structure forces for dynamics simulations of biomolecules is presented. The model introduces information on the microscopic nature of the liquid in the vicinity of polar and charged groups and the associated non-pairwise character of the forces, thus improving upon conventional continuum representations. The solvent is treated as a polar and polarizable medium, with dielectric properties described by an inhomogeneous version of the Onsager theory. This treatment leads to an effective position-dependent dielectric permittivity that incorporates saturation effects of the electric field and the spatial variation of the liquid density. The non-pairwise additivity of the liquid-structure forces is represented by centers of force located at specific points in the liquid phase. These out-of-the-solute centers are positioned at the peaks of liquid density and exert local, external forces on the atoms of the solute. The density is calculated from a barometric law, using a Lennard-Jones-type solute-liquid effective interaction potential. The conceptual aspects of the model and its exact numerical solutions are discussed for single alkali and halide ions and for ion-pair interactions. The practical aspects of the model and the simplifications introduced for efficient computation of forces in molecular solutes are discussed in the context of polar and charged amino acid dimers. The model reproduces the contact and solvent-separated minima and the desolvation barriers of intermolecular potentials of mean force of amino acid dimers, as observed in atomistic dynamics simulations. Possible refinements based on an improved treatment of molecular correlations are discussed.

Ab initio computational modeling of loops in G-protein-coupled receptors: lessons from the crystal structure of rhodopsin

With the help of the crystal structure of rhodopsin an ab initio method has been developed to calculate the three-dimensional structure of the loops that connect the transmembrane helices (TMHs). The goal of this procedure is to calculate the loop structures in other G-protein coupled receptors (GPCRs) for which only model coordinates of the TMHs are available. To mimic this situation a construct of rhodopsin was used that only includes the experimental coordinates of the TMHs while the rest of the structure, including the terminal domains, has been removed. To calculate the structure of the loops a method was designed based on Monte Carlo (MC) simulations which use a temperature annealing protocol, and a scaled collective variables (SCV) technique with proper structural constraints. Because only part of the protein is used in the calculations the usual approach of modeling loops, which consists of finding a single, lowest energy conformation of the system, is abandoned because such a single structure may not be a representative member of the native ensemble. Instead, the method was designed to generate structural ensembles from which the single lowest free energy ensemble is identified as representative of the native folding of the loop. To find the native ensemble a successive series of SCV-MC simulations are carried out to allow the loops to undergo structural changes in a controlled manner. To increase the chances of finding the native funnel for the loop, some of the SCV-MC simulations are carried out at elevated temperatures. The native ensemble can be identified by an MC search starting from any conformation already in the native funnel. The hypothesis is that native structures are trapped in the conformational space because of the high-energy barriers that surround the native funnel. The existence of such ensembles is demonstrated by generating multiple copies of the loops from their crystal structures in rhodopsin and carrying out an extended SCV-MC search. For the extracellular loops e1 and e3, and the intracellular loop i1 that were used in this work, the procedure resulted in dense clusters of structures with Calpha-RMSD approximately 0.5 angstroms. To test the predictive power of the method the crystal structure of each loop was replaced by its extended conformations. For e1 and i1 the procedure identifies native clusters with Calpha-RMSD approximately 0.5 angstroms and good structural overlap of the side chains; for e3, two clusters were found with Calpha-RMSD approximately 1.1 angstroms each, but with poor overlap of the side chains. Further searching led to a single cluster with lower Calpha-RMSD but higher energy than the two previous clusters. This discrepancy was found to be due to the missing elements in the constructs available from experiment for use in the calculations. Because this problem will likely appear whenever parts of the structural information are missing, possible solutions are discussed.

Mechanical Unfolding of Segment-Swapped Protein G Dimer: Results from Replica Exchange Molecular Dynamics Simulations

The protein G dimer (pdb code 1Q10) is a mutated dimeric form of the immunoglobulin-binding domain B1 of streptococcal protein G, in which the two monomeric units have swapped elements of their secondary structure. We have used replica exchange molecular dynamics simulations to study how this dimer responds to a mechanical force that pulls the N-terminus of one unit and the C-terminus of the other apart. We have further compared the mechanical response of the dimer to that of the protein G monomer. When the pulling force is low enough, the mechanical unfolding can be viewed as a thermally activated barrier crossing process. For each protein, we have computed the corresponding free energy barrier and its dependence on the pulling force. While the dimer is found to be less resistant to mechanical unfolding than its monomeric counterpart, the two proteins exhibit essentially the same mechanical unfolding mechanism involving separation of the terminal parallel strands. On the basis of our results, we speculate that the mechanical properties of natural adhesives, composites, fibers, and other materials may be optimized not only at a single molecule level but also at the mesoscopic level through the interactions among individual chains.

Preferential hydration of DNA: the magnitude and distance dependence of alcohol and polyol interactions

The physical forces that underlie the exclusion of solutes from macromolecular surfaces can be probed in a similar way as the measurement of forces between macromolecules in condensed arrays using the osmotic stress technique and x-ray scattering. We report here the dependence of alcohol exclusion or, equivalently, the preferential hydration of DNA on the spacing between helices in condensed arrays. The actual forces describing exclusion are quite different from the commonly assumed steric crowding coupled with weak binding. For a set of 12 nonpolar alcohols, exclusion is due to repulsive hydration interactions with the charged DNA surface. Exclusion amplitudes do not depend simply on size, but rather on the balance between alkyl carbons and hydroxyl oxygens. Polyols are included at very close spacings. The distance dependence of polyol inclusion, however, is quite different from nonpolar alcohol exclusion, suggesting the underlying mechanism of interaction is different.