Hydrophobic Peptide Channels and Encapsulated Water Wires

Kohn-Sham Density Functional Calculations Reveal Proton Wires in the Enolization and Carboxylase Reactions Catalyzed by Rubisco

Ribulose 1,5-bisphosphate (RuBP) carboxylase-oxygenase (Rubisco) plays a fundamental role in the carbon cycle by fixing the atmospheric CO₂ used in photosynthesis. Rubisco is all the more remarkable because it must catalyze some difficult multistep reaction chemistry involving proton transfers within the one active site. In the present study, we have used Kohn-Sham density functional theory at the B3LYP/6-31G* level with basis set superposition error and dispersion corrections (B3LYP-gCP-D3) to examine the possibility that the proton transfers can take place through molecular wires (including active-site water molecules) via the classical Grotthuss proton-shuttle mechanism. The results support an essential role for water molecules found in the crystal structures of Rubisco complexes as facilitators of proton transport in all the rate-limiting (catalytic) reaction steps through a network of short proton wires within the Rubisco active site. We suggest that completion of the initial product turnover (cycle) requires two excess protons produced in the initial carbamylation that is required for Rubisco activation. By use of proton wires, a large number of reaction steps may be accommodated within a single active site without necessitating the input of excessive conformational strain energy arising from the movement of residue side chains into positions where direct protonation of substrates can occur. The involvement of the identified types of proton wires in the kinetic mechanism is capable of providing a unique explanation for various experimental observations, including deuterium isotope effects and the results of site-directed mutagenesis experiments, and may thus provide a realistic solution to the problem of Rubisco's challenging chemistry.

Acyclic Janus-AT Nucleoside Host Channels Precisely Lock Water into Single-File Wires with Local Rotational Flexibility

Confining polar water molecules to particular geometries demands sophisticated intermolecular interactions, and not many small synthetic molecules have accomplished such a task. Herein, regioisomeric acyclic Janus-AT nucleosides (1 and 2), with a self-complementary fused genetic alphabet and conformationally flexible side chains, have been selectively synthesized. 1 and 2 adopt disparate base-pair motifs from the π-π stacked hydrophobic base moieties and distinct hydrogen bond (HB) interconnections from the hydrophilic sugar residues, which in turn lead to divergent, intricate intermolecular interaction networks with different capacities to confine water molecules. Under the precise control of the host framework of the N⁸ -regioisomer, separate ordered single-file water wires can be locked through special three-HB clamps into unique inter- and intra-wire geometrical alignments. Localized dynamic synchronized rotations within the fixed framework coordinated by both the host hydroxy groups and guest water molecules were observed in a temperature-induced reversible single-crystal-to-single-crystal transition (SCSCT).

Molecular Shape and the Hydrophobic Effect

This review focuses on papers published since 2000 on the topic of the properties of solutes in water. More specifically, it evaluates the state of the art of our understanding of the complex relationship between the shape of a hydrophobe and the hydrophobic effect. To highlight this, we present a selection of references covering both empirical and molecular dynamics studies of small (molecular-scale) solutes. These include empirical studies of small molecules, synthetic hosts, crystalline monolayers, and proteins, as well as in silico investigations of entities such as idealized hard and soft spheres, small solutes, hydrophobic plates, artificial concavity, molecular hosts, carbon nanotubes and spheres, and proteins.

Experimental Binding Energies in Supramolecular Complexes

On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.

Hydrogen Bonding between Metal-Ion Complexes and Noncoordinated Water: Electrostatic Potentials and Interaction Energies

The hydrogen bonding of noncoordinated water molecules to each other and to water molecules that are coordinated to metal-ion complexes has been investigated by means of a search of the Cambridge Structural Database (CSD) and through quantum chemical calculations. Tetrahedral and octahedral complexes that were both charged and neutral were studied. A general conclusion is that hydrogen bonds between noncoordinated water and coordinated water are much stronger than those between noncoordinated waters, whereas hydrogen bonds of water molecule in tetrahedral complexes are stronger than in octahedral complexes. We examined the possibility of correlating the computed interaction energies with the most positive electrostatic potentials on the interacting hydrogen atoms prior to interaction and obtained very good correlation. This study illustrates the fact that electrostatic potentials computed for ground-state molecules, prior to interaction, can provide considerable insight into the interactions.

A terminally protected dipeptide: from crystal structure and self-assembly, through co-assembly with carbon-based materials, to a ternary catalyst for reduction chemistry in water

A terminally protected, hydrophobic dipeptide Boc-L-Cys(Me)-L-Leu-OMe (1) was synthesized and its 3D-structure was determined by single crystal X-ray diffraction analysis. This peptide is able to hierarchically self-assemble in a variety of superstructures, including hollow rods, ranging from the nano- to the macroscale, and organogels. In addition, 1 is able to drive fullerene (C60) or multiwalled carbon nanotubes (MWCNTs) in an organogel by co-assembling with them. A hybrid 1-C60–MWCNT organogel was prepared and converted (through a high vacuum-drying process) into a robust, high-volume, water insoluble, solid material where C60 is well dispersed over the entire superstructure. This ternary material was successfully tested as a catalyst for: (i) the reduction reaction of water-soluble azo compounds mediated by NaBH4 and UV-light with an overall performance remarkably better than that provided by C60 alone, and (ii) the NaBH4-mediated reduction of benzoic acid to benzyl alcohol. Our results suggest that the self-assembly properties of 1 might be related to the occurrence in its single crystal structure of a sixfold screw axis, a feature shared by most of the linear peptides known so far to give rise to nanotubes.

Assembly of encapsulated water in hybrid bisamides: helical and zigzag water chains

The addition of water promotes the self-assembly of hybrid bisamides by bridging between the molecules and stabilizes the helical or zigzag one-dimensional water chains.

The Dynamics, energetics and selectivity of water chain-containing aquapores created by the self-assembly of aquafoldamer molecules

Self-assembled hollow tubular aquapores were found to be stable, very dynamic yet highly selective toward recognition of water molecules.

The hydrophobic effect revisited--studies with supramolecular complexes imply high-energy water as a noncovalent driving force

Traditional descriptions of the hydrophobic effect on the basis of entropic arguments or the calculation of solvent-occupied surfaces must be questioned in view of new results obtained with supramolecular complexes. In these studies, it was possible to separate hydrophobic from dispersive interactions, which are strongest in aqueous systems. Even very hydrophobic alkanes associate significantly only in cavities containing water molecules with an insufficient number of possible hydrogen bonds. The replacement of high-energy water in cavities by guest molecules is the essential enthalpic driving force for complexation, as borne out by data for complexes of cyclodextrins, cyclophanes, and cucurbiturils, for which complexation enthalpies of up to -100 kJ mol(-1) were reached for encapsulated alkyl residues. Water-box simulations were used to characterize the different contributions from high-energy water and enabled the calculation of the association free enthalpies for selected cucurbituril complexes to within a 10% deviation from experimental values. Cavities in artificial receptors are more apt to show the enthalpic effect of high-energy water than those in proteins or nucleic acids, because they bear fewer or no functional groups in the inner cavity to stabilize interior water molecules.

Sparsely populated residue conformations in protein structures: revisiting "experimental" Ramachandran maps

The Ramachandran map clearly delineates the regions of accessible conformational (φ-ψ) space for amino acid residues in proteins. Experimental distributions of φ, ψ values in high-resolution protein structures, reveal sparsely populated zones within fully allowed regions and distinct clusters in apparently disallowed regions. Conformational space has been divided into 14 distinct bins. Residues adopting these relatively rare conformations are presented and amino acid propensities for these regions are estimated. Inspection of specific examples in a completely "arid", fully allowed region in the top left quadrant establishes that side-chain and backbone interactions may provide the energetic compensation necessary for populating this region of φ-ψ space. Asn, Asp, and His residues showed the highest propensities in this region. The two distinct clusters in the bottom right quadrant which are formally disallowed on strict steric considerations correspond to the gamma turn (C7 axial) conformation (Bin 12) and the i + 1 position of Type II' β turns (Bin 13). Of the 516 non-Gly residues in Bin 13, 384 occupied the i + 1 position of Type II' β turns. Further examination of these turn segments revealed a high propensity to occur at the N-terminus of helices and as a tight turn in β hairpins. The β strand-helix motif with the Type II' β turn as a connecting element was also found in as many as 57 examples.

A water wire in L-prolyl-L-serine monohydrate

Despite the extra functional group in the serine side chain, the crystal packing arrangement of the title compound {systematic name: (S)-3-hydroxy-2-[(S)-pyrrolidine-2-carboxamido]propanoic acid monohydrate}, C8H14N2O4·H2O, is essentially the same as observed for a series of L-Pro-L-Nop peptide hydrates, where Nop is a strictly nonpolar residue. This is rendered possible by a monoclinic P2(1) packing arrangement with Z' = 2 that deviates from orthorhombic P2(1)2(1)2(1) symmetry only for the seryl hydroxy groups, which form infinite O-H···O-H hydrogen-bonded chains along the 5.3 Å a axis. At the same time, cocrystallized water molecules form parallel water wires.

Ice-like encapsulated water by two cholic acid moieties

Starting from the structure of ice (in which each water molecule is surrounded by other four water molecules forming a tetrahedron with a value of 4.51Å for the edge O-O distance), and the knowledge that this value also corresponds to the O7-O12 distance of the skeleton of cholic acid, it is hypothesized that two steroid cholic acid moieties, with an appropriate steroid-steroid distance and a belly-to-belly orientation, could encapsulate a single water molecule between them. To check this hypothesis two succinyl derivatives of cholic acid (a monomer and the related head-head dimer in which the succinyl group is the linking bridge) were designed. The expected "ice-like" structure is found in the crystal of the dimer. There is a hydrogen bond synergy between those participating in the "ice-like" structure, and those in which the bridge is involved with the O7-H hydroxy group and the side chain of the steroid.

Molecular wire of urea in carbon nanotube: a molecular dynamics study

We perform molecular dynamics simulations of narrow single-walled carbon nanotubes (SWNTs) in aqueous urea to investigate the structure and dynamical behavior of urea molecules inside the SWNT. Even at low urea concentrations (e.g., 0.5 M), we have observed spontaneous and continuous filling of SWNT with a one-dimensional urea wire (leaving very few water molecules inside the SWNT). The urea wire is structurally ordered, both translationally and orientationally, with a contiguous hydrogen-bonded network and concerted urea's dipole orientations. Interestingly, despite the symmetric nature of the whole system, the potential energy profile of urea along the SWNT is asymmetric, arising from the ordering of asymmetric urea partial charge distribution (or dipole moment) in confined environment. Furthermore, we study the kinetics of confined urea and find that the permeation of urea molecules through the SWNT decreases significantly (by a factor of ∼20) compared to that of water molecules, due to the stronger dispersion interaction of urea with SWNT than water, and a maximum in urea permeation happens around a concentration of 5 M. These findings might shed some light on the better understanding of unique properties of molecular wires (particularly the wires formed by polar organic small molecules) confined within both artificial and biological nanochannels, and are expected to have practical applications such as the electronic devices for signal transduction and multiplication at the nanoscale.

Modelling peptide nanotubes for artificial ion channels

We investigate the van der Waals interaction of D,L-Ala cyclopeptide nanotubes and various ions, ion-water clusters and C(60) fullerenes, using the Lennard-Jones potential and a continuum approach which assumes that the atoms are smeared over the peptide nanotube providing an average atomic density. Our results predict that Li(+), Na(+), Rb(+) and Cl(-) ions and ion-water clusters are accepted into peptide nanotubes of 8.5 Å internal diameter whereas the C(60) molecule is rejected. The model indicates that the C(60) molecule is accepted into peptide nanotubes of 13 Å internal diameter, suggesting that the interaction energy depends on the size of the molecule and the internal diameter of the peptide nanotube. This result may be useful for the design of peptide nanotubes for drug delivery applications. Further, we also find that the ions prefer a position inside the peptide ring where the energy is minimum. In contrast, Li(+)-water clusters prefer to be in the space between each peptide ring.

Single-file water in nanopores

Water molecules confined to pores with sub-nanometre diameters form single-file hydrogen-bonded chains. In such nanoscale confinement, water has unusual physical properties that are exploited in biology and hold promise for a wide range of biomimetic and nanotechnological applications. The latter can be realized by carbon and boron nitride nanotubes which confine water in a relatively non-specific way and lend themselves to the study of intrinsic properties of single-file water. As a consequence of strong water-water hydrogen bonds, many characteristics of single-file water are conserved in biological and synthetic pores despite differences in their atomistic structures. Charge transport and orientational order in water chains depend sensitively on and are mainly determined by electrostatic effects. Thus, mimicking functions of biological pores with apolar pores and corresponding external fields gives insight into the structure-function relation of biological pores and allows the development of technical applications beyond the molecular devices found in living systems. In this Perspective, we revisit results for single-file water in apolar pores, and examine the similarities and the differences between these simple systems and water in more complex pores.

Characterization of bent helical conformations in polymorphic forms of a designed 18-residue peptide containing a central Gly-Pro segment

An 18-residue sequence Boc-Aib-Val-Ala-Leu-Aib-Val-Ala-Leu-Gly-Pro-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-OMe (UK18) was designed to examine the effect of introducing a Gly-Pro segment into the middle of a potentially helical peptide. The crystal structures of two polymorphic forms yielded a view of the conformation of three independent molecules. Form 1 (space group P2(1)2(1)2(1,) a = 14.620Å; b = 26.506Å, c = 28.858Å, Z = 4) has one molecule in the asymmetric unit, with one cocrystallized water molecule. Form 2 (space group P2(1)2(1)2(1,) a = 9.696Å; b = 19.641Å, c = 114.31Å, Z = 8) has two molecules in the asymmetric unit with four cocrystallized water molecules. In Form 1, residues 1 to 18 adopt ϕ,ψ values that lie in the right-handed helical (α(R) ) region of the Ramachandran map. Two residues, Leu (8) (ϕ = -92.0°, ψ = -7.5°) and Leu (17) (ϕ = -94.7°, ψ = -1.7°) adopt conformations that deviate significantly from helical values. In Form 2, molecule A, residues 2 to 16 lie in the α(R) region of ϕ,ψ space, with Leu (8) (ϕ = -94.9°, ψ = -2.9°) deviating significantly from helical values. Aib (1) and Aib (18) adopt left-handed (α(L)) helical conformation. Significant distortion is observed at Leu (17) (ϕ = -121.3°, ψ = -31.3°). Molecule B, Form 2, adopts a right-handed helix over residues 1 to 17. In all three molecules, a distinct bend in the helix is observed, with the bend angle values varying from 40.8° to 58.9°.

A model proton-transfer system in the condensed phase: NH4(+)OOH(-), a crystal with short intermolecular H-bonds

The crystal structure of NH(4)(+)OOH(-) is determined from single-crystal x-ray data obtained at 150 K. The crystal belongs to the space group P2(1)/c and has four molecules in a unit cell. The structure consists of discrete NH(4)(+) and OOH(-) ions. The OOH(-) ions are linked by short hydrogen bonds (2.533 Å) to form parallel infinite chains. The ammonium ions form links between these chains (the N⋯O distances vary from 2.714 to 2.855 Å) giving a three-dimensional network. The harmonic IR spectrum and H-bond energies are computed at the Perdew-Burke-Ernzerhof (PBE)/6-31G(∗∗) level with periodic boundary conditions. A detailed analysis of the shared (bridging) protons' dynamics is obtained from the CPMD simulations at different temperatures. PBE functional with plane-wave basis set (110 Ry) is used. At 10 K the shared proton sits near the oxygen atom, only a few proton jumps along the chain are detected at 70 K while at 270 K numerous proton jumps exist in the trajectory. The local-minimum structure of the space group Cc is localized. It appears as a result of proton transfer along a chain. This process is endothermic (∼2 kJ/mol) and is described as P2(1)/c↔2Cc. The computed IR spectrum at 10 K is close to the harmonic one, the numerous bands appear at 70 K while at 270 K it shows a very broad absorption band that covers frequencies from about 1000 to 3000 cm(-1). The advantages of the NH(4)(+)OOH(-) crystal as a promising model for the experimental and DFT based molecular dynamics simulation studies of proton transfer along the chain are discussed.

X-ray crystallographic structure of an artificial beta-sheet dimer

This paper describes the X-ray crystallographic structure of a designed cyclic beta-sheet peptide that forms a well-defined hydrogen-bonded dimer that mimics beta-sheet dimers formed by proteins. The 54-membered ring macrocyclic peptide (1a) contains molecular template and turn units that induce beta-sheet structure in a heptapeptide strand that forms the dimerization interface. The X-ray crystallographic structure reveals the structures of the two "Hao" amino acids that help template the beta-sheet structure and the two delta-linked ornithine turn units that link the Hao-containing template to the heptapeptide beta-strand. The Hao amino acids adopt a conformation that resembles a tripeptide in a beta-strand conformation, with one edge of the Hao unit presenting an alternating array of hydrogen-bond donor and acceptor groups in the same pattern as that of a tripeptide beta-strand. The delta-linked ornithines adopt a conformation that resembles a hydrogen-bonded beta-turn, in which the ornithine takes the place of the i+1 and i+2 residues. The dimers formed by macrocyclic beta-sheet 1a resemble the dimers of many proteins, such as defensin HNP-3, the lambda-Cro repressor, interleukin 8, and the ribonuclease H domain of HIV-1 reverse transcriptase. The dimers of 1a self-assemble in the solid state into a barrel-shaped trimer of dimers in which the three dimers are arranged in a triangular fashion. Molecular modeling in which one of the three dimers is removed and the remaining two dimers are aligned face-to-face provides a model of the dimers of dimers of closely related macrocyclic beta-sheet peptides that were observed in solution.