Hydrophobic Packing Research Articles

Optimization of Interstrand Hydrophobic Packing Interactions within Unnatural DNA Base Pairs

As part of an effort to expand the genetic alphabet, we have evaluated a large number of predominantly hydrophobic unnatural base pairs. We now report the synthesis and stability of unnatural base pairs formed between simple phenyl rings modified at different positions with methyl groups. Surprisingly, several of the unnatural base pairs are virtually as stable as a natural base pair in the same sequence context. The results show that neither hydrogen-bonding nor large aromatic surface area are required for base pair stability within duplex DNA and that interstrand interactions between small aromatic rings may be optimized for both stability and selectivity. These smaller nucleobases are not expected to induce the distortions in duplex DNA or at the primer terminus that seem to limit replication of larger unnatural base pairs, and they therefore represent a promising approach to the expansion of the genetic alphabet.

Replacement of Staphylococcal Nuclease Hydrophobic Core Residues with Those from Thermophilic Homologues Indicates Packing is Improved in Some Thermostable Proteins

The importance of tight hydrophobic core packing in stabilizing proteins found in thermophilic organisms has been vigorously disputed. Here, portions of the cores found in three thermophilic homologues were transplanted into the core of staphylococcal nuclease, a protein of modest stability. Packing of the core was evaluated by comparing interaction energy of the three mutants to the comprehensive mutant library built up previously at these same sites in staphylococcal nuclease. It was found that the interaction energy of one thermophilic sequence is extraordinarily favorable and the interaction energies of other two transplanted thermophilic sequences are good, comparable to the interaction energies of mutant cores based on cores found in mesophilic homologues. As expected when transferring just a portion of the core sequence, the mutant proteins were destabilized overall relative to wild-type staphylococcal nuclease. The overall conclusion is that improvement of packing interactions is a mechanism to confer stability employed in some proteins from thermophiles, but not all.

Stabilizing roles of residual structure in the empty heme binding pockets and unfolded states of microsomal and mitochondrial apocytochrome b5.

The microsomal (Mc) and mitochondrial (OM) isoforms of mammalian cytochrome b5 are the products of different genes, which likely arose via duplication of a primordial gene and subsequent functional divergence. Despite sharing essentially identical folds, heme-polypeptide interactions are stronger in OM b5s than in Mc b5s due to the presence of two conserved patches of hydrophobic amino acid side chains in the OM heme binding pockets. This is of fundamental interest in terms of understanding heme protein structure-function relationships, because stronger heme-polypeptide interactions in OM b5s in comparison to Mc b5s may represent a key source of their more negative reduction potentials. Herein we provide evidence that interactions amongst the amino acid side chains contributing to the hydrophobic patches in rat OM (rOM) b5 persist when heme is removed, rendering the empty heme binding pocket of rOM apo-b5 more compact and less conformationally dynamic than that in bovine Mc (bMc) apo-b5. This may contribute to the stronger heme binding by OM apo-b5 by reducing the entropic penalty associated with polypeptide folding. We also show that when bMc apo-b5 unfolds it adopts a structure that is more compact and contains greater nonrandom secondary structure content than unfolded rOM apo-b5. We propose that a more robust beta-sheet in Mc apo-b5s compensates for the absence of the hydrophobic packing interactions that stabilize the heme binding pocket in OM apo-b5s.

Folding propensity of cyclohexylether-delta-peptides.

[structure: see text] Linear (n = 2-18) and cyclic oligomers (n = 3-8) of a cyclohexylether-delta-amino acid (COA) were prepared in high yield and stereopurity. CD spectra of the linear oligomers were indicative of secondary structure formation. X-ray crystal structures of cyclic COA oligomers revealed hydrophobic packing and internal 5- and 10-membered-ring hydrogen bonds. Ether and amide oxygens reside preferably in an ap orientation. This conformational locking is apparently broken by a C-2 substituent in an asymmetric cyclotrimer, for which a zeolithe-like tubular structure was found.

Cation-pi interactions studied in a model coiled-coil peptide.

Cation-pi interactions between aromatic amino acids and the positively charged residues lysine and arginine have been proposed to play an important role in stabilizing protein structure. We have used a peptide that adopts a coiled coil structure as a model system to evaluate the energetic contribution of cation-pi interactions to protein folding. Peptides were designed in which phenylalanine, tyrosine, and tryptophan were placed at a solvent-exposed position of the helix, one turn removed from an arginine residue that could provide a favorable cation-pi interaction. Only the arginine-phenylalanine pairing provided significant stabilization of the peptide structure and it appears that hydrophobic packing, rather than the cation-pi effect, is more likely to be responsible for the stability of this peptide. We conclude that any stabilizing effect of cation-pi interactions in these peptides is much smaller than that predicted from computational studies.

Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction.

pi-pi, Cation-pi, and hydrophobic packing interactions contribute specificity to protein folding and stability to the native state. As a step towards developing improved models of these interactions in proteins, we compare the side-chain packing arrangements in native proteins to those found in compact decoys produced by the Rosetta de novo structure prediction method. We find enrichments in the native distributions for T-shaped and parallel offset arrangements of aromatic residue pairs, in parallel stacked arrangements of cation-aromatic pairs, in parallel stacked pairs involving proline residues, and in parallel offset arrangements for aliphatic residue pairs. We then investigate the extent to which the distinctive features of native packing can be explained using Lennard-Jones and electrostatics models. Finally, we derive orientation-dependent pi-pi, cation-pi and hydrophobic interaction potentials based on the differences between the native and compact decoy distributions and investigate their efficacy for high-resolution protein structure prediction. Surprisingly, the orientation-dependent potential derived from the packing arrangements of aliphatic side-chain pairs distinguishes the native structure from compact decoys better than the orientation-dependent potentials describing pi-pi and cation-pi interactions.

Inactivation of triosephosphate isomerase from Trypanosoma cruzi by an agent that perturbs its dimer interface.

We characterized by crystallographic, calorimetric and biochemical methods the action of a low molecular weight compound, 3-(2-benzothiazolylthio)-1-propanesulfonic acid (compound 8) that binds to the dimer interface of triosephosphate isomerase from Trypanosoma cruzi (TcTIM) and thereby abolishes its function with a high level of selectivity. The kinetics of TcTIM inactivation by the agent and isothermal titration calorimetry experiments showed that the binding of two molecules of the compound per enzyme is needed for inactivation. The binding of the first molecule is endothermic, and that of the second exothermic. Crystals of TcTIM in complex with one molecule of the inactivating agent that diffracted to a resolution of 2A were obtained. The compound is at the dimer interface at less than 4A from residues of the two subunits. Compound 8 is more effective at low than at high protein concentrations, indicating that it perturbs the association between the two TcTIM monomers. Calorimetric and kinetic data of experiments in which TcTIM was added to a solution of the inactivating agent showed that at low concentrations of the compound, inactivation is limited by binding, whereas at high concentrations of the agent, the events that follow binding become rate-limiting. The portion of the interface of TcTIM that binds the benzothiazole derivative and its equivalent region in human TIM differs in amino acid composition and hydrophobic packing. Thus, we show that by focusing on protein-protein interfaces, it is possible to discover low molecular weight compounds that are selective for enzymes from parasites.

Database-Derived Potentials Dependent on Protein Size for In Silico Folding and Design

Knowledge-based potentials are widely used in simulations of protein folding, structure prediction, and protein design. Their advantages include limited computational requirements and the ability to deal with low-resolution protein models compatible with long-scale simulations. Their drawbacks comprehend their dependence on specific features of the dataset from which they are derived, such as the size of the proteins it contains, and their physical meaning is still a subject of debate. We address these issues by probing the theoretical validity of these potentials as mean-force potentials that take the solvent implicitly into account and involve entropic contributions due to atomic degrees of freedom and solvation. The dependence on the size of the system is checked on distance-dependent amino acid pair potentials, derived from six protein structure sets containing proteins of increasing length N. For large inter-residue distances, they are found to display the theoretically predicted 1/N behavior weighted by a factor depending on the boundaries and the compressibility of the system. For short distances, different trends are observed according to the nature of the residue pairs and their ability to form, for example, electrostatic, cation- π or π− π interactions, or hydrophobic packing. The results of this analysis are used to devise a novel protein size-dependent distance potential, which displays an improved performance in discriminating native sequence-structure matches among decoy models.

Structural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces.

S1 domains occur in four of the major enzymes of mRNA decay in Escherichia coli: RNase E, PNPase, RNase II, and RNase G. Here, we report the structure of the S1 domain of RNase E, determined by both X-ray crystallography and NMR spectroscopy. The RNase E S1 domain adopts an OB-fold, very similar to that found with PNPase and the major cold shock proteins, in which flexible loops are appended to a well-ordered five-stranded beta-barrel core. Within the crystal lattice, the protein forms a dimer stabilized primarily by intermolecular hydrophobic packing. Consistent with this observation, light-scattering, chemical crosslinking, and NMR spectroscopic measurements confirm that the isolated RNase E S1 domain undergoes a specific monomer-dimer equilibrium in solution with a K(D) value in the millimolar range. The substitution of glycine 66 with serine dramatically destabilizes the folded structure of this domain, thereby providing an explanation for the temperature-sensitive phenotype associated with this mutation in full-length RNase E. Based on amide chemical shift perturbation mapping, the binding surface for a single-stranded DNA dodecamer (K(D)=160(+/-40)microM) was identified as a groove of positive electrostatic potential containing several exposed aromatic side-chains. This surface, which corresponds to the conserved ligand-binding cleft found in numerous OB-fold proteins, lies distal to the dimerization interface, such that two independent oligonucleotide-binding sites can exist in the dimeric form of the RNase E S1 domain. Based on these data, we propose that the S1 domain serves a dual role of dimerization to aid in the formation of the tetrameric quaternary structure of RNase E as described by Callaghan et al. in 2003 and of substrate binding to facilitate RNA hydrolysis by the adjacent catalytic domains within this multimeric enzyme.

Repacking of hydrophobic residues in a stable mutant of apocytochrome b562 selected by phage-display and proteolysis.

To test a hydrophobic core-directed protein design approach, we previously have used phage-display and proteolysis to select stably folded proteins from a library of mutants of apocytochrome b562. The consensus sequence of the selected mutants has hydrophilic residues at two of the three positions that are designed to form a hydrophobic core. To understand this unexpected result, we determined the high-resolution structure of one of the selected mutants using multi-dimensional nuclear magnetic resonance (NMR). The structure shows that the two hydrophilic residues in the consensus sequence were on the surface of the structure. Instead, two of their neighboring hydrophobic residues reorganized their side-chain conformations and formed the hydrophobic core. This result suggests that the hydrophobic core-directed protein design by phage-display and proteolysis is a valid method in general but alternative hydrophobic packing needs to be considered in the initial design. The unexpected repacking of the hydrophobic residues also highlights the plastic nature of protein structures.

Assembly of a Ca2+-dependent BK channel signaling complex by binding to beta2 adrenergic receptor.

Large-conductance voltage and Ca2+-activated potassium channels (BKCa) play a critical role in modulating contractile tone of smooth muscle, and neuronal processes. In most mammalian tissues, activation of beta-adrenergic receptors and protein kinase A (PKAc) increases BKCa channel activity, contributing to sympathetic nervous system/hormonal regulation of membrane excitability. Here we report the requirement of an association of the beta2-adrenergic receptor (beta2AR) with the pore forming alpha subunit of BKCa and an A-kinase-anchoring protein (AKAP79/150) for beta2 agonist regulation. beta2AR can simultaneously interact with both BKCa and L-type Ca2+ channels (Cav1.2) in vivo, which enables the assembly of a unique, highly localized signal transduction complex to mediate Ca2+- and phosphorylation-dependent modulation of BKCa current. Our findings reveal a novel function for G protein-coupled receptors as a scaffold to couple two families of ion channels into a physical and functional signaling complex to modulate beta-adrenergic regulation of membrane excitability.

A tradeoff between protein stability and conformational mobility in homotrimeric dUTPases

Oligomerization directs active site formation in homotrimeric 2 ′-deoxyuridine triphosphate pyrophosphatases (dUTPases). Stability of the homotrimer is a central determinant in enzyme function. The present comparative studies of bacterial and fruitfly dUTPases with homologous 3D structures by differential scanning microcalorimetry; fluorescence, circular dichorism and infrared spectroscopies, demonstrate that unfolding is a two-state highly cooperative transition in both dUTPases excluding a significantly populated intermediate state of dissociated and folded monomers. The eukaryotic protein is much less resistant against either thermal or guanidine hydrochloride-induced denaturation. Results suggest that hydrophobic packing of the inner threefold channel of the dUTPase homotrimer greatly contributes to stability.

Redesigning the Folding Energetics of a Model Three-helix Bundle Protein by Site-directed Mutagenesis

Because of their limited size and complexity, de novo designed proteins are particularly useful for the detailed investigation of folding thermodynamics and mechanisms. Here, we describe how subtle changes in the hydrophobic core of a model three-helix bundle protein (GM-0) alter its folding energetics. To explore the folding tolerance of GM-0 toward amino acid sequence variability, two mutant proteins (GM-1 and GM-2) were generated. In the mutants, cavities were created in the hydrophobic core of the protein by either singly (GM-1; L35A variant) or doubly (GM-2; L35A/I39A variant) replacing large hydrophobic side chains by smaller Ala residues. The folding of GM-0 is characterized by two partially folded intermediate states exhibiting characteristics of molten globules, as evidenced by pressure-unfolding and pressure-assisted cold denaturation experiments. In contrast, the folding energetics of both mutants, GM-1 and GM-2, exhibit only one folding intermediate. Our results support the view that simple but biologically important folding motifs such as the three-helix bundle can reveal complex folding plasticity, and they point to the role of hydrophobic packing as a determinant of the overall stability and folding thermodynamic of the helix bundle.

Hydrophobically Directed Selective Reduction of Ketones.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Water of hydration in coagels

Vitamin C-based alkanoyl-6-O-ascorbic acid esters, ASCn, are a class of surfactants, interesting both on account of their phase behaviour, and of the properties of the supramolecular assemblies they form. When dispersed in water at room, or lower, temperatures above ca. 5% w/w concentration, they form coagels. At higher temperatures, the microstructure changes to micellar solutions for surfactants of low hydrocarbon chain length n. The longer chained systems form gel phases. The transition enthalpy change is dominated by rearrangements in hydrophobic chain packing. On the other hand the Krafft point seems instead to be dictated mainly by interactions between the polar headgroups and the solvent. The coagel phase is usually thought of as formed of surfactant lamellae separated by thin interlayers of strongly bound, essentially “frozen”, water molecules. In this work, DSC measurements were performed to explore the interactions between water and the surfactant molecules. Two kinds of water were detected: interlayer hydration water and bulk water. The number of hydration water molecules per polar headgroup was inferred from the experimental results. Further insights into the coagel structure were gained from X-ray diffraction and optical microscopy. The effects of glycerin (GLY), propylene glycol (PG), and poly(ethylene glycol) (PEG), as co-solvents were investigated by conductivity and DSC experiments. Glycerin seems to stabilize the coagel, probably through the formation of hydrogen bonds that compete for the polar headgroups with the strongly bound water molecules. By contrast, PG and PEG decrease the compactness of the lamellar structure. This is most likely because these compounds can penetrate into the lipid portion of the lamellae, and reduce the hydrophobic interactions that hold the compact assemblies together.

Crystal Structure of a cAMP-dependent Protein Kinase Mutant at 1.26 Å: New Insights into the Catalytic Mechanism

The catalytic subunit of cAMP-dependent protein kinase has served as a paradigm for the entire kinase family. In the course of studying the structure–function relationship of the P+1 loop (Leu198–Leu205) of the kinase, we have solved the crystal structure of the Tyr204 to Ala mutant in complexes with Mg·ATP and an inhibitory peptide at 1.26Å, with overall structure very similar to that of the wild-type protein. However, at the nucleotide binding site, ATP was found largely hydrolyzed, with the products ADP-PO4 retained in the structure. High-resolution refinement suggests that 26% of the molecules contain the intact ATP, whereas 74% have the hydrolyzed products. The observation of the substrate and product states in the same structure adds significant information to our understanding of the phosphoryl transfer process. Structural examination of the mutation site substantiates and extends the emerging concept that the hydrophobic core in the large lobe of the kinase might serve as a stable platform for anchoring key segments involved in catalysis. We propose that Tyr204 is critical for anchoring the P+1 loop to the core. Further analysis has highlighted two major connections between the P+1 loop and the catalytic loop (Arg165–Asn171). One emphasizes the hydrophobic packing of Tyr204 and Leu167 mediated through residues from the αF-helix, recently recognized as a signal integration motif, which together with the αE-helix forms the center of the hydrophobic core network. The other connection is mediated by the hydrogen bond interaction between Thr201 and Asp166, in a substrate-dependent manner. We speculate that the latter interaction may be important for the kinase to sense the presence of substrate and prepare itself for the catalytic reaction. Thus, the P+1 loop is not merely involved in substrate binding; it mediates the communication between substrate and catalytic residues.

Model structures of the N-methyl- d-aspartate receptor subunit NR1 explain the molecular recognition of agonist and antagonist ligands

Molecular models of the ligand-binding domain of N-methyl- d-aspartate subunit R1 (NR1) were made using the published crystal structures of rat glutamate receptor B (GluRB), the bacterial glutamate receptor (GluR0), and the glutamine-binding protein (QBP) of Escherichia coli. Separate models of NR1 were built to represent the ligand-binding conformation for agonist (glycine, d- and l-isomers of serine and alanine, and the partial agonist ligand d-cycloserine) and antagonist (5,7-dichloro-4-oxo-1,4-dihydroquinoline-2-carboxylic acid (DCKA) and E-3-(2-phenyl-2-carboxyethenyl)-4,6-dichloro-1- H-indole-2-carboxylic acid (MDL 105,519)) ligands. Side-chain conformations of residues within the NR1 ligand-binding site were selected that optimized the hydrophobic packing and hydrogen bonding among residues, while taking into account published data comparing receptor mutants with wild-type NR1. Ligands docked to the model structures provide a rational explanation for the observed differences in binding affinity and receptor activation among agonist and antagonist ligands. NR1 prefers smaller ligands (glycine, serine, and alanine) in comparison with GluRB and GluR0 that bind l-glutamate: the bulky side chain of W731 in NR1 dramatically reduces the size of the ligand-binding site, functioning to selectively restrict recognition to glycine and the d-isomers of serine and alanine. Nevertheless, many of the interactions seen for ligands bound to GluRB, GluR0, and periplasmic-binding proteins are present for the ligands docked to the model structures of NR1.

Preparation of hydrophobic interaction chromatographic packings based on monodisperse poly(glycidylmethacrylate- co-ethylenedimethacrylate) beads and their application

The monodisperse, poly(glycidylmethacrylate- co-ethylenedimethacrylate) beads with macroporous in the range of 8.0–12.0 μm were prepared by a single-step swelling and polymerization method. The seed particles prepared by dispersion polymerization exhibited good absorption of the monomer phase. The pore size distribution of the beads was evaluated by gel permeation chromatography and mercury instrusion method. Based on this media, a hydrophobic interaction chromatographic (HIC) stationary phase for HPLC was synthesized by a new chemically modified method. The prepared resin has advantages for biopolymer separation, high column efficiency, low column backpressure, high protein mass recovery and good resolution for proteins. The dynamic protein loading capacity of the synthesized HIC packings was 40.0 mg/ml. Six proteins were fast separated in less than 8.0 min using the synthesized HIC stationary phase. The HIC resin was firstly used for the purification and simultaneous renaturation of recombinant human interferon-γ (rhIFN-γ) in the extract solution containing 7.0 mol/l guanidine hydrochloride with only one step. The purity and specific bioactivity of the purified of rhIFN-γ was found more than 95% and 1.3×10 8 IU/mg, respectively.

Hydrophobically directed selective reduction of ketones.

Three hydrophobic borohydrides carrying phenyl, pentafluorophenyl, and beta-naphthyl groups were used to reduce ketones in water and in methanol. With ketones carrying phenyl, naphthyl, or biphenyl substituents, there was preferential reduction in methanol of competing acetyl groups, either intermolecular or intramolecular, but preferential reduction of the aryl ketones in water. In the most extreme case, there was a 40-fold selectivity reversal. Lithium borohydride showed no such change in selectivity and favored acetyl reduction in both solvents. Salt and cosolvent effects indicate that hydrophobic packing is involved in the reaction of hydrophobic reagents with the aryl ketones. Some special interaction of the pentafluorophenyl group with aryl rings was also detected.

Crystallographic analysis of an "anticalin" with tailored specificity for fluorescein reveals high structural plasticity of the lipocalin loop region.

The artificial lipocalin FluA with novel specificity toward fluorescein was derived via combinatorial engineering from the bilin-binding protein, BBP by exchange of 16 amino acids in the ligand pocket. Here, we describe the crystal structure of FluA at 2.0 A resolution in the space group P2(1) with two protein-ligand complexes in the asymmetric unit. In both molecules, the characteristic beta-barrel architecture with the attached alpha-helix is well preserved. In contrast, the four loops at one end of the beta-barrel that form the entrance to the binding site exhibit large conformational deviations from the wild-type protein, which can be attributed to the sidechain replacements. Specificity for the new ligand is furnished by hydrophobic packing, charged sidechain environment, and hydrogen bonds with its hydroxyl groups. Unexpectedly, fluorescein is bound in a much deeper cavity than biliverdin IX(gamma) in the natural lipocalin. Triggered by the substituted residues, unmutated sidechains at the bottom of the binding site adopt conformations that are quite different from those observed in the BBP, illustrating that not only the loop region but also the hydrophobic interior of the beta-barrel can be reshaped for molecular recognition. Particularly, Trp 129 participates in a tight stacking interaction with the xanthenolone moiety, which may explain the ultrafast electron transfer that occurs on light excitation of the bound fluorescein. These structural findings support our concept of using lipocalins as a scaffold for the engineering of so-called "anticalins" directed against prescribed targets as an alternative to recombinant antibody fragments.