Van Der Waals Packing Research Articles

Are aromatic carbon donor hydrogen bonds linear in proteins?

Proteins fold and maintain structure through the collective contributions of a large number of weak, noncovalent interactions. The hydrogen bond is one important category of forces that acts on very short distances. As our knowledge of protein structure continues to expand, we are beginning to appreciate the role that weak carbon-donor hydrogen bonds play in structure and function. One property that differentiates hydrogen bonds from other packing forces is propensity for forming a linear donor-hydrogen-acceptor orientation. To ascertain if carbon-donor hydrogen bonds are able to direct acceptor linearity, we surveyed the geometry of interactions specifically involving aromatic sidechain ring carbons in a data set of high resolution protein structures. We found that while donor-acceptor distances for most carbon donor hydrogen bonds were tighter than expected for van der Waals packing, only the carbons of histidine showed a significant bias for linear geometry. By categorizing histidines in the data set into charged and neutral sidechains, we found only the charged subset of histidines participated in linear interactions. B3LYP/6-31G**++ level optimizations of imidazole and indole-water interactions at various fixed angles demonstrates a clear orientation dependence of hydrogen bonding capacity for both charged and neutral sidechains. We suggest that while all aromatic carbons can participate in hydrogen bonding, only charged histidines are able to overcome protein packing forces and enforce linear interactions. The implications for protein modeling and design are discussed.

Structural Basis for the Conformational Integrity of the Arabidopsis thaliana HY5 Leucine Zipper Homodimer

The leucine zipper (LZ) domain of the HY5 transcription factor from Arabidopsis thaliana has unique primary structural properties, including major occupation by the Leu residues as well as two buried polar residues in the a positions and a localized distribution of charged and polar residues in the first three heptad repeats. In this study, we solved the crystal structure of the HY5 LZ domain and show that the peculiarities in the primary sequence yield unusual structural characteristics. For example, the HY5 LZ domain exhibits a bipartite charge distribution characterized by a highly negative electrostatic surface potential in its N-terminal half and a nearly neutral potential in its C-terminal half. The LZ N-terminal region also contains two consecutive putative trigger sites for dimerization of the coiled coils. In addition, two buried asparagines at a positions 19 and 33 in the HY5 LZ domain display distinct modes of polar interaction. Whereas Asn(19) shows a conformational flip-flop, Asn(33) is engaged in a permanent hydrogen bond network. CD spectropolarimetry and analytical ultracentrifugation experiments performed with versions of the HY5 LZ domain containing mutations in the a positions yielded further evidence that position a amino acid residues are crucial for achieving an oligomeric state and maintaining stability. However, a low correlation between position a amino acid preference, core packing geometry, and rotamer conformations suggests that the oligomeric state of the LZ domain is not governed entirely by known structural properties. Taken together, our results suggest structural factors conferring conformational integrity of the HY5 LZ homodimer that are more complicated than proposed previously.

Self‐assembly of coiled‐coil tetramers in the 1.40 Å structure of a leucine‐zipper mutant

The hydrophobic core of the GCN4 leucine-zipper dimerization domain is formed by a parallel helical association between nonpolar side chains at the a and d positions of the heptad repeat. Here we report a self-assembling coiled-coil array formed by the GCN4-pAe peptide that differs from the wild-type GCN4 leucine zipper by alanine substitutions at three charged e positions. GCN4-pAe is incompletely folded in normal solution conditions yet self-assembles into an antiparallel tetraplex in crystals by formation of unanticipated hydrophobic seams linking the last two heptads of two parallel double-stranded coiled coils. The GCN4-pAe tetramers in the lattice associate laterally through the identical interactions to those in the intramolecular dimer-dimer interface. The van der Waals packing interaction in the solid state controls extended supramolecular assembly of the protein, providing an unusual atomic scale view of a mesostructure.

Structure determination of symmetric homo‐oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing

Structural studies of symmetric homo-oligomers provide mechanistic insights into their roles in essential biological processes, including cell signaling and cellular regulation. This paper presents a novel algorithm for homo-oligomeric structure determination, given the subunit structure, that is both complete, in that it evaluates all possible conformations, and data-driven, in that it evaluates conformations separately for consistency with experimental data and for quality of packing. Completeness ensures that the algorithm does not miss the native conformation, and being data-driven enables it to assess the structural precision possible from data alone. Our algorithm performs a branch-and-bound search in the symmetry configuration space, the space of symmetry axis parameters (positions and orientations) defining all possible C(n) homo-oligomeric complexes for a given subunit structure. It eliminates those symmetry axes inconsistent with intersubunit nuclear Overhauser effect (NOE) distance restraints and then identifies conformations representing any consistent, well-packed structure to within a user-defined similarity level. For the human phospholamban pentamer in dodecylphosphocholine micelles, using the structure of one subunit determined from a subset of the experimental NMR data, our algorithm identifies a diverse set of complex structures consistent with the nine intersubunit NOE restraints. The distribution of determined structures provides an objective characterization of structural uncertainty: backbone RMSD to the previously determined structure ranges from 1.07 to 8.85 A, and variance in backbone atomic coordinates is an average of 12.32 A(2). Incorporating vdW packing reduces structural diversity to a maximum backbone RMSD of 6.24 A and an average backbone variance of 6.80 A(2). By comparing data consistency and packing quality under different assumptions of oligomeric number, our algorithm identifies the pentamer as the most likely oligomeric state of phospholamban, demonstrating that it is possible to determine the oligomeric number directly from NMR data. Additional tests on a number of homo-oligomers, from dimer to heptamer, similarly demonstrate the power of our method to provide unbiased determination and evaluation of homo-oligomeric complex structures.

Molecular ladders based upon binuclear bis-chelate platforms

Two coordination compounds of Zn(II) with a doubly deprotonated bis(β-diketone) 1,3-(CO-CH2-CO-Ph)2Ph (H2L), [Zn2(DMSO)4L2] (I) and [Zn2(bipy)2L2]·4(DMSO) (II) (bipy = 4,4′-bipyridyl; DMSO = dimethylsulfoxide), have been prepared and characterized with XRD method. Both structures are based on a binuclear flat fragment Zn2L2. The crystal structure I reveals van der Waals packing of molecules in which four DMSO ligands are coordinated axially to the cations of the binuclear fragments. The crystal structure II comprises a linear coordination polymer in which adjacent binuclear fragments are connected through bridging bipy ligands to form a molecular ladder type of architecture. Guest DMSO molecules reside in the voids of the crystal packing. The newly obtained host coordination polymer is compared with similar polymers based upon metal dibenzoylmethanate bis-chelate platforms.

Mistletoe lectin I in complex with galactose and lactose reveals distinct sugar-binding properties

The structures of mistletoe lectin I (ML-I) from Viscum album complexed with lactose and galactose have been determined at 2.3 A resolution and refined to R factors of 20.9% (Rfree = 23.6%) and 20.9 (Rfree = 24.6%), respectively. ML-I is a heterodimer and belongs to the class of ribosome-inactivating proteins of type II, which consist of two chains. The A-chain has rRNA N-glycosidase activity and irreversibly inhibits eukaryotic ribosomes. The B-chain is a lectin and preferentially binds to galactose-terminated glycolipids and glycoproteins on cell membranes. Saccharide binding is performed by two binding sites in subdomains alpha1 and gamma2 of the ML-I B-chain separated by approximately 62 A from each other. The favoured binding of galactose in subdomain alpha1 is achieved via hydrogen bonds connecting the 4-hydroxyl and 3-hydroxyl groups of the sugar moiety with the side chains of Asp23B, Gln36B and Lys41B and the main chain of 26B. The aromatic ring of Trp38B on top of the preferred binding pocket supports van der Waals packing of the apolar face of galactose and stabilizes the sugar-lectin complex. In the galactose-binding site II of subdomain gamma2, Tyr249B provides the hydrophobic stacking and the side chains of Asp235B, Gln238B and Asn256B are hydrogen-bonding partners for galactose. In the case of the galactose-binding site I, the 2-hydroxyl group also stabilizes the sugar-protein complex, an interaction thus far rarely detected in galactose-specific lectins. Finally, a potential third low-affinity galactose-binding site in subunit beta1 was identified in the present ML-I structures, in which a glycerol molecule from the cryoprotectant buffer has bound, mimicking the sugar compound.

Hydrophobic Helical Hairpins: Design and Packing Interactions in Membrane Environments

Helix-helix interactions within membranes are dominated by van der Waals packing motifs and side chain-side chain hydrogen bond formation, which act in tandem to determine the residues that comprise the interface between two given helices. To explore in a systematic manner the tertiary contacts between transmembrane helices, we have designed and expressed in Escherichia coli highly hydrophobic helix-loop-helix constructs of prototypic sequence K(1)KKKKKKFAIAIAIIAWAX(19)AIIAIAIAIKSPGSKIAIAIAIIAZ(44)AWAIIAIAIAFKKKKKKK(62), where "small" (Ala) and "large" (Ile) residues were used to maximize the tertiary contact area. Evidence that the two transmembrane (TM) segments in the AI construct contain an interface conducive for folding into a hairpin structure was obtained from the results that (i) the single TM AI(pep) peptide derived from the AI hairpin forms SDS-resistant dimers on PAGE gels and (ii) the corresponding sequence forms a strong dimer when examined in vivo in TOXCAT assays. Site-directed mutagenesis of AI hairpins was carried out to incorporate each of the 20 commonly occurring amino acids at X positions. Analysis on Western blots using an oligomerization assay in 12% NuPage-sodium dodecyl sulfate (SDS) indicated that mutants with X = E, D, Q, R, N, H, and K largely formed SDS-resistant dimers-which likely correspond to H-bonded four-helix bundles-while all the others (e.g., X = F, W, L, I, M, V, C, Y, A, T, S, G, and P) remained monomeric. Systematic studies of X/Z double mutants indicated that formation of hairpin dimers is the result of the disruption of stabilizing interactions between the antiparallel helices within the AI construct. The overall results suggest that, in situations where hydrophobic van der Waals packing energy between helices is sufficient to prevent significant rotation about the major axes of interacting helices, intrahairpin side chain-side chain H-bond formation will occur mainly when pairs of polar residues are interfacially located and proximal. Knowledge of the relative contributions of these forces should be of value, for example, in clarifying the context--and the structural consequences--of disease-related mutations.

Computer modeling of polyleucine-based coiled coil dimers in a realistic membrane environment: insight into helix-helix interactions in membrane proteins.

Simulated annealing was performed to model parallel dimers of alpha-helical transmembrane peptides with the sequence L(11)XL(12), predicting left-handed coiled coil geometry in all cases. Insertion of peptides containing threonine, asparagine, alanine, phenylalanine, and leucine in position 12 into realistic model membranes showed these structures were stable for 20 ns of molecular dynamics simulation time. Threonine could participate in intermolecular hydrogen bonds, but predominantly formed hydrogen bonds to the backbone of the helix it resided on. These hydrogen bonds, although infrequent, appeared to promote closer association of polyleucine helices. Asparagine participated in multiple, rapidly fluctuating intermolecular and intramolecular hydrogen bonds, and may have slightly destabilized optimum van der Waals packing in favor of optimum hydrogen bonding. Coordinated rotations of transmembrane helices about their axes were observed, indicating helices may rotate around one another during the folding of membrane proteins or other processes. These rotations were inhibited by phenylalanine, suggesting a role for bulky residues in modulating membrane protein dynamics.

Side-chain Contributions to Membrane Protein Structure and Stability

The molecular forces that stabilize membrane protein structure are poorly understood. To investigate these forces we introduced alanine substitutions at 24 positions in the B helix of bacteriorhodopsin and examined their effects on structure and stability. Although most of the results can be rationalized in terms of the folded structure, there are a number of surprises. (1) We find a remarkably high frequency of stabilizing mutations (17%), indicating that membrane proteins are not highly optimized for stability. (2) Helix B is kinked, with the kink centered around Pro50. The P50A mutation has no effect on stability, however, and a crystal structure reveals that the helix remains bent, indicating that tertiary contacts dominate in the distortion of this helix. (3) We find that the protein is stabilized by about 1 kcal/mol for every 38 Å 2 of surface area buried, which is quite similar to soluble proteins in spite of their dramatically different environments. (4) We find little energetic difference, on average, in the burial of apolar surface or polar surface area, implying that van der Waals packing is the dominant force that drives membrane protein folding.

Sequence Context Strongly Modulates Association of Polar Residues in Transmembrane Helices

Polar residues are capable of mediating the association of membrane-embedded helices through the formation of side-chain/side-chain inter-helical hydrogen bonds. However, the extent to which native van der Waals packing of the residues surrounding the polar locus can enhance, or interfere with, the interaction of polar residues has not yet been studied. We examined the propensities of four polar residues (aspartic acid, asparagine, glutamic acid, and glutamine) to promote self-association of transmembrane (TM) domains in several biologically derived sequence environments, including (i) four naturally occurring TM domains that contain a Glu or Gln residue (Tnf5/CD40 ligand, C79a/Ig-α, C79b/Ig-β, and Fut3/α-fucosyltransferase); and (ii) variants of bacteriophage M13 major coat protein TM segment with Asp and Asn at interfacial and non-interfacial positions. Self-association was quantified by the TOXCAT assay, which measures TM helix self-oligomerization in the Escherichia coli inner membrane. While an appropriately placed polar residue was found in several cases to significantly stabilize TM helix–helix interactions through the formation of an interhelical hydrogen bond, in other cases the strongly polar residues did not enhance the association of the two helices. Overall, these results suggest that an innate structural mechanism may operate to control non-specific association of membrane-embedded polar residues.

Polar Residues in Membrane Domains of Proteins: Molecular Basis for Helix−Helix Association in a Mutant CFTR Transmembrane Segment

Polar side chains constitute over 20% of residues in the transmembrane (TM) helices of membrane proteins, where they may serve as hydrogen bond interaction sites for phenotypic polar mutations that arise in membrane protein-related diseases. To systematically explore the structural consequences of H-bonds between TM helices, we focused on TM4 of the cystic fibrosis conductance regulator (CFTR) and its cystic fibrosis- (CF-) phenotypic mutation, V232D, as a model system. Synthetic peptides corresponding to wild-type (TM4-wt) (residues 219-242: LQASAFCGLGFLIVLALFQAGLGR) and mutant (TM4-V232D) sequences both adopt helical structures in SDS micelles and display dimer bands on SDS-PAGE arising from disulfide bond formation via wild-type residue Cys-225. However, the TM4-V232D peptide additionally forms a ladder of noncovalent oligomers, including tetramers, hexamers, and octamers, mediated by a hydrogen bond network involving Asp-Gln side chain-side chain interactions. Ala-scanning mutagenesis of the TM4 sequence indicated that ladder formation minimally required the simultaneous presence of the Cys-225, Asp-232, and Gln-237 residues. As random hydrophobic sequences containing these three residues at TM4 equivalent positions did not oligomerize, specific van der Waals packing interactions between helix side chains were also shown to play a crucial role. Overall, the results suggest that polar mutations in membrane domains, in conjunction with critically positioned polar partner residues, potentially constitute a source of aberrant helix interactions that could contribute to loss of function when they arise in protein transmembrane domains.

Inclusion Ability of 4-Phenylpyridine-Extended Nickel(II) Dibenzoylmethanate, a New Metal−Complex Host

A new host complex, [Ni(4-PhPy)2(DBM)2], has been prepared by modification of nickel dibenzoylmethanate (Ni(DBM)2; DBM = C6H5COCHCOC6H5-) with 4-phenylpyridine (4-PhPy). Of 17 organic solvents that were tested as guest candidates, 6 inclusion compounds were isolated, mostly as bulk products. All compounds were characterized with XRD methods. With benzene, fluoro-, chloro-, and bromobenzenes, toluene, and o-xylene, 1:1 inclusions form; they are all green, relatively stable, and isostructural (triclinic, P1, Z = 2). The guest species accommodate flattened cages formed upon van der Waals packing of host molecules. The guest inclusion influences the distortion in the bischelate fragment of the host molecule, as the dihedral angle between two chelate rings ranges up to 12°. This distortion is probably responsible for the green color of these phases. The series of inclusions exhibits an order of thermal stability opposite to that which would be expected from the volativity of the neat guests; the order indicat...

(6,17-Dimethyl-8,15-diphenyldibenzo[b,i][1,4,8,11]-tetra-aza[14]annulenato)nickel(II) in solids: two guest-free polymorphs and inclusion compounds with methylene chloride and fullerene (C(60))-carbon disulfide.

Two guest-free polymorphs and two inclusion compounds of the macrocyclic title complex [NiL] have been isolated and characterized with single-crystal and/or powder XRD, solid-state (13)C NMR, and other methods. The inclusion compound with methylene chloride, [NiL](CH(2)Cl(2)), is stable in air and thermally stable up to approximately 128 degrees C. Its crystal structure is consistent with van der Waals packing of the host [NiL] and guest CH(2)Cl(2) molecules. The host complex has square-planar coordination of the nickel(II) center with four nitrogen atoms of the macrocycle with an average Ni-N distance of 1.86 A. The molecule has a saddle-shaped conformation with the guest molecule located between one phenylene and two phenyl rings of the host molecule. Isostructural compounds with chloroform and 2-chloropropane form only as mixtures along with a guest-free host polymorph. The inclusion compound with C(60) has a composition 3[NiL]*(C(60))*2(CS(2)) and here also the crystal structure is consistent with a van der Waals type of packing. Three crystallographically inequivalent [NiL] molecules have geometries similar to that in the inclusion compound with methylene chloride. The concave surfaces of the complex molecules form a spherical cavity for the C(60) molecule. At -100 degrees C the C(60) molecule is disordered over two orientations centered at the same site. (13)C NMR studies at room temperature show that the C(60) molecule is undergoing rapid pseudo-isotropic rotation. The stability and other properties of the title and related complexes are discussed.

Insights into the stability of native and partially folded states of ubiquitin: effects of cosolvents and denaturants on the thermodynamics of protein folding.

The thermodynamics of the native<-->A state and native<-->unfolded transitions for ubiquitin have been characterized in detail using the denaturants methanol and guanidinium chloride (Gdn.HCl) both separately and in combination. Gdn.HCl destabilizes the partially folded alcohol-induced A state such that the effects of alcoholic solvents on the native<-->unfolded transition can be investigated directly via a two-state model. The combined denaturing effects of methanol and Gdn.HCl appear to conform to a simple additive model. We show that ubiquitin folds and unfolds cooperatively in all cases, forming the same "native" state; however, the thermodynamics of the N<-->U transition change dramatically between alcoholic and Gdn.HCl solutions, with folding in aqueous methanol associated with large negative enthalpy and entropy terms at 298 K with a gradual falloff in DeltaC(p) at higher methanol concentrations, as previously reported for the N<-->A transition (Woolfson, D. N., Cooper, A., Harding, M. M., Williams, D. H., and Evans, P. A. (1993) J. Mol. Biol. 229, 502-511.). Both the N<-->U and the N<-->A transitions are enthalpy driven to a similar extent. We conclude that under these conditions van der Waals interactions in the packing of the nonpolar protein core, which is common to both the N<-->U and the N<-->A transitions, appear to drive folding in the absence of entropic effects associated with release of ordered solvent (hydrophobic effect). Solvent transfer studies of hydrocarbons into alcoholic solvents, with and without Gdn.HCl, are consistent with a large enthalpic driving force for burial of a nonpolar surface, with a linear dependence of protein stability (DeltaG(N)(<-->)(U)) on cosolvent concentration reflected in a similar linear dependence of hydrocarbon solubility. The data demonstrate that the hydrophobic effect is not a prerequisite for specific stabilization of the native state or the A state and that van der Waals packing of the nonpolar core appears to be the dominant factor in stabilization of the native state.

Nickel(II) and zinc(II) dibenzoylmethanates: molecular and crystal structure, polymorphism, and guest- or temperature-induced oligomerization.

Four forms of nickel(II) and two of zinc(II) dibenzoylmethanates have been isolated and characterized with powder and single-crystal X-ray diffraction analyses, differential scanning calorimetry, magnetic susceptibility measurements, and solid-state 13C cross-polarization/magic angle spinning NMR. Nickel dibenzoylmethanate, Ni(DBM)2 (DBM = PhCOCHCOPh-), forms three polymorphic forms (light-green, brown, and green) and a fourth clathrate form with guest benzene included. The light-green polymorph is metastable. Substituted benzenes induce recrystallization of the polymorph into a stable brown form (C30H22NiO4; a = 26.502(3) A, b = 5.774(1) A, c = 16.456(2) A, beta = 116.03(1) degrees; monoclinic, C2/c; Z = 4). Unlike the other forms, the brown form is diamagnetic and is comprised of monomers of the low-spin [Ni(DBM)2] complex. The Ni(II) is chelated by two DBM ligands in a square planar environment by four donor oxygen atoms. When heated, the brown form transforms to a green form which is stable above 202 degrees C (C90H66Ni3O12; a = 13.819(2) A, b = 16.252(2) A, c = 17.358(2) A, beta = 108.28(1) degrees; monoclinic, P2(1)/n; Z = 2). This polymorph is formed by van der Waals packing of trimers [Ni3(DBM)6] containing linear Ni3 clusters with an Ni-Ni distance of 2.81 A. The cluster is surrounded by six DBM ligands, providing a distorted octahedral environment about each Ni by six oxygen atoms. Benzene stabilizes the trimeric structure at room temperature, forming a [Ni3(DBM)6].2(benzene) inclusion compound (Ni-Ni distance of 2.83 A) with guest benzene molecules located in channels (C90H66Ni3O12 + 2(C6H6); a = 17.670(2) A, b = 20.945(3) A, c=11.209(2) A, beta = 102.57(1) degrees; monoclinic, P2(1)/c; Z = 2). Zinc dibenzoylmethanate has been prepared in two polymorphic forms. The monomeric form contains [Zn(DBM)2] molecules with the zinc center in a distorted tetrahedral environment of four oxygens from the two chelated DBMs (C30H22O4Zn; a = 10.288(2) A, b = 10.716(2) A, c = 12.243(2) A, alpha = 89.19(1) degrees, beta = 75.39(1) degrees, gamma = 64.18(1) degrees; triclinic, P1; Z = 2). Another, dimeric form contains [Zn2(DBM)4] species, with two zinc atoms separated by a distance of 3.14 A and each zinc coordinated by five oxygen atoms (C60H44O8Zn2; a = 25.792(3) A, b = 7.274(1) A, c = 24.307(2) A, beta = 90.58(1) degrees; monoclinic, C2/c; Z = 4). The polymorphic variety of the title complexes and the peculiarities of the Ni(II) and Zn(II) coordination environments are discussed in the context of using the complexes as precursors for new metal complex hosts.

4-Vinylpyridine-Modified Nickel and Cobalt Dibenzoylmethanates as New Hosts: Inclusions with Carbon Tetrachloride and Chlorobenzene

Bis(4-vinylpyridine)bis(dibenzoylmethanato)metal(II), [M(ViPy)2(DBM)2] (M = Ni(II), Co(II); ViPy = 4-Vinylpyridine; DBM = C6H5COCHCOC6H5 −, dibenzoylmethanate) is a new metal-complex host. Its inclusions with carbon tetrachloride (host:guest = 1:2; triclinic, P 1, Z = 1) and chlorobenzene (host:guest = 1:1; monoclinic, P2 1 /c, Z = 4) are consistent with the van der Waals packing of neutral complex (host) and solvent (guest) molecules. In the host unit, four oxygens from two chelate DBM-units provide a square-planar environment around the metal center that is extended to octahedral coordination by two apical nitrogens from two vinylpyridine moieties in the trans-position. In the carbon tetrachloride inclusions, the host traps two guest molecules in large prolate spheroidal cavities. In the chlorobenzene inclusions, guest species are located inside 8-shaped serpentine channels along the y-axis. The nickel and cobalt versions of the inclusion compounds were found to be very similar.

Pressure-induced interlinking of carbon nanotubes

We predict new forms of carbon consisting of one- and two-dimensional networks of interlinked single-wall carbon nanotubes, some of which are energetically more stable than van der Waals packing of the nanotubes on a hexagonal lattice. These interlinked nanotubes are further transformed with higher applied external pressures to more dense and complicated stable structures, in which curvature-induced carbon ${\mathrm{sp}}^{3}$ rehybridizations are formed. We also discuss the energetics of the bond formation between nanotubes and the electronic properties of these predicted novel structures.

Effect of amino-acid substitutions on Alzheimer's amyloid-beta peptide-glycosaminoglycan interactions.

One of the major clinical features of Alzheimer's disease is the presence of extracellular amyloid plaques that are associated with glycosaminoglycan-containing proteoglycans. It has been proposed that proteoglycans and glycosaminoglycans facilitate amyloid fibril formation and/or stabilize these aggregates. Characterization of proteoglycan-protein interactions has suggested that basic amino acids in a specific conformation are necessary for glycosaminoglycan binding. Amyloid-beta peptide (Abeta) has a cluster of basic amino acids at the N-terminus (residues 13-16, His-His-Gln-Lys), which are considered critical for glycosaminoglycan interactions. To understand the molecular recognition of glycosaminoglycans by Abeta, we have examined a series of synthetic peptides with systematic alanine substitutions. These include: His13-->Ala, His14-->Ala, Lys16-->Ala, His13His14Lys16-->Ala and Arg5His6-->Ala. Alanine substitutions result in differences in both the secondary and fibrous structure of Abeta1-28 as determined by circular dichroism spectroscopy and electron microscopy. The results demonstrate that the His-His-Gln-Lys region of Abeta, and in particular His13, is an important structural domain, as Ala substitution produces a dysfunctional folding mutant. Interaction of the substituted peptides with heparin and chondroitin sulfate glycosaminoglycans demonstrate that although electrostatic interactions contribute to binding, nonionic interactions such as hydrogen bonding and van der Waals packing play a role in glycosaminoglycan-induced Abeta folding and aggregation.

Asparagine-mediated self-association of a model transmembrane helix.

In membrane proteins, the extent to which polarity, hydrogen bonding, and van der Waals packing interactions of the buried, internal residues direct protein folding and association of transmembrane segments is poorly understood. The energetics associated with these various interactions should differ substantially between membrane versus water-soluble proteins. To help evaluate these energetics, we have altered a water-soluble, two-stranded coiled-coil peptide to render its sequence soluble in membranes. The membrane-soluble peptide associates in a monomer-dimer-trimer equilibrium, in which the trimer predominates at the highest peptide/detergent ratios. The oligomers are stabilized by a buried Asn side chain. Mutation of this Asn to Val essentially eliminates oligomerization of the membrane-soluble peptide. Thus, within a membrane-like environment, interactions involving a polar Asn side chain provide a strong thermodynamic driving force for membrane helix association.

Role of helix-helix interactions in assembly of the bacteriorhodopsin lattice.

The purple membrane of Halobacterium salinarium is a two-dimensional lattice of lipids and the integral membrane protein bacteriorhodopsin (BR). To determine whether helix-helix interactions within the membrane core stabilize this complex, we substituted amino acid residues at the helix-helix interface between BR monomers and examined the assembly of the protein into the lattice. Lattice assembly was demonstrated to fit a cooperative self-assembly model that exhibits a critical concentration in vivo. Using this model as the basis for a quantitative assay of lattice stability, bulky substitutions at the helix-helix interface between BR monomers within the membrane core were shown to be destabilizing, probably due to steric clash. Ala substitutions of two residues at the helix-helix interface also reduced stability, suggesting that the side chains of these residues participate in favorable van der Waals packing interactions. However, the stabilizing interactions were restricted to a small region of the interface, and most of the substitutions had little effect. Thus, the contribution of helix-helix interactions to lattice stability appears limited, and favorable interactions between other regions of neighboring BR monomers or between BR and lipid molecules must also contribute.