Betabellins 15D and 16D, de Novo designed beta-sandwich proteins that have amyloidogenic properties.

The betabellin structure is a de novo designed beta-sandwich protein consisting of two 32-residue beta-sheets packed against one another by hydrophobic interactions. d-Amino acid residues are used to energetically favor formation of type-I' beta turns. Air oxidation of betabellin 15S (B15S) (HSLTAKIpkLTFSIAphTYTCAVpkYTAKVSH, where p denotes d-Pro, h denotes d-His, and k denotes d-Lys) yields betabellin 15D (B15D), a 64-residue disulfide-bridged protein. The amino acid sequence of B15D contains a conformationally constrained d-Pro residue at the i + 1 position of each type-I' beta turn. To test whether d-Pro residues are necessary for folding at these positions, the six d-Pro residues of B15D are replaced by d-Ala residues in betabellin 16D (B16D). Previously, transmission electron microscopy showed that B15D forms unbranched, 35-A wide fibrils that associate into bundles in 5.0 mM 3-(N-morpholino)propanesulfonate and 250 mM NaCl at pH 7; under these conditions, B16D forms ribbon-like assemblies. The B15D fibrils resemble the protofilaments that constitute amyloid fibrils. The present studies show that both B15D and B16D have characteristics of amyloidogenic proteins: the unbranched fibrils and ribbons stained with Congo red and displayed a green birefringence, exhibited a cross-beta structure, and bound 1-anilino-8-naphthalenesulfonate. Thus, these de novo designed beta-sandwich proteins should provide useful models for studying the mechanism of amyloid protofilament formation and assembly into amyloid fibrils and for designing potential inhibitors of amyloidogenesis.

Biophysical characterization of betabellin 16D: a beta-sandwich protein that forms narrow fibrils which associate into broad ribbons.

The betabellin structure is a de novo designed beta-sandwich protein consisting of two 32-residue beta sheets packed against one another by hydrophobic interactions. Betabellin 16S (B16S), a 32-residue peptide chain (HSLTAKIakLTFSIAahTYTCAVakYTAKVSH, where a is DAla, h is DHis, and k is DLys), did not have beta structure in water at pH 6.5. Air oxidation of B16S furnished betabellin 16D (B16D), a 64-residue disulfide-bridged two-chain protein, which also did not fold in water at pH 6.5. However, the extent of beta structure observed for B16D increased with pH and ionic strength of the solution and the B16D concentration as observed by circular dichroism spectropolarimetry. Transmission electron microscopy showed that B16D formed narrow fibrils that associated into broad ribbons in 5.0 mM Mops and 0.25 M NaCl at pH 6.9.

Metal-ion binding and limited proteolysis of betabellin 15D, a designed beta-sandwich protein.

Betabellin 15D is a 64-residue, disulfide-bridged homodimer. When folded into a beta structure, the protein is predicted to have two clusters of three histidine residues, each cluster able to bind a divalent metal ion. When the protein was incubated with Cu2+, Zn2+, Co2+, or Mn2+, metal complexes of betabellin 15D were observed by electrospray-ionization mass spectrometry. The relative abundances of the ionic complexes suggested an order of affinities of Cu2+ > Zn2+ > Co2+ > Mn2+, consistent with solution-phase affinities for nitrogen- or sulfur-containing ligands. Limited proteolysis of betabellin 15D by immobilized pepsin, as measured by nanoelectrospray-ionization mass spectrometry, showed that the Phe12-Ser13 peptide bond of betabellin 15D was cleaved more slowly in the presence of Cu2+ than in its absence. Because Cu2+ has little or no effect on the catalytic rate of pepsin, the slower cleavage of the Phe12-Ser13 peptide bond may be due to its decreased accessibility caused by Cu(2+)-induced folding of betabellin 15D.

Structural basis of the oligomerization of hepatitis delta antigen.

BACKGROUND: The hepatitis D virus (HDV) is a small satellite virus of hepatitis B virus (HBV). Coinfection with HBV and HDV causes severe liver disease in humans. The small 195 amino-acid form of the hepatitis delta antigen (HDAg) functions as a trans activator of HDV replication. A larger form of the protein containing a 19 amino acid C-terminal extension inhibits viral replication. Both of these functions are mediated in part by a stretch of amino acids predicted to form a coiled coil (residues 13-48) that is common to both forms. It is believed that HDAg forms dimers and higher ordered structures through this coiled-coil region. RESULTS: The high-resolution crystal structure of a synthetic peptide corresponding to residues 12 to 60 of HDAg has been solved. The peptide forms an antiparallel coiled coil, with hydrophobic residues near the termini of each peptide forming an extensive hydrophobic core with residues C-terminal to the coiled-coil domain in the dimer protein. The structure shows how HDAg forms dimers, but also shows the dimers forming an octamer that forms a 50 A ring lined with basic sidechains. This is confirmed by cross-linking studies of full-length recombinant small HDAg. CONCLUSIONS: HDAg dimerizes through an antiparallel coiled coil. Dimers then associate further to form octamers through residues in the coiled-coil domain and residues C-terminal to this region. Our findings suggest that the structure of HDAg represents a previously unseen organization of a nucleocapsid protein and raise the possibility that the N terminus may play a role in binding the viral RNA.

Engineering of betabellin-15D: a 64 residue beta sheet protein that forms long narrow multimeric fibrils.

The betabellin target structure is a beta-sandwich protein consisting of two 32 residue beta-sheets packed against one another by interaction of their hydrophobic faces. The 32 residue chain of betabellin-15S (HSLTAKIpkLTFSIAphTYTCAV pkYTAKVSH, where p=DPro, k=DLys, and h=DHis) did not fold in water at pH 6.5. Air oxidation of betabellin-15S provided betabellin-15D, the 64 residue disulfide bridged two-chain molecule, which also remained unfolded in water at pH 6.5. By circular dichroic spectropolarimetry, the extent of beta structure observed for betabellin-15D increased with the pH and ionic strength of the solution and the betabellin-15D concentration. By electron microscopy, in 5.0 mM MOPS and 0.25 M NaCl at pH 6.9, betabellin-15D formed long narrow multimeric fibrils. A molecular model was constructed to show that the dimensions of these betabellin-15D fibrils are consistent with a single row of beta-sandwich molecules joined by multiple intersheet H-bonds.

Synthetic peptides from mouse Fc receptor (MoFc gamma RII) that alter the binding of IgG to MoFc gamma RII.

Fc receptors are transmembrane proteins, found on the surfaces of immune cells, that aid in the removal of foreign pathogens by binding to antibody-coated targets via the Fc regions of the antibodies. Using peptides synthesized on pins, overlapping dodecapeptides (170) were synthesized to cover the extracellular region of the mouse Fc receptor for IgG, moFc gamma RII. The peptides were screened for antibody binding activity by using multivalent immune complexes composed of anti-dinitrophenyl monoclonal mouse IgG1 (ANO6) and dinitrophenyl conjugated to human serum albumin (DNP-HSA). Assays were also carried out with an anti-moFc gamma RII monoclonal rat IgG (2.4G2). The peptides that interacted with these antibodies prompted the synthesis of two soluble peptides: peptide A [Fc gamma RII-(108-119), RCHSWRNKLLNRamide] and peptide B [Fc gamma RII-(153-165), CKGSLGRTLHQSKamide]. Monomeric S-alkylated (A, B), homodimeric (AA, BB), heterodimeric (AB), and scrambled homodimeric (CC, DD) forms of these peptides were synthesized and examined for their ability to inhibit immune-complex binding to immobilized soluble Fc gamma RII. Peptides AA and CC completely inhibited immune-complex binding while each of the other peptides partially inhibited binding (AB, 80%; A, 80%; BB, 65%; DD, 64%; B, 52%). The pair of monomeric moFc gamma RII peptides and the set of five dimeric peptides showed the same increase in binding inhibition with increasing net positive charge per residue. These results suggest that the Fc region of IgG binds to the solvent-exposed B/C and F/G loops of the moFc gamma RII receptor through predominantly electrostatic forces.

Photochemical energy conversion in a helical oligoproline assembly.

A general method is described for constructing a helical oligoproline assembly having a spatially ordered array of functional sites protruding from a proline-II helix. Three different redox-active carboxylic acids were coupled to the side chain of cis-4-amino-L-proline. These redox modules were incorporated through solid-phase peptide synthesis into a 13-residue helical oligoproline assembly bearing in linear array a phenothiazine electron donor, a tris(bipyridine)ruthenium(II) chromophore, and an anthraquinone electron acceptor. Upon transient 460-nm irradiation in acetonitrile, this peptide triad formed with 53% efficiency an excited state containing a phenothiazine radical cation and an anthraquinone radical anion. This light-induced redox-separated state had a lifetime of 175 ns and stored 1.65 eV of energy.

The linked phi psi chain plot for visual comparison of the backbone conformation of peptides and proteins.

A new graphic method is described for presenting in two dimensions the phi and psi dihedral angles that describe the backbone conformation of a peptide or protein chain. For each residue in sequence, phi and psi are plotted as dots on the y-axis above the next two points on the x-axis representing the residue number. Each dot is linked to the next dot by a slanting line segment (link) and each cis-peptide bond (omega approximately 0 degrees) between residues X and Y is indicated by marking dots psi X and phi Y with a diamond. This linked phi psi chain plot is more useful than an unlinked phi psi chain plot for visually recognizing helices, sheets and turns and for graphically comparing several protein structures. Overlaying the linked phi psi chain plots for 15 beta-hairpins classified as type-I' beta-turns revealed that three were significantly different from the rest. The dihedral angles (mean +/- standard deviation) of the loop residues (L1, L2) for a cluster of 12 beta-hairpins with an inverse-common, type-I' beta-turn (phi L1 = 52 +/- 7 degrees, psi L1 = 40 +/- 8 degrees, phi L2 = 80 +/- 9 degrees, psi L2 = -1 +/- 13 degrees) are similar to the standard dihedral angles for the type-1' turn (60, 30, 90 and 0 degrees, respectively).

Engineering of five 88-residue receptor-adhesive modular proteins containing a parallel alpha-helical coiled coil and two RGD ligand sites.

Several 88-residue proteins were designed, synthesized and examined as receptor-adhesive modular proteins (RAMPs). Three covalent and two noncovalent dimers were made from two 44-residue peptide chains containing three structural modules: RGD-A23a (ligand-spacer-coil) and A9a-RGD (coil-spacer-ligand). The ligand module contained the tripeptide Arg-Gly-Asp (RGD). The coil modules A9a and A23a were five-heptad alpha-helices engineered by Hodges and co-workers [Int. J. Peptide Protein Res. (1992) 40, 171-179]. By circular dichroic spectroscopy, each of these five RAMPs contained an alpha-helical coiled coil. The disulfide-bridged dimer RGD-A23a/RGD-A23a and its reduced form (RGD-A23a)2 had two N-terminal RGD sites. The disulfide-bridged dimer A9a-RGD/A9a-RGD and its reduced form (A9a-RGD)2 had two C-terminal RGD sites. However, the disulfide-bridged heterodimer RGD-A23a/A9a-RGD had one RGD site at each terminus with a 50 Angstrum coiled coil between them. The temperature at the midpoint of unfolding for each of the covalent homodimers RGD-A23a/RGD-A23a (67 degrees C) and A9a-RGD/A9a-RGD (69 degrees C) was slightly higher than that of the corresponding noncovalent homodimer (RGD-A23a)2 (62 degrees C) or (A9a-RGD)2 (68 degrees C) but much lower than that of the covalent heterodimer RGD-A23a/A9a-RGD (79 degrees C). The enthalpy and entropy of thermal unfolding were also significantly greater for the heterodimer than for the four homodimers, consistent with the heterodimer having the most stable coiled coil. Although the distance between its RGD sites was at least 50 Angstrum greater than that for the homodimers, this heterodimeric RAMP was only as active as the homodimers A9a-RGD/A9a-RGD and (A9a-RGD)2 in inhibiting the adhesion of A2058 melanoma cells to extracellular matrix proteins.(ABSTRACT TRUNCATED AT 250 WORDS)

Self-association of a synthetic peptide from the N terminus of the hepatitis delta virus protein into an immunoreactive alpha-helical multimer.

The formation of hepatitis delta antigen (HDAg) multimers is required for full biologic activity of this protein and for replication of the hepatitis delta virus. To determine the residues responsible for multimerization, three peptides [ delta 12-49, delta 25-60(Y), delta 12-60(Y)] from the putative coiled-coil multimer-forming domain of HDAg were chemically synthesized and biophysically characterized by circular dichroic spectroscopy, deuterium-exchange mass spectrometry, gel filtration, chemical crosslinking, and ultracentrifugation. By circular dichroism the 50-residue peptide delta 12-60(Y) was half-denatured above 80 degrees C and was 97% alpha-helical at 5 degrees C and 84% alpha-helical at 37 degrees C. By deuterium exchange, peptide delta 12-60(Y) was 93% alpha-helical at 25 degrees C. Its high alpha-helicity and melting temperature are due to the formation of an alpha-helical multimer consisting of four or more chains. All three synthetic peptides reacted with human anti-HDAg antibodies in an enzyme-linked immunosorbent assay, but only peptide delta 12-60(Y) was detected in a sandwich radioimmunoassay in which successful antigens must display at least two antibody-binding sites, which correlates with the ability of this peptide to form multimers. Peptide delta 12-60(Y) also interfered with the self-association of natural HDAg into multimers. These results have significant practical implications for development of improved diagnostic tests, antiviral agents, and possibly even vaccines for prevention of hepatitis delta virus disease.

Designed polyanionic coiled-coil proteins: acceleration of heparin cofactor II inhibition of thrombin.

Novel polyanionic proteins were designed to increase the rate of heparin cofactor II (HC) inhibition of alpha-thrombin, an essential protease in the coagulation cascade. Two alpha-helical coiled-coil proteins, a 62-residue dimer containing 8 Glu residues (E8C) and a 104-residue dimer containing 14 Glu residues (E14C), plus two 31-residue control peptides containing 8 Glu residues each (E8A and E8B), were chemically synthesized, structurally characterized and enzymatically assayed. Circular dichroic spectrophotometry indicated that both E8C and E14C formed stable two-chain alpha-helical coiled coils at pH 7 and 25 degrees C. The control peptides were only partially alpha-helical. E14C remained folded at 90 degrees C but E8C was half unfolded at 49 degrees C. Coiled-coil proteins E8C and E14C maximally accelerated by 35- and 33-fold, respectively, the rate of HC inhibition of alpha-thrombin. None of these compounds accelerated antithrombin inhibition of alpha-thrombin, and neither control peptide accelerated HC inhibition of alpha-thrombin. Acceleration of the HC inhibition of alpha-thrombin showed bimodal dependence on the concentration of the polyanionic protein, which is consistent with formation of a HC-coiled-coil-thrombin ternary complex. The results suggest that antithrombotic polyanionic alpha-helical coiled-coil proteins can be designed and synthesized and that the occurrence of secondary structure can be correlated with biological activity.

Deuterium exchange of alpha-helices and beta-sheets as monitored by electrospray ionization mass spectrometry.

Deuterium exchange was monitored by electrospray ionization mass spectrometry (ESI-MS) to study the slowly exchanging (hydrogen bonded) peptide hydrogens of several alpha-helical peptides and beta-sheet proteins. Polypeptides were synthetically engineered to have mainly disordered, alpha-helical, or beta-sheet structure. For 3 isomeric 31-residue alpha-helical peptides, the number of slowly exchanging hydrogens as measured by ESI-MS in 50% CF3CD2OD (pD 9.5) provided estimates of their alpha-helicities (26%, 40%, 94%) that agreed well with the values (17%, 34%, 98%) measured by circular dichroic spectroscopy in the same nondeuterated solvent. For 3 betabellins containing a pair of beta-sheets and a related disordered peptide, their order of structural stability (12D > 12S > 14D > 14S) shown by their deuterium exchange rates in 10% CD3OD/0.5% CD3CO2D (pD 3.8) as measured by ESI-MS was the same as their order of structural stability to unfolding with increasing temperature or guanidinium chloride concentration as measured by circular dichroic spectroscopy in water. Compared to monitoring deuterium exchange by proton NMR spectrometry, monitoring deuterium exchange by ESI-MS requires much less sample (1-50 micrograms), much shorter analysis time (10-90 min), and no chemical quenching of the exchange reaction.

Engineering of betabellin 14D: disulfide-induced folding of a beta-sheet protein.

The betabellin target structure consists of 2 32-residue beta sheets packed against each other by hydrophobic interactions. We have designed, chemically synthesized, and biophysically characterized betabellin 14S, a single chain, and betabellin 14D, the disulfide-bridged double chain. The 32-residue nongenetic betabellin-14 chain (HSLTASIkaLTIHVQakTATCQVkaYTVHISE, a = D-Ala, k = D-Lys) has a palindromic pattern of polar (p), nonpolar (n), end (e), and beta-turn (t,r) residues (epnpnpnttnpnpnprrpnpnpnttnpnpnpe). Each half contains the same 14-residue palindromic pattern (underlined). Pairs of D-amino acid residues are used to favor formation of inverse-common (type-I') beta turns. In water at pH 6.5, the single chain of betabellin 14S is not folded, but the disulfide-linked betabellin 14D is folded into a stable beta-sheet structure. Thus, folding of the covalent dimer beta-bellin 14D is induced by formation of the single interchain disulfide bond. The binary pattern of alternating polar and nonpolar residues of its beta-sheets is not sufficient to induce folding. Betabellin 14D is a very water-soluble (10 mg/mL), small (64 residues), nongenetic (12 D residues) beta-sheet protein with properties (well-dispersed proton NMR resonances; Tm = 58 degrees C and delta Hm = 106 kcal/mol at pH 5.5) like those of a native protein structure.

Rational design of a three-heptad coiled-coil protein and comparison by molecular dynamics simulation with the GCN4 coiled coil: presence of interior three-center hydrogen bonds.

alpha-Helical coiled coils have a 7-residue repeating pattern (abcdefg) where a and d are usually hydrophobic. We have designed a 2-stranded 44-residue coiled-coil protein (P44) consisting of 2 22-residue alpha-helices linked by 2 terminal disulfide groups to test whether the disulfide bridges could stabilize a 3-heptad coiled coil. P44 should be stabilized by intrahelical hydrogen bonds, interhelical disulfide and salt bridges, and interior hydrophobic interactions. A computer model of P44 was built and its stability was studied by molecular dynamics simulation with explicit water. This doubly crosslinked 3-heptad coiled coil did not unfold during a 300-ps simulation with explicit water. This doubly crosslinked 3-heptad coiled coil did not unfold during a 300-ps simulation. But reduced P44 with 4 thiol groups did unfold. For comparison, the 62-residue crystal structure of the 4-heptad coiled coil of transcription activator GCN4 did not unfold during a 300-ps simulation. Thus P44 may be a stable folded protein in aqueous solution. These simulations revealed the presence of 2 local hydrogen bond networks involving intra-helical 3-center hydrogen bonds in the hydrophobic interior of the coiled coils of GCN4 and P44. The NH hydrogen at d makes a 3-center hydrogen bond whose major component is to the i - 4 C = O oxygen at g and minor component is to the solvent-inaccessible i - 3 C = O oxygen at a. Likewise, the NH hydrogen at g makes a 3-center hydrogen bond with the i - 4 C = O oxygen at c and the buried i - 3 C = O oxygen at d.

Mapping of the alpha-actinin binding site within the beta 1 integrin cytoplasmic domain.

The actin cross-linking protein alpha-actinin binds to the cytoplasmic domain of the beta 1 subunit of integrin, suggesting that alpha-actinin may form a direct link between the actin cytoskeleton and the transmembrane fibronectin receptor. In this study, we have used short synthetic peptides to localize the binding site for alpha-actinin within the cytoplasmic domain of beta 1 integrin. Four 13-residue peptides were tested in both an affinity chromatographic assay and a solid-phase binding assay. The results indicated that two regions of sequence contribute to the binding of alpha-actinin: one near where the beta 1 cytoplasmic tail emerges from the membrane and a second segment located near the C terminus of the cytoplasmic tail. This binding pattern was investigated in more detail using an adaptation of the mimotope assay, in which each of the 32 overlapping sequential decapeptide segments from the beta 1 cytoplasmic domain was assembled on the head of a different plastic pin. The peptide-pin constructs were used to detect the binding of 125I-alpha-actinin. As predicted from our initial results, alpha-actinin was found to bind to two distinct clusters of peptide segments. This represents a novel use of the mimotope pin assay to map interactive sites on structural proteins.

Superpotent synthetic tripeptide mimics of the mud-crab pumping pheromone.

Soluble pheromones released by the mud crab, Rhithropanopeus harrisii (Gould) during egg hatching cause the female crab to contract her abdomen rapidly (the pumping response). This stereotypical behavior can be induced in the laboratory by exposing egg-bearing females to solutions containing certain amino acids or peptides. Twelve amino acids exhibited response thresholds of 10(-3)-10(-10) M, the most potent (norleucine, methionine and tryptophan) having a hydrophobic sidechain. Four synthetic tripeptides of the form Gly-X-Arg, where the hydrophobic residue X was isoleucine, norleucine, methionine or phenylalanine, were superpotent agonists over a limited concentration range. Gly-Ile-Arg was a significant agonist at 10(-17) and 10(-16) M, both Gly-Nle-Arg and Gly-Met-Arg at 10(-20) and 10(-19) M, and Gly-Phe-Arg at 10(-21), 10(-20) and 10(-19) M. At the subattomolar concentration of 10(-20) M the superpotent pheromone mimics Gly-Met-Arg and Gly-Phe-Arg produced not only a statistically significant increase in the relative number of pumping mud crabs but also a substantial increase in the pumping rate ratio. In contrast, at 10(-13) M the tripeptide Gly-Met(O)-Arg with an internal residue of methionine sulfoxide blocked the abdominal pumping response of egg-bearing mud crabs.

Free energies for refolding of the common beta turn into the inverse-common beta turn: simulation of the role of D/L chirality.

Quantitative estimates of the Gibbs free-energy change (delta G) for refolding of one beta-turn conformation into another would assist rational protein design. For beta-turn models, we studied a chirally representative set of nine peptides of the form CH3CO-L1-L2-NHCH3, where loop residues L1 (i + 1) and L2 (i + 2) are achiral Gly (G), L-Ala (A), or D-Ala (a). The stabilities of their common (type I) and inverse-common (type I') beta-turn conformers (GGI is the type-I GG conformer, etc.) were estimated by free-energy simulations using explicit water molecules. An alpha-hydrogen atom of a Gly residue at L1 or L2 was replaced by a methyl group by slow growth. The resulting conformers were less stable than GGI and GGI' by about 1-3 kcal/mol (delta G = 0.9 kcal/mol for AGI and aGI', 1.0 kcal/mol for GAI and GaI', 2.1 kcal/mol for aGI and AGI', and 2.8 kcal/mol for GaI and GAI'; 1 kcal = 4.18 kJ). The delta G value for simultaneous growth of one methyl group at L1 and another at L2 was the sum of the two component delta G values. The delta G values for I-->I' refolding of the common beta-turn conformer into the inverse-common beta-turn conformer ranged over 6 kcal/mol (-3.0 for aa, -1.8 for Ga, -1.1 for aG, -0.7 for Aa, 0 for GG, 0.7 for aA, 1.1 for AG, 1.8 for GA, and 3.0 for AA). Thus, replacing L-Ala by D-Ala at both L1 and L2 of a common beta turn may contribute as much as 6 kcal/mol toward its refolding as an inverse-common beta turn.

Differentiation between selected pairs of tripeptide diastereomers by tandem mass spectrometry on a hybrid tandem mass spectrometer.

Low-energy collisionally activated decomposition (CAD) and unimolecular decomposition of the [M+H]+ ions for X-L-Pro-L-Phe, where X is L-Ala, D-Ala, L-Asp, or D-Asp, allow easy differentiation between the LLL and DLL diastereomers. Tandem mass spectrometric (MS/MS) studies of the [M+H]+ ions formed by fast-atom bombardment (FAB) at various ion kinetic energies (Elab values) on a hybrid tandem instrument produced ions of different intensities for the diastereomers. The ratio of NH3 to H2O loss is 0.3 for the L-Ala peptide but 1.7 for the D-Ala isomer at 5 eV. In some L-Ala spectra, the [M+H-NH3]+ ion does not appear at all. The y2 ion is up to twice as abundant in the L-Ala spectra as in the D-Ala, while the b2 ion is somewhat more abundant for CAD of the D-Ala peptide for most collision energies investigated. The D-Asp peptide produces a b2 ion that is more than half-again as abundant as in the case of the L-Asp isomer, and an [M+H-H2O]+ ion that is up to twice as abundant in the D-Asp CAD spectra as in those of the L-Asp. The y1, a2, and phenylalanine immonium ions are each up to twice as abundant in the L-Asp spectra as in those of the D-Asp isomer. The major differences are correlated with force-field calculations on hydrogen-bonded tautomers.

Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992.

Looking at proteins is an active process of interpretation and selection, emphasizing some features and deleting others. Multiple representations are needed, for such purposes as showing motions or conveying both the chain connectivity and the three-dimensional shape simultaneously. In studying and comparing protein structures, ideas are suggested about the determinants of tertiary structure and of folding (e.g., that Greek key beta barrels may fold up two strands at a time). The design and synthesis of new proteins "from scratch" provides a route toward the experimental testing of such ideas. It has also been a fruitful new perspective from which to look at structures, requiring such things as statistics on very narrowly defined structural categories and explicit attention to "negative design" criteria that actively block unwanted alternatives (e.g., reverse topology of a helix bundle, or edge-to-edge aggregation of beta sheets). Recently, the field of protein design has produced a rather unexpected general result: apparently we do indeed know enough to successfully design proteins that fold into approximately correct structures, but not enough to design unique, native-like structures. The degree of order varies considerably, but even the best designed material shows multiple conformations by NMR, more similar to a "molten globule" folding intermediate than to a well ordered native tertiary structure. In response to this conclusion, we are now working on systems that test useful questions with approximate structures (such as determining which factors most influence the choice of helix-bundle topology) and also analyzing how natural proteins achieve unique core conformations (e.g., for side chains on the interior side of a beta sheet, illustrated in the kinemages).

Synthesis of redox derivatives of lysine and related peptides containing phenothiazine or tris(2,2'-bipyridine)ruthenium(II).

Boc-L-Lysine derivatives and lysine-containing peptides bearing the electron donor 10H-phenothiazine (PTZ) or the redox chromophore tris(2,2'-bipyridine)ruthenium(II) dication ([Rub3]2+, where b is 2,2'-bipyridine) have been synthesized and characterized. SeO2 oxidation (53% yield) of 4,4'-dimethyl-2,2'-bipyridine, Ag2O oxidation (85% yield) of the monoaldehyde, complexation (96% yield) of 4'-methyl-2,2'-bipyridine-4-carboxylic acid (m-OH) with Rub2Cl2, activation (81% yield) of the acid [Rub2m-OH]2+ (PF6-)2, and condensation (83% yield) of the succinimido ester [Rub2m-OSu]2+ (PF6-)2 with Boc-Lys furnished the protected redox-chromophore module [Boc-Lys(Rub2m)-OH]2+ (PF6-)2 in 29% overall yield over five steps. The first two steps constitute the first practical synthesis of the monocarboxylic acid m-OH (45% overall yield). Also prepared were m-OSu, Boc-Lys(m)-OH, Boc-Lys(m)-OCH3, and [Rub2m-NHCH3]2+ (PF6-)2. Activation (91% yield) of 3-(10H-phenothiazine-10)propanoic acid (PTZpn-OH) and condensation (92% yield) of the succinimido ester PTZpn-OSu with Boc-Lys furnished the protected electron-donor module Boc-Lys(PTZpn)-OH (84% overall yield). The latter was used in solid-phase syntheses of two redox tripeptides, CH3CO-Ala-Lys(PTZpn)-Ala-OH and [Rub2m-Ala-Lys(PTZpn)-Ala-OH]2+ (PF6-)2. The electrochemical properties of these redox amino acids and peptides were similar to those of PTZpn-OH, [Rub2m-OH]2+ (PF6-)2, or [Rub2m-NHCH3]2+ (PF6-)2. Lys(PTZpn), [Lys(Rub2m)]2+ (PF6-)2, and other redox modules may be useful for engineering light-harvesting proteins, photovoltaic cells, and other molecular electronic devices.