Weakly polar interactions in proteins

Possible ligand-receptor interactions for NK1 antagonists as observed in their crystal structures

Crystal structures of nine non-peptide tachykinin NK1 antagonists have been analysed for the intermolecular interactions of their pharmacophoric groups with neighbouring molecules in the crystals. Experimental data on interaction geometries of these antagonists with their environment can be of help in understanding the mechanism of binding to the human NK1 receptor. Several interaction geometries have been identified that are consistent with both structure-activity relationships and reported receptor interactions for the compounds analysed. In addition, an interaction site for the side-chain of Gln-165 in the human NK1 receptor that is probably involved in donating a hydrogen bond to the benzylamino nitrogen or benzylether oxygen of the quinuclidine and piperidine antagonists is explicitly postulated. Also, a superposition based on pharmacophoric elements in the crystal structure conformations of two prototypic NK1 antagonists, CP-96,345 (1) and CP-99,994 (4), suggests how both compounds might interact with the human NK1 receptor in a similar manner.

The estradiol pharmacophore: ligand structure-estrogen receptor binding affinity relationships and a model for the receptor binding site

The accumulated knowledge on the binding of estradiol (E2) and its analogs and the results of affinity-labeling studies have been reviewed and are used herein to derive a binding site model for the estrogen receptor (ER). Estradiol is nonpolar and hydrophobic, except at its molecular termini. Most of its skeletal flexibility resides in the B-ring, and it probably binds in a low-energy conformation. The phenolic OH group in the A-ring contributes about 1.9 kcal/mol to the binding free energy and probably acts primarily as a hydrogen bond donor. The 17 beta-hydroxyl group in the D-ring contributes approximately 0.6 kcal/mol to the binding and probably acts as a hydrogen bond acceptor, either directly or via a water molecule. There also seems to be a degree of flexibility in the region of the receptor that encompasses the D-ring. The aromatic ring contributes about 1.5 kcal/mol, probably through weak polar interactions with receptor residues that contact the beta-face of the steroid. The receptor seems to surround the ligand, so that all four rings contribute significantly to binding. Small hydrophobic substituents enhance binding affinity at positions 4, 12 beta, 14, and 16 alpha; whereas, larger hydrophobic substituents are tolerated at positions 7 alpha, 11 beta, and 17 alpha. In general, the ER is intolerant of polar substituents. Based on E2 analogs bearing affinity-labeling groups, cysteine residues might be present in the binding site in the area of C-4, C-17 alpha, and C-17 beta, and a lysine residue might be located near C-16. Models that represent the limits of deformability of the ligand binding site, the position of preformed pockets, and space occupied by the receptor are presented. The various elements in this model for the binding of steroidal estrogens by the estrogen receptor are consistent with evidence emerging from the crystal structures of related nuclear hormone receptor ligand complexes.

Enzymes from cold-adapted microorganisms. The class C beta-lactamase from the antarctic psychrophile Psychrobacter immobilis A5

A heat-labile beta-lactamase has been purified from culture supernatants of Psychrobacter immobilis A5 grown at 4 degrees C and the corresponding chromosomal ampC gene has been cloned and sequenced. All structural and kinetic properties clearly relate this enzyme to class C beta-lactamases. The kinetic parameters of P. immobilis beta-lactamase for the hydrolysis of some beta-lactam antibiotics are in the same range as the values recorded for the highly specialized cephalosporinases from pathogenic mesophilic bacteria. By contrast, the enzyme displays a low apparent optimum temperature of activity and a reduced thermal stability. Structural factors responsible for the latter property were analysed from the three-dimensional structure built by homology modelling. The deletion of proline residues in loops, the low number of arginine-mediated H-bonds and aromatic-aromatic interactions, the lower global hydrophobicity and the improved solvent interactions through additional surface acidic residues appear to be the main determinants of the enzyme flexibility.

Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation

Residue-specific potentials between pairs of side-chains and pairs of side-chain-backbone interaction sites have been generated by collecting radial distribution data for 302 protein structures. Multiple atomic interactions have been utilized to enhance the specificity and smooth the distance-dependence of the potentials. The potentials are demonstrated to successfully discriminate correct sequences in inverse folding experiments. Many specific effects are observable in the non-bonded potentials; grouping of residue types is inappropriate, since each residue type manifests some unique behavior. Only a weak dependence is seen on protein size and composition. Effective contact potentials operating in three different environments (self, solvent-exposed and residue-exposed) and over any distance range are presented. The effective contact potentials obtained from the integration of radial distributions over the distance interval r < or = 6.4 A are in excellent agreement with published values. The hydrophobic interactions are verified to be dominantly strong in this range. Comparison of these with a newly derived set of effective contact potentials for closer inter-residue separations (r < or = 4.0 A) demonstrates drastic changes in the most favorable interactions. In the closer approach case, where the number of pairs with a given residue is approximately one, the highly specific interactions between charged and polar side-chains predominate. These closer approach values could be utilized to select successively the relative positions and directions of residue side-chains in protein simulations, following a hierarchical algorithm optimizing side-chain-side-chain interactions over the two successively closer distance ranges. The homogeneous contribution to stability is stronger than the specific contribution by about a factor of 5. Overall, the total non-bonded interaction energy calculated for individual proteins follows a dependence on the number of residues of the form of n1.28, indicating an enhanced stability for larger proteins.

A comparison of the crystal packing in benzene with the geometry seen in crystalline cyclophane-benzene complexes: guidelines for rational receptor design

Self-recognition in crystalline benzene is compared with the recognition of benzene in inclusion complexes of three cyclophane receptors. It is shown that the structural organization of aromatic rings, which determines the packing in the molecular crystal and the binding geometry in the preorganized cavity of the cyclophane host molecules, follows the same principles. It is concluded that the examination of the spatial requirements of the aromatic-aromatic interaction motifs found in crystals should allow one to design host bonding skeletons with high binding selectivity and affinity for a specific aromatic guest.

The structural and functional basis of antibody catalysis

Ten years have passed since the initial reports that antibodies could be programmed to have enzymatic activity by immunization with a transition-site analog. Much of the research over the last decade has focused on defining the scope and generality of antibody catalysis; however, during the past two years the first few crystal structures of catalytic antibody transition-state analogs have been reported. This review analyzes four such structures of catalytic antibodies that catalyze markedly different reactions, including ester hydrolysis, sulfide oxidation, and a pericyclic rearrangement. Structure-function relations for these catalysts are discussed and compared to the structure and function of natural enzymes, as well as the chemistry that occurs in solution.

Dynamics of a type VI reverse turn in a linear peptide in aqueous solution

BACKGROUND

Peptide sequences with aromatic groups flanking a cis-proline residue are known to have a high propensity for adopting compact structures in which the aromatic sidechains pack against the proline ring. In particular, the sequence Ser-Tyr-Pro-Phe-Asp-Val (and variants of this) is known by NMR to form a high proportion of type VI turns in aqueous solution. We set out to explore the energetic and dynamic features of such sequences using molecular dynamics simulation techniques.

RESULTS

The conformation properties of the linear pentapeptide NH3(+)-Ala-Tyr-cisPro-Tyr-Asp-NMA (cis-AYPYD) have been explored in three solvated molecular dynamics simulations. The first began from an NMR-derived model structure containing a type VIa turn and close-stacking interactions between the tyrosine and proline sidechains. During 20 ns of simulation, the peptide made transitions between type VIa and VIb turns, but did not 'unfold' to more extended conformers, consistent with the unusual stability for folded forms observed by NMR for this sequence. Distances monitored by nuclear Overhauser peaks and sidechain rotamer populations in the trajectory are in good agreement with NMR data. Two additional 5 ns trajectories were begun from more extended conformers. The first folded into a conformer much like the NMR-derived structure within 3 ns and remained folded for the remainder of the trajectory. The second was begun from a structure in which the sidechain orientations were deliberately misfolded relative to that required for turn formation; this structure did not make a transition to a turn-like state.

CONCLUSIONS

The kinetic stability of folded forms of AYPYD, along with the observation of spontaneous folding from an extended conformation, indicates that the special stability seen experimentally is reflected in computer simulations. The results provide new information about the stabilization of secondary structure in short peptides, particularly by aromatic-proline interactions, and offer a description of pathways of interconversion of type VIa and VIb turns.

The measurement of molecular diversity: a three-dimensional approach

This paper describes a method for selecting a small, highly diverse subset from a large pool of molecules. The method has been employed in the design of combinatorial synthetic libraries for use in high-throughput screening for pharmaceutical lead generation. It computes diversity in terms of the main factors relevant to ligand-protein binding, namely the three-dimensional arrangement of steric bulk and of polar functionalities and molecular entropy. The method was used to select a set of 20 carboxylates suitable for use as side-chain precursors in a polyamine-based library. The method depends on estimates of various physical-chemical parameters involved in ligand-protein binding; experiments examined the sensitivity of the method to these parameters. This paper compares the diversity of randomly and rationally selected side-chain sets; the results suggest that careful design of synthetic combinatorial libraries may increase their effectiveness several-fold.

Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator

Ying-Yang 1 protein (YY1) supports specific, unidirectional initiation of messenger RNA production by RNA polymerase II from two adjacent start sites in the adeno-associated virus P5 promoter, a process which is independent of the TATA box-binding protein (TBP). The 2.5-A resolution YY1-initiator element cocrystal structure reveals four zinc fingers recognizing a YY1-binding consensus sequence. Upstream of the transcription start sites protein-DNA contacts involve both strands and downstream they are virtually restricted to the template strand, permitting access to the active center of RNA polymerase II and ensuring specificity and directionality. The observed pattern of protein-DNA contacts also explains YY1 binding to a preformed transcription bubble, and YY1 binding to a DNA/RNA hybrid analog of the P5 promoter region containing a nascent RNA transcript. A model is proposed for YY1-directed, TBP-independent transcription initiation.

Characterization of a buried neutral histidine residue in Bacillus circulans xylanase: NMR assignments, pH titration, and hydrogen exchange

Bacillus circulans xylanase contains two histidines, one of which (His 156) is solvent exposed, whereas the other (His 149) is buried within its hydrophobic core. His 149 is involved in a network of hydrogen bonds with an internal water and Ser 130, as well as a potential weak aromatic-aromatic interaction with Tyr 105. These three residues, and their network of interactions with the bound water, are conserved in four homologous xylanases. To probe the structural role played by His 149, NMR spectroscopy was used to characterize the histidines in BCX. Complete assignments of the 1H, 13C, and 15N resonances and tautomeric forms of the imidazole rings were obtained from two-dimensional heteronuclear correlation experiments. An unusual spectroscopic feature of BCX is a peak near 12 ppm arising from the nitrogen bonded 1H epsilon 2 of His 149. Due to its solvent inaccessibility and hydrogen bonding to an internal water molecule, the exchange rate of this proton (4.0 x 10(-5) s-1 at pH*7.04 and 30 degrees C) is retarded by > 10(6)-fold relative to an exposed histidine. The pKa of His 156 is unperturbed at approximately 6.5, as measured from the pH dependence of the 15N- and 1H-NMR spectra of BCX. In contrast, His 149 has a pKa < 2.3, existing in the neutral N epsilon 2H tautomeric state under all conditions examined. BCX unfolds at low pH and 30 degrees C, and thus His 149 is never protonated significantly in the context of the native enzyme. The structural importance of this buried histidine is confirmed by the destablizing effect of substituting a phenylalanine or glutamine at position 149 in BCX.

Crystal structure of the hepatitis C virus NS3 protease domain complexed with a synthetic NS4A cofactor peptide

An estimated 1% of the global human population is infected by hepatitis C viruses (HCVs), and there are no broadly effective treatments for the debilitating progression of chronic hepatitis C. A serine protease located within the HCV NS3 protein processes the viral polyprotein at four specific sites and is considered essential for replication. Thus, it emerges as an attractive target for drug design. We report here the 2.5 angstrom resolution X-ray crystal structure of the NS3 protease domain complexed with a synthetic NS4A activator peptide. The protease has a chymotrypsin-like fold and features a tetrahedrally coordinated metal ion distal to the active site. The NS4A peptide intercalates within a beta sheet of the enzyme core.

Evolutionary relationships among extradiol dioxygenases

A structure-validated alignment of 35 extradiol dioxygenase sequences including two-domain and one-domain enzymes was derived. Strictly conserved residues include the metal ion ligands and several catalytically essential active site residues, as well as a number of structurally important residues that are remote from the active site. Phylogenetic analyses based on this alignment indicate that the ancestral extradiol dioxygenase was a one-domain enzyme and that the two-domain enzymes arose from a single genetic duplication event. Subsequent divergence among the two-domain dioxygenases has resulted in several families, two of which are based on substrate preference. In several cases, the two domains of a given enzyme express different phylogenies, suggesting the possibility that such enzymes arose from the recombination of genes encoding different dioxygenases. A phylogeny-based classification system for extradiol dioxygenases is proposed.

Functional mimicry of a protein hormone by a peptide agonist: the EPO receptor complex at 2.8 A

The functional mimicry of a protein by an unrelated small molecule has been a formidable challenge. Now, however, the biological activity of a 166-residue hematopoietic growth hormone, erythropoietin (EPO), with its class 1 cytokine receptor has been mimicked by a 20-residue cyclic peptide unrelated in sequence to the natural ligand. The crystal structure at 2.8 A resolution of a complex of this agonist peptide with the extracellular domain of EPO receptor reveals that a peptide dimer induces an almost perfect twofold dimerization of the receptor. The dimer assembly differs from that of the human growth hormone (hGH) receptor complex and suggests that more than one mode of dimerization may be able to induce signal transduction and cell proliferation. The EPO receptor binding site, defined by peptide interaction, corresponds to the smaller functional epitope identified for hGH receptor. Similarly, the EPO mimetic peptide ligand can be considered as a minimal hormone, and suggests the design of nonpeptidic small molecule mimetics for EPO and other cytokines may indeed be achievable.

Three quaternary structures for a single protein

The structure of a multisubunit protein (immunoglobulin light chain) was solved in three crystal forms, differing only in the solvent of crystallization. The three structures were obtained at high ionic strength and low pH, high ionic strength and high pH, and low ionic strength and neutral pH. The three resulting "snapshots" of possible structures show that their variable-domain interactions differ, reflecting their stabilities under specific solvent conditions. In the three crystal forms, the variable domains had different rotational and translational relationships, whereas no alteration of the constant domains was found. The critical residues involved in the observed effect of the solvent are tryptophans and histidines located between the two variable domains in the dimeric structure. Tryptophan residues are commonly found in interfaces between proteins and their subunits, and histidines have been implicated in pH-dependent conformation changes. The quaternary structure observed for a multisubunit protein or protein complex in a crystal may be influenced by the interactions of the constituents within the molecule or complex and/or by crystal packing interactions. The comparison of buried surface areas and hydrogen bonds between the domains forming the molecule and between the molecules forming the crystals suggest that, for this system, the interactions within the molecule are most likely the determining factors.

Structure of the heme d of Penicillium vitale and Escherichia coli catalases

A heme d prosthetic group with the configuration of a cis-hydroxychlorin gamma-spirolactone has been found in the crystal structures of Penicillium vitale catalase and Escherichia coli catalase hydroperoxidase II (HPII). The absolute stereochemistry of the two heme d chiral carbon atoms has been shown to be identical. For both catalases the heme d is rotated 180 degrees about the axis defined by the alpha-gamma-meso carbon atoms, with respect to the orientation found for heme b in beef liver catalase. Only six residues in the heme pocket, preserved in P. vitale and HPII, differ from those found in the bovine catalase. In the crystal structure of the inactive N201H variant of HPII catalase the prosthetic group remains as heme b, although its orientation is the same as in the wild type enzyme. These structural results confirm the observation that heme d is formed from protoheme in the interior of the catalase molecule through a self-catalyzed reaction.

Structure and Activity of Membrane Receptors: Modeling and Computational Simulation of Ligand Recognition in a Three-Dimensional Model of the 5-Hydroxytryptamine(1A) Receptor

A three-dimensional molecular model of the transmembrane domain of the 5-HT(1A) receptor (5-HT(1A)R) is presented in the context of a general strategy for modeling the macromolecular structure of a guanine nucleotide binding, regulatory protein coupled receptor (GPCR). The model of the 5-HT(1A)R rests on the definition of the putative residues of the ligand-binding site guided by criteria based on specific models proposed from structure-activity studies and on published results of modifications of GPCRs using methods of molecular biology. The resulting requirements for matching recognition sites in the agonist-binding pocket define the molecular details of the interaction between the agonist 5-HT and the human 5-HT(1A)R that includes: (1) the interaction between the protonated amine moiety and the conserved negative Asp-116, located in TMH 3; (2) the hydrogen bond between the hydroxyl group and Thr-199, located in TMH 5; and (3) the interaction complex between the aromatic ring portion of the ligand and the neutral form of His-192, located in TMH 5. Results from quantum mechanical calculations of the interaction between an agonist and the proposed recognition pocket of the 5-HT(1A)R model suggest a trigger of the receptor activation mechanism resulting from ligand binding. The antagonist-binding pocket of the human 5-HT(1A)R is inferred from the interaction sites of pindolol with the receptor model: (1) the ionic interaction between the protonated amine of the ligand and the side chain of the conserved Asp-116, located in TMH 3; and (2) the hydrogen bonds between the ether oxygen and the hydroxyl group of the ligand and Asn-385, located in TMH 7. Use of the model is proposed to facilitate the identification of the structural elements of agonists and antagonists that are key for their specific functions, in order to achieve the design of new compounds with predetermined pharmacological properties. Copyright 1996 S. Karger AG, Basel

How are close residues of protein structures distributed in primary sequence?

Structurally neighboring residues are categorized according to their separation in the primary sequence as proximal (1-4 positions apart) and otherwise distal, which in turn is divided into near (5-20 positions), far (21-50 positions), very far ( > 50 positions), and interchain (from different chains of the same structure). These categories describe the linear distance histogram (LDH) for three-dimensional neighboring residue types. Among the main results are the following: (i) nearest-neighbor hydrophobic residues tend to be increasingly distally separated in the linear sequence, thus most often connecting distinct secondary structure units. (ii) The LDHs of oppositely charged nearest-neighbors emphasize proximal positions with a subsidiary maximum for very far positions. (iii) Cysteine-cysteine structural interactions rarely involve proximal positions. (iv) The greatest numbers of interchain specific nearest-neighbors in protein structures are composed of oppositely charged residues. (v) The largest fraction of side-chain neighboring residues from beta-strands involves near positions, emphasizing associations between consecutive strands. (vi) Exposed residue pairs are predominantly located in proximal linear positions, while buried residue pairs principally correspond to far or very far distal positions. The results are principally invariant to protein sizes, amino acid usages, linear distance normalizations, and over- and underrepresentations among nearest-neighbor types. Interpretations and hypotheses concerning the LDHs, particularly those of hydrophobic and charged pairings, are discussed with respect to protein stability and functionality. The pronounced occurrence of oppositely charged interchain contacts is consistent with many observations on protein complexes where multichain stabilization is facilitated by electrostatic interactions.

Identification of histatins as tannin-binding proteins in human saliva

Tannins have a number of detrimental biological effects and these include interference with normal growth and metabolism if they are present in the feed of various animals. Proline-rich proteins (PRPs) in saliva have been shown to provide protection against tannin, but little is known about the mechanism of protection and interaction of other salivary proteins with tannin. To identify tannin-binding human salivary proteins, parotid and submandibular/sublingual saliva samples were adsorbed with tannin. PRPs, and in particular a group of low-M(r) proteins, were readily precipitated by tannin. The low-M(r) proteins were purified from parotid saliva and demonstrated to be histatins, a family of well-characterized histidine-rich salivary proteins. The ability of synthetic histatin 5, as well as an acidic PRP (PRP-1) and gelatin to precipitate quebracho condensed tannin and tannic acid was determined. At pH 7.4 histatin 5 was the most effective precipitant of both condensed tannin and tannic acid and it also precipitated the largest amount of condensed tannin at pH 3.0, but the smallest amount of tannic acid at that pH. In contrast PRP-1 showed a greater ability to precipitate both condensed tannin and tannic acid at pH 3.0 than at pH 7.4. Under most circumstances histatin 5 was therefore more effective in precipitating tannins than proteins with high proline content which generally have been recognized as strong precipitants of tannin. Pre-incubation of tannic acid with alpha-amylase inhibited the enzyme, but addition of histatin 5 or the acidic PRP PIF-s protected amylase from inhibition by tannin. Similarly salivary proteins may protect other biological activities in the digestive tract from inhibition by dietary tannin.

Molecular modeling studies of HIV-1 reverse transcriptase nonnucleoside inhibitors: total energy of complexation as a predictor of drug placement and activity

Computer modeling studies have been carried out on three nonnucleoside inhibitors complexed with human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT), using crystal coordinate data from a subset of the protein surrounding the binding pocket region. Results from the minimizations of solvated complexes of 2-cyclopropyl-4-methyl-5,11-dihydro-5H-dipyrido[3,2-b :2',3'-e][1,4] diazepin-6-one (nevirapine), alpha-anilino-2, 6-dibromophenylacetamide (alpha-APA), and 8-chloro-tetrahydro-imidazo(4,5,1-jk)(1,4)-benzodiazepin-2(1H)-thi one (TIBO) show that all three inhibitors maintain a very similar conformational shape, roughly overlay each other in the binding pocket, and appear to function as pi-electron donors to aromatic side-chain residues surrounding the pocket. However, side-chain residues adapt to each bound inhibitor in a highly specific manner, closing down around the surface of the drug to make tight van der Waals contacts. Consequently, the results from the calculated minimizations reveal that only when the inhibitors are modeled in a site constructed from coordinate data obtained from their particular RT complex can the calculated binding energies be relied upon to predict the correct orientation of the drug in the pocket. In the correct site, these binding energies correlate with EC50 values determined for all three inhibitors in our laboratory. Analysis of the components of the binding energy reveals that, for all three inhibitors, solvation of the drug is endothermic, but solvation of the protein is exothermic, and the sum favors complex formation. In general, the protein is energetically more stable and the drug less stable in their complexes as compared to the reactant conformations. For all three inhibitors, interaction with the protein in the complex is highly favorable. Interactions of the inhibitors with individual residues correlate with crystallographic and site-specific mutational data. pi-Stacking interactions are important in binding and correlate with drug HOMO RHF/6-31G* energies. Modeling results are discussed with respect to the mechanism of complex formation and the design of nonnucleoside inhibitors that will be more effective against mutants of HIV-1 RT that are resistant to the currently available drugs.

A structural motif for the voltage-gated potassium channel pore

Mutation studies have identified a region of the S5-S6 loop of voltage-gated K+ channels (P region) responsible for teraethylammonium (TEA) block and permeation/selectivity properties. We previously modeled a similar region of the Na+ channel as four beta-hairpins with the C strands from each of the domains forming the external vestibule and with charged residues at the beta-turns forming the selectivity filter. However, the K+ channel P region amino acid composition is much more hydrophobic in this area. Here we propose a structural motif for the K+ channel pore based on the following postulates (Kv2.1 numbering). (i) The external TEA binding site is formed by four Tyr-380 residues; P loop residues participating in the internal TEA binding site are four Met-371 and Thr-372 residues. (ii) P regions form extended hairpins with beta-turns in sequence ITMT. (iii) only C ends of hairpins form the inner walls of the pore. (iv) They are extended nonregular strands with backbone carbonyl oxygens of segment VGYGD facing the pore with the conformation BRLRL. (v) Juxtaposition of P loops of the four subunits forms the pore. Fitting the external and internal TEA sites to TEA molecules predicts an hourglass-like pore with the narrowest point (GYG) as wide as 5.5 A, suggesting that selectivity may be achieved by interactions of carbonyls with partially hydrated K+. Other potential cation binding sites also exist in the pore.

Role of Tyr residues in the contact region of anti-lysozyme monoclonal antibody HyHEL10 for antigen binding

It has been shown that Tyr residues are unusually localized in the regions of antibodies responsible for contact with antigens (Padlan, E. A. (1990) Proteins Struct. Funct. Genet. 7, 112-124). In order to clarify the role of these Tyr residues in antigen binding, the interaction between hen egg white lysozyme (HEL) and its monoclonal antibody HyHEL10, whose structure has been well studied in complex with its antigen, was investigated. Four Tyr residues in the VH chain (HTyr-33, HTyr-50, HTyr-53, and HTyr-58) were replaced with Ala, Leu, Phe, or Trp, and the interactions between these mutant Fv fragments and HEL were studied by inhibition assay of the enzymatic activity of HEL and isothermal titration calorimetry. Twelve mutant Fv fragments could be expressed, but two mutants (HY50W and HY58W) could not be obtained in the Escherichia coli expression system, and a further two mutants (HY33A and HY50A) could not be purified by affinity chromatography. It was shown by inhibition assay that Tyr residues at each mutated site made positive contributions to the interaction to different degrees. Thermodynamic studies showed that the role of Tyr residues in antigen binding was to obtain enthalpic energy. The roles of Tyr residues in antibody HyHEL10 for the association with antigen, HEL, can be summarized as follows: 1) formation of hydrogen bonds by the hydroxyl group, 2), creating more favorable interactions through the aromatic ring and decreasing the entropic loss upon binding, and 3) allowing hydrophobic interaction through the side chain. The four Tyr residues studied here were found to play significant roles in the association in various ways.

Core domain of hirudin from the leech Hirudinaria manillensis: chemical synthesis, purification, and characterization of a Trp3 analog of fragment 1-47

Hirudin is a small (approximately 7 kDa) disulfide-cross-linked polypeptide known as the most potent and specific thrombin inhibitor. We have previously shown that the N-terminal proteolytic fragment 1-47 of hirudin HM2 from Hirudinaria manillensis maintains inhibitory action toward thrombin [Vindigni, A., et al. (1994) Eur. J. Biochem. 226, 323-333]. Here we report the solid-phase chemical synthesis of an analog of fragment 1-47 bearing a Tyr3-->Trp exchange (Y3W analog). The crude, reduced peptide was purified by reverse-phase HPLC and subjected to oxidative folding to the disulfide-cross-linked species. The folding process of the Y3W analog was slower than that of the natural fragment 1-47, but nevertheless still occurred almost quantitatively as the natural species. The overall final yield of the synthetic product was approximately 35%, and its identity and homogeneity was established by a number of analytical techniques, including electrospray mass spectometry. The unique alignment of the three disulfide bridges of the Y3W analog was established by peptide mapping as Cys6-Cys14, Cys16-Cys28, and Cys22-Cys37 and shown to be identical to that of the natural fragment. The results of far- and near-ultraviolet circular dichroism and fluorescence emission measurements provided evidence that the Y3W analog retains the structural features of the natural species. The thermodynamic quantities (delta GD, delta Hm, delta Sm, and delta Cp) characterizing the reversible and cooperative thermal unfolding processes of the Y3W analog (Tm = 60.5 degrees C) and the natural fragment species (Tm = 62.5 degrees C) were evaluated. Despite the relatively high Tm values, the stability of both fragment species at 37 degrees C was only approximately 10 kJ mol-1, well below the average 50 kJ mol-1 typical of single-domain globular proteins. The synthetic Y3W species was found to be approximately 5-fold more active (KI = 30 +/- 5 nM) than the natural fragment 1-47 (KI = 150 +/- 20 nM) in inhibiting thrombin. Of interest was that the difference in the free energies of binding to thrombin at 37 degrees C, delta delta Gb, between the Y3W analog and natural species (4.2 kJ mol-1) was that expected for the difference in hydrophobicity between the two polypeptides resulting from the Tyr-->Trp exchange. The results of this study indicate that solid-phase chemical synthesis represents a convenient and high-yield procedure to prepare analogs of the biologically active, N-terminal core domain of hirudin with improved functional properties.

Molecular modeling of the substrate specificity of prohormone convertases SPC2 and SPC3

In this paper we describe the results of molecular modeling of the structures of the active sites of two subtilisin-like prohormone convertases (SPCs), SPC2 (PC2) and SPC3 (PC1/PC3). These enzymes are members of a recently discovered family of cellular proteases involved in the processing of precursor proteins. Although these proteases all possess catalytic domains similar to the bacterial subtilisins no tertiary structural data from x-ray analysis are yet available. We have shown that despite the high structural homology of the subtilisins and the SPCs, the structure of the loop which lies immediately below the active sites differs due to the presence of a cis-peptide bond (Tyr167-Pro168) in this loop in the subtilisins and its absence in the SPCs. Accordingly, we have proposed a new alignment for the amino acid sequences of the SPCs in this region. Both SPC2 and SPC3 participate in the processing of prohormones at dibasic cleavage sites, typically Lys-Arg or Arg-Arg. To investigate the structural basis of the substrate specificity of these SPCs, we have carried out molecular mechanic calculations of the optimal arrangement and interactions of peptide substrates containing several residues of arginine or lysine, i.e. Arg, Ala-Ala-Ala-Arg, Arg-Ala-Ala-Arg, Arg-Ala-Arg-Arg, Arg-Ala-Lys-Arg, in the putative active sites. Such subtilisin-based modeling has allowed us to identify those negatively charged residues, Asp and Glu, in the S1, S2, and S4 subsites, which can directly interact with basic residues in the substrates via formation of salt bridges and thereby contribute to the substrate selectivity of the SPCs.

On the lack of coordination between protein folding and flavin insertion in Escherichia coli for flavocytochrome b2 mutant forms Y254L and D282N

Wild-type flavocytochrome b2 (L-lactate dehydrogenase) from Saccharomyces cerevisiae, as well as a number of its point mutants, can be expressed to a reasonable level as recombinant proteins in Escherichia coli (20-25 mg per liter culture) with a full complement of prosthetic groups. At the same expression level, active-site mutants Y254L and D282N, on the other hand, were obtained with an FMN/heme ratio significantly less than unity, which could not be raised by addition of free FMN. Evidence is provided that the flavin deficit is due to incomplete prosthetic group incorporation during biosynthesis. Flavin-free and holo-forms for both mutants could be separated on a Blue-Trisacryl M column. The far-UV CD spectra of the two forms of each mutant protein were very similar to one another and to that of the wild-type enzyme, suggesting the existence of only local conformational differences between the active holo-enzymes and the nonreconstitutable flavin-free forms. Selective proteolysis with chymotrypsin attacked the same bond for the two mutant holo-enzymes as in the wild-type one, in the protease-sensitive loop. In contrast, for the flavin-free forms of both mutants, cleavage occurred at more than a single bond. Identification of the cleaved bonds suggested that the structural differences between the mutant flavin-free and holo-forms are located mostly at the C-terminal end of the barrel, which carries the prosthetic group and the active site. Altogether, these findings suggest that the two mutations induce an alteration of the protein-folding process during biosynthesis in E. coli; as a result, the synchrony between folding and flavin insertion is lost. Finally, a preliminary kinetic characterization of the mutant holo-forms showed the Km value for lactate to be little affected; kcat values fell by a factor of about 70 for the D282N mutant and of more than 500 for the Y254L mutant, compared to the wild-type enzyme.

Benz[a]anthracene diols: predicted carcinogenicity and structure-estrogen receptor binding affinity relationships

Benz[a]anthracenes are ubiquitous environmental carcinogens that exert estrogenic and antiestrogenic effects directly or via hydroxylated metabolites. In this paper, the structure-estrogen receptor binding relationships of four 3,9-benz[a]anthracene diols are described: unsubstituted, 7-methyl, 12-methyl, and 7,12-dimethyl. Compounds unsubstituted at the 12-position have flat molecular topology, whereas methyl substitution at the 12-position in the bay region induces twisting of the molecular framework. The oxygen-oxygen distances (11.94-11.98 A) are similar to diethylstilbestrol (12.1 A). The binding affinities range from 0.43% to 26% that of estradiol. Methyl substitution at the 7-position enhances affinity; 12-methyl substitution decreases it. These results are contrary to many estrogen receptor (ER) ligand systems, in which the compounds with the flatter molecular geometries typically have lower binding affinity. Molecular graphics were used to analyze the fit of the four compounds with a receptor excluded volume model for the ER. These studies suggest that these compounds bind to the ER in a manner in which the anthracene fragment acts as the steroid AB-ring mimic (i.e, the benz[a]anthracene 9-position corresponds to the estradiol 3-position). Molecular orbital (AM1) calculations were used to calculate the charges of selected atoms. The 7-methyl compound was found to have greater charge similarity to estradiol than the other three compounds. The high affinity of the 7-methyl compound is ascribed to its charge similarity to estradiol, hydrophobic interactions in the receptor region that would accommodate a substituent in the planar 6-position of a delta 6,7-steroid, and favorable dispersive interactions with the receptor secondary to its extended planar system. Molecular orbital calculations also suggest that some of the benz[a]anthracene monophenols and diphenols have sufficiently low ionization potentials to act as carcinogens by a radical cation process.

Competing interactions contributing to alpha-helical stability in aqueous solution

The stability of a 15-residue peptide has been investigated using CD spectroscopy and molecular simulation techniques. The sequence of the peptide was designed to include key features that are known to stabilize alpha-helices, including ion pairs, helix dipole capping, peptide bond capping, and aromatic interactions. The degree of helicity has been determined experimentally by CD in three solvents (aqueous buffer, methanol, and trifluoroethanol) and at two temperatures. Simulations of the peptide in the aqueous system have been performed over 500 ps at the same two temperatures using a fully explicit solvent model. Consistent with the CD data, the degree of helicity is decreased at the higher temperature. Our analysis of the simulation results has focused on competition between different side-chain/side-chain and side-chain/main-chain interactions, which can, in principle, stabilize the helix. The unfolding in aqueous solution occurs at the amino terminus because the side-chain interactions are insufficient to stabilize both the helix dipole and the peptide hydrogen bonds. Loss of capping of the peptide backbone leads to water insertion within the first peptide hydrogen bond and hence unfolding. In contrast, the carboxy terminus of the alpha-helix is stable in both simulations because the C-terminal lysine residue stabilizes the helix dipole, but at the expense of an ion pair.

Structural basis of inhibitor affinity to variants of human carbonic anhydrase II

The activities and structures of certain L198 variants of human carbonic anhydrase II (CAII) have been reported recently [Krebs, J. F., Rana, F., Dluhy, R. A., & Fierke, C. A. (1993) Biochemistry 32, 4496-4505; Nair, S. K., & Christianson, D. W. (1993) Biochemistry 32, 4506-4514]. In order to understand the structural basis of enzyme-inhibitor affinity, we now report the dissociation rate and equilibrium constants for acetazolamide and dansylamide binding to 13 variants of CAII containing substituted amino acids at position 198. These data indicate that inhibitor affinity is modulated by the hydrophobicity and charge of the 198 side chain. Furthermore, we have determined crystal structures of L198R, L198E, and L198F CAIIs complexed with the transition state analog acetazolamide. The substituted benzyl side chain of L198F CAII does not occlude the substrate association pocket, and it is therefore not surprising that this substitution has minimal effects on catalytic properties and inhibitor binding. Nevertheless, the F198 side chain undergoes a significant conformation change in order to accommodate the binding of acetazolamide; the same behavior is observed for the engineered side chain of L198R CAII. In contrast, the engineered side chain of L198E CAII does not alter its conformation upon inhibitor binding. We conclude that the mobility and hydrophobicity or residue 198 side chains affect enzyme-inhibitor (and enzyme-substrate) affinity, and these structure-function relationships are important for understanding the behavior of carbonic anhydrase isozyme III, which bears a wild-type F198 side chain.(ABSTRACT TRUNCATED AT 250 WORDS)

Molecular and crystal structure of an amphiphile: 4'-propoxybiphenyl-4-methyl-N,N-dimethylamineoxide dihydrate

A novel amphiphile, 4'-propoxybiphenyl-4-methyl-N,N-dimethylamineoxide, has been synthesized, crystallized (P2(1)/a, a = 9.084 A, b = 8.911 A, c = 22.460 A, beta = 96.224 degrees) and its crystal structure was determined. The amphiphile forms a bilayer in which the amineoxide oxygen of each molecule binds two water molecules. In the hydrophobic part of the bilayer the biphenyls form edge-to-face contacts, in the polar layer there is a hydrogen bonding network. The potential use of the compound as a detergent for membrane proteins has been demonstrated and the relevance of the amineoxide hydrate for other detergents discussed.

Protein thermal denaturation, side-chain models, and evolution: amino acid substitutions at a conserved helix-helix interface

Random mutant libraries with substitutions at the interface between the N- and C-terminal helices of Saccharomyces cerevisiae iso-1-cytochrome c were screened. All residue combinations that have been identified in naturally occurring cytochrome c sequences are found in the libraries. Mutants with these combinations are biologically functional. Enthalpies, heat capacities, and midpoint temperatures of denaturation are used to determine the entropy and Gibbs free energy of denaturation (delta GD) for the ferri form of the wild-type protein and 13 interface variants. Changes in delta GD cannot be allocated solely to enthalpic or entropic effects, but there is no evidence of enthalpy-entropy compensation. The lack of additivity of delta GD values for single versus multiple amino acid substitutions indicates that the helices interact thermodynamically. Changes in delta GD are not in accord with helix propensities, indicating that interactions between the helices and the rest of the protein outweigh helix propensity. Comparison of delta GD values for the interface variants and nearly 90 non-cytochrome c variants to side-chain model data leads to several conclusions. First, hydrocarbon side chains react to burial-like transfer from water to cyclohexane, but even weakly polar side chains respond differently. Second, despite octanol being a poor model for protein interiors, octanol-to-water transfer free energies are useful stability predictors for changing large hydrocarbon side chains to smaller ones. Third, unlike cyclohexane and octanol, the Dayhoff mutation matrix predicts stability changes for a variety of substitutions, even at interacting sites.(ABSTRACT TRUNCATED AT 250 WORDS)

Structural analysis of the active site of porcine pancreatic elastase based on the X-ray crystal structures of complexes with trifluoroacetyl-dipeptide-anilide inhibitors

The X-ray crystal structures of two new (trifluoroacetyl)dipeptide p-(trifluoromethyl)anilide (TFA-dipeptide-TFM) inhibitors complexed to porcine pancreatic elastase are presented. TFA-Val-Ala-TFM and TFA-Phe-Ala-TFM both bind to elastase with the TFA group in the S1 subsite, Val or Phe in the S2 subsite, Ala in the S3 subsite, and the TFM group in the S4 subsite. Five other TFA-dipeptide-anilide/elastase crystal structures are available (two TFA-X-Ala-p-(trifluoromethyl)anilide, X = Lys, Leu, and three TFA-Lys-X-p-isopropylanilide, X = Pro, Leu, Phe). The four inhibitors with the trifluoromethyl substituent on the anilide ring bind in a single mode to elastase, whereas superposition of the three inhibitors with the isopropyl substituent on the anilide ring show three different modes of binding to the protein [Mattos, C., et al. (1994) Nature Struct. Biol. 1, 55-58]. The seven structures are taken together in a detailed analysis of the active site of porcine pancreatic elastase. The inhibition constants for the inhibitors are used in combination with the crystal structures to understand the specificity of the different elastase subsites.