Visualizing substructural fingerprints.

Substructural fingerprints have proven very useful for chemical library and diversity analysis, but their high dimensionality makes them poorly suited to principal components analysis and to standard nonlinear mapping methods. By using a combination of optimizable K-dissimilarity selection (OptiSim) and a modified stress function that suppresses effects of distances that fall beyond a characteristic horizon, it is possible to relax principal components analysis coordinates into more consistently meaningful projections from fingerprint space into two dimensions. The nonlinear maps so obtained are useful for characterizing combinatorial libraries, for comparing sublibraries, and for exploring the distribution of biological properties across structural space.

Molecular skins: a new concept for quantitative shape matching of a protein with its small molecule mimics.

A novel analytical method for comparing molecular shapes by optimizing the intersection of molecular "SKINS" has been developed. This method provides a quantitative measure of the shape similarity by maximizing the intersection volume of molecular surfaces with a finite thickness; a molecular skin. We report shape matching of a small tripeptide inhibitor (DFKi) of elastase class proteins with the 56 residue turkey ovomucoid inhibitor (TOMI). To match a large elastase inhibitor such as TOMI with a small inhibitor or drug, we found that it is necessary to use a skin match rather than molecular volume. Skin based comparisons of TOMI protein with DFKi successfully found the alignment expected from comparison of their respective crystallographic complexes with elastase (i.e. HLE/TOMI complex and PPE/tripeptide complex). In the skin comparison of the tripeptide with the TOMI protein, blind searching for skin matches involved optimization of the skin intersection from 172 starting positions randomly selected from a set of 500 points on the TOMI van der Waals surface [within 9.5 A of the Leu-18 on the TOMI binding loop (1 point/A2)]. The tripeptide center of mass was placed at these points and its orientation was randomized before optimization was initiated. The best skin intersection, 86.4 A3, was found three times and corresponds to the experimental alignment. The next best skin intersection was 78.1 A3 giving a discrimination factor in this case of 10%. Searches over the entire surface of the TOMI protein did not identify any new matches with skin intersection greater than 78.1 A3. Matching the DFKi with a TOMI structure relaxed from its crystal conformation by molecular dynamics gives similar results.

Molecular shape comparison of angiotensin II receptor antagonists.

A new and powerful analytical method for comparing molecular shapes by optimizing the overlap of molecular volumes has been developed. This shape comparison method provides both a quantitative measure of the shape similarity of molecules and a means to align molecules such that shape similarity if maximized. Our MSC method has been enhanced with an option to allow discrimination between groups with different chemical properties. Atoms or groups of atoms may be assigned to different classes based on specific properties such as electrostatic potential, hydrogen bonding ability, or hydrophobicity. This enables matches based on criteria such as alignment of hydrophobic groups or hydrogen bond acceptor groups. In this study, we report shape comparisons of angiotensin II (AII) receptor antagonists from two structural classes, 4-(biphenyl-4-ylmethoxy)-quinoline derivatives such as ICI D8731 and N-(biphenyl-4-ylmethyl)imidazole derivatives, such as DuP753. Starting with a list of low-energy conformations for the two molecules, each conformation of the first molecule is paired with each of the conformations of the second molecule. For each of these conformational pairs, an MSC comparison, which generates multiple MSC maxima, is initiated. Eight high scoring conformational pairings were found with shape matching based on the intersection of the total molecular volume, while nine high-scoring pairs were identified with matching by atom type. MSC identifies conformational pairs with high shape similarity, as measured by the intersection volume, and thus generates and prioritizes several alternative models for the AII antagonist pharmacophore.

Electrostatic field around cytochrome c: theory and energy transfer experiment.

Energy transfer in the "rapid diffusion" limit from electronically excited terbium(III) chelates in three different charge states to horse heart ferricytochrome c was measured as a function of ionic strength. Theoretical rate constants calculated by numerical integration of the Forster integral (containing the Poisson-Boltzmann-generated protein electrostatic potential) were compared with the experimental data to evaluate the accuracy of protein electrostatic field calculations at the protein/solvent interface. Two dielectric formalisms were used: a simple coulombic/Debye-Hückel procedure and a finite difference method [Warwicker, J. & Watson, H. C. (1982) J. Mol. Biol. 157, 671-679] that accounts for the low-dielectric protein interior and the irregular protein/solvent boundary. Good agreement with experiment was obtained and the ionic-strength dependence of the reaction was successfully reproduced. The sensitivity of theoretical rate constants to the choices of effective donor sphere size and the energy transfer distance criterion was analyzed. Electrostatic potential and rate-constant calculations were carried out on sets of structures collected along two molecular dynamics trajectories of cytochrome c. Protein conformational fluctuations were shown to produce large variations in the calculated energy transfer rate constant. We conclude that protein fluctuations and the resulting transient structures can play significant roles in biological or catalytic activities that are not apparent from examination of a static structure. For calculating protein electrostatics, large-scale low-frequency conformational fluctuations, such as charged side-chain reorientation, are established to be as important as the computational method for incorporating dielectric boundary effects.

Molecular dynamics effects on protein electrostatics.

Electrostatic calculations have been carried out on a number of structural conformers of tuna cytochrome c. Conformers were generated using molecular dynamics simulations with a range of solvent simulating, macroscopic dielectric formalisms, and one solvent model that explicitly included solvent water molecules. Structures generated using the lowest dielectric models were relatively tight, with side chains collapsed on the surface, while those from the higher dielectric models had more internal and external fluidity, with surface side chains exploring a fuller range of conformational space. The average structure generated with the explicitly solvated model corresponded most closely with the crystal structure. Individual pK values, overall titration curves, and electrostatic potential surfaces were calculated for average structures and structures along each simulation. Differences between structural conformers within each simulation give rise to substantial changes in calculated local electrostatic interactions, resulting in pK value fluctuations for individual sites in the protein that vary by 0.3-2.0 pK units from the calculated time average. These variations are due to the thermal side chain reorientations that produce fluctuations in charge site separations. Properties like overall titration curves and pH dependent stability are not as sensitive to side chain fluctuations within a simulation, but there are substantial effects between simulations due to marked differences in average side chain behavior. These findings underscore the importance of proper dielectric formalism in molecular dynamics simulations when used to generate alternate solution structures from a crystal structure, and suggest that conformers significantly removed from the average structure have altered electrostatic properties that may prove important in episodic protein properties such as catalysis.

Electrostatic interactions in the assembly of Escherichia coli aspartate transcarbamylase.

Although ionizable groups are known to play important roles in the assembly, catalytic, and regulatory mechanisms of Escherichia coli aspartate transcarbamylase, these groups have not been characterized in detail. We report the application of static accessibility modified Tanford-Kirkwood theory to model electrostatic effects associated with the assembly of pairs of chains, subunits, and the holoenzyme. All of the interchain interfaces except R1-R6 are stabilized by electrostatic interactions by -2 to -4 kcal-m-1 at pH 8. The pH dependence of the electrostatic component of the free energy of stabilization of intrasubunit contacts (C1-C2 and R1-R6) is qualitatively different from that of intersubunit contacts (C1-C4, C1-R1, and C1-R4). This difference may allow the transmission of information across subunit interfaces to be selectively regulated. Groups whose calculated pK or charge changes as a result of protein-protein interactions have been identified and the results correlated with available information about their function. Both the 240s loop of the c chain and the region near the Zn(II) ion of the r chain contain clusters of ionizable groups whose calculated pK values change by relatively large amounts upon assembly. These pK changes in turn extend to regions of the protein remote from the interface. The possibility that networks of ionizable groups are involved in transmitting information between binding sites is suggested.

Characterization of murine IL-1 beta. Isolation, expression, and purification.

One cDNA clone encoding a truncated murine IL-1 beta (M IL-1 beta) sequence was isolated from a murine macrophage cDNA library. We reconstituted the coding sequence of the 152-residue mature protein and expressed it in Escherichia coli. rM IL-1 beta was purified to homogeneity and characterized by oligonucleotide and NH2-terminal sequence analysis. Purified rM IL-1 beta exhibited biologic activity equivalent to 7.8 x 10(7) units/mg in the murine thymocyte proliferation assay and 9.9 x 10(3) units/mg in the human gingival fibroblast PGE2 production assay, indicative of species specificity. The isoelectric point of rM IL-1 was found to be 8.85. The circular dichroism spectrum revealed that the secondary structure of M IL-1 is indistinguishable from that of the human protein. Receptor binding studies indicated the rM IL-1 bound to murine EL-4.1 thymoma cells in a specific and dose-dependent fashion with an affinity of 32 pM. Competition binding data suggested that murine and human IL-1 compete for a single class of receptor. Antisera were generated in rabbits against both murine and human IL-1. Results of ELISA binding and antisera neutralization assays indicated that there are common antigenic sites between the two IL-1 beta molecules. These domains are of functional importance because they are capable of mediating the neutralization of biologic activity.

Site-specific semisynthetic variant of human hemoglobin.

A single round of Edman degradation was employed to remove the NH2-terminal valine from isolated alpha chains of human hemoglobin. Reconstitution of normal beta chains with truncated or substituted alpha chains was used to form truncated (des-Val1-alpha 1) and substituted ([[1-13C]Gly1]alpha 1) tetrameric hemoglobin analogs. Structural homology of the analogs with untreated native hemoglobin was established by using several spectroscopic and physical methods. Functional studies indicate that the reconstituted tetrameric protein containing des-Val1-alpha chains has a higher affinity for oxygen, is less influenced by chloride ions or 2,3-bisphosphoglycerate, and shows lower cooperativity than native hemoglobin. These results confirm the key functional role of the alpha-chain NH2 terminus in mediating cooperative oxygen binding across the dimer interface. The NH2-terminal pK1/2 value was determined for the [13C]glycine-substituted analog to be 7.46 +/- 0.09 at 15 degrees C in the carbon monoxide-liganded form. This value, measured directly by 13C NMR, agrees with the determination made by the less-direct 13CO2 method and confirms the role of this residue as a contributor to the alkaline Bohr effect; however, it is inconsistent with the presence of an NH2-terminal salt bridge to the carboxylate of Arg-141 of the alpha chain in the liganded form.

Molecular dynamics of a cytochrome c-cytochrome b5 electron transfer complex.

Cytochrome c and cytochrome b5 form an electrostatically associated electron transfer complex. Computer models of this and related complexes that were generated by docking the x-ray structures of the individual proteins have provided insight into the specificity and mechanism of electron transfer reactions. Previous static modeling studies were extended by molecular dynamics simulations of a cytochrome c-cytochrome b5 intermolecular complex. The simulations indicate that electrostatic interactions at the molecular interface results in a flexible association complex that samples alternative interheme geometries and molecular conformations. Many of these transient geometries appear to be more favorable for electron transfer than those formed in the initial model complex. Of particular interest is a conformational change that occurred in phenylalanine 82 of cytochrome c that allowed the phenyl side chain to bridge the two cytochrome heme groups.

Muteins of human interleukin-1 that show enhanced bioactivities.

Using recombinant DNA techniques, we have made a series of amino-terminal muteins of human interleukin-1 (IL-1). Two of the muteins demonstrated 4-7-fold increase in bioactivity as compared to that of the native IL-1. The enhanced biological potency coincides with an increase in both receptor binding affinity and in vivo tumor inhibitory activity. By site specific mutagenesis, we have shown that the arginine at the fourth position of IL-1 is one of the key residues in the function of IL-1. Circular dichroism studies of the amino-terminus analogs showed little structural rearrangement. The change in bioactivity might be due to a change in the stability of the muteins, in the side chain interactions with receptors or in the minor change in folding near the receptor binding site.

Electrostatic analysis of the interaction of cytochrome c with native and dimethyl ester heme substituted cytochrome b5.

The stability of the complex formed between cytochrome c and dimethyl ester heme substituted cytochrome b5 (DME-cytochrome b5) has been determined under a variety of experimental conditions to evaluate the role of the cytochrome b5 heme propionate groups in the interaction of the two native proteins. Interaction between cytochrome c and the modified cytochrome b5 was found to produce a difference spectrum in the visible range that is very similar to that generated by the interaction of the native proteins and that can be used to monitor complex formation between the two proteins. At pH 8 [25 degrees C (HEPPS), I = 5 mM], DME-cytochrome b5 and cytochrome c form a 1:1 complex with an association constant KA of 3 (1) X 10(6) M-1. This pH is the optimal pH for complex formation between these two proteins and is significantly higher than that observed for the interaction between the two native proteins. The stability of the complex formed between DME-cytochrome b5 and cytochrome c is strongly dependent on ionic strength with KA ranging from 2.4 X 10(7) M-1 at I = 1 mM to 8.2 X 10(4) M-1 at I = 13 mM [pH 8.0 (HEPPS), 25 degrees C]. Calculations for the native, trypsin-solubilized form of cytochrome b5 and cytochrome c confirm that the intermolecular complex proposed by Salemme [Salemme, F. R. (1976) J. Mol. Biol. 102, 563] describes the protein-protein orientation that is electrostatically favored at neutral pH.(ABSTRACT TRUNCATED AT 250 WORDS)

Distribution of ions around DNA, probed by energy transfer.

Measurements of the effect of DNA on rates of bimolecular energy transfer between ions provide a direct indication of how cations cluster in regions near DNA and how anions are repelled from the same regions. Energy transfer from luminescent lanthanide ions (in the "rapid-diffusion" limit) probes collision frequencies that are dependent on the equilibrium spatial distributions of ions. The addition of 1 mM DNA (phosphate) to a 2 mM salt solution increases the overall collision frequency between monovalent cations by a factor of 6 +/- 1.5; it increases the divalent-monovalent cation collision frequency by a factor of 29 +/- 3; and it decreases the divalent cation-monovalent anion collision frequency by a factor of 0.24 +/- 0.03. Comparisons are made with the changes in collision frequencies predicted by several different theoretical descriptions of ion distributions. The closest agreement with experimental results for monovalent ions at 1 mM DNA is obtained with a static accessibility-modified discrete charge calculation, based on a detailed molecular model of B-DNA. At high DNA concentration (10 mM), the best results are obtained by numerical solutions of the Poisson-Boltzmann equation for a "soft-rod" model of DNA. Poisson-Boltzmann calculations for a "hard-rod" model greatly overestimate the effects of DNA on collision frequencies, as does a calculation based on counterion-condensation theory.

Electrostatic deformation of DNA by a DNA-binding protein.

Complementary electrostatic interactions between negatively charged B-DNA and a positively charged array on the lambda Cro repressor protein are shown to substantially contribute to the formation energy of sequence-specific and nonspecific Cro-DNA complexes. The electrostatic interactions favor Cro binding to a bent form of DNA, a geometry which optimizes hydrogen-bonding contacts between Cro and exposed base pair groups in the DNA major groove.

pH-dependent processes in proteins.

Recent improvements in the understanding of electrostatic interactions in proteins serve as a focus for the general topic of pH-dependent processes in proteins. The general importance of pH-dependent processes is first set out in terms of hydrogen ion equilibria, stability, ligand interactions, assembly, dynamics, and events in related molecular systems. The development of various theoretical treatments includes various formalisms in addition to the solvent interface model developed by Shire et al. as an extension of the Tanford-Kirkwood treatment. A number of detailed applications of the model are presented and future potentialities are sketched.

Electrostatics and flexibility in protein-DNA interactions.

CAP, cro, and lambda repressor represent a class of gene-regulatory proteins that bind specifically to DNA using a common bihelical motif. Examination of these structures suggest a possible mechanism for the binding of protein to DNA. The first step would be the formation of a non-specific protein-DNA complex energetically driven by the electrostatic interaction of asymetrically distributed charges on the surface of the protein that complement the charges on DNA. This attraction keeps the protein near the DNA, limiting diffusion to one dimension. As the protein slides, random thermal fluctuations twist and dip the protein over irregularities in the structure of the DNA. During these excursions, surface complementarity is sampled until the specific binding site is found. At this point the intervening solvent is displaced allowing the two molecules maximize their electrostatic and hydrogen bonding interactions.