Mutation is modulated: implications for evolution.

Evolution occurs through genome variation followed by selection. Because DNA sequence context affects the activity of enzymes that copy, move and repair DNA, there are intrinsic variations in the probability of genetic variation along a genome. These intrinsic variations can be affected by selective pressure. Codon changes that do not alter the encoded amino acids may still have effects on the local rate of sequence change. Large gene families could encode a successful genetic framework by which to evolve new, functional members. The speed of adaptation to environmental challenges may be improved when the distinct mechanisms of genetic change come under regulatory control. Natural selection operates on mechanisms that generate and modulate diversity as it does on all biological functions.

Chance favors the prepared genome.

Most descriptions of mutation have emphasized its negative consequences, and randomness with respect to biological function. This book seeks to balance the discussion by emphasizing mechanisms that both diversify the genome and increase the probability that a genome's descendants will survive. This chapter provides a framework for, and overview of, the diverse contributions to this book; these contributions will be stimulating companions, well into the 21st Century, as we work to comprehend the information contained in genomic databases. Genomes that encode "better" amino acid sequences are at a selective advantage. Genomes that generate diversity also are at an advantage to the extent that they can navigate efficiently through the space of possible sequence changes. Biochemical systems that tend to increase the ratio of useful to destructive genetic change may harness preexisting information (horizontal gene transfer, DNA translocation and/or DNA duplication), focus the location, timing, and extent of genetic change, adjust the dynamic range of a gene's activity, and/or sample regulatory connections between sites distributed across the genome. Rejecting entirely random genetic variation as the substrate of genome evolution is not a refutation, but rather provides a deeper understanding, of the theory of natural selection of Darwin and Wallace. The fittest molecular strategies survive, along with descendants of the genomes that encode them.

A solution-phase strategy for the synthesis of chemical libraries containing small organic molecules: a universal and dipeptide mimetic template.

A general approach to the solution phase, parallel synthesis of chemical libraries, which allows the preparation of multi-milligram quantities of each individual member, is exemplified with both a universal and dipeptide mimetic template. In each step of the sequence, the reactants, unreacted starting material, reagents and their byproducts are removed by simple liquid/ liquid or liquid/solid extractions providing the desired intermediates and final compounds in high purities (> or = 90-100%) independent of the reaction yields and without deliberate reaction optimization.

Chemical ecology: a view from the pharmaceutical industry.

Biological diversity reflects an underlying molecular diversity. The molecules found in nature may be regarded as solutions to challenges that have been confronted and overcome during molecular evolution. As our understanding of these solutions deepens, the efficiency with which we can discover and/or design new treatments for human disease grows. Nature assists our drug discovery efforts in a variety of ways. Some compounds synthesized by microorganisms and plants are used directly as drugs. Human genetic variations that predispose to (or protect against) certain diseases may point to important drug targets. Organisms that manipulate molecules within us to their benefit also may help us to recognize key biochemical control points. Drug design efforts are expedited by knowledge of the biochemistry of a target. To supplement this knowledge, we screen compounds from sources selected to maximize molecular diversity. Organisms known to manipulate biochemical pathways of other organisms can be sources of particular interest. By using high throughput assays, pharmaceutical companies can rapidly scan the contents of tens of thousands of extracts of microorganisms, plants, and insects. A screen may be designed to search for compounds that affect the activity of an individual targeted human receptor, enzyme, or ion channel, or the screen might be designed to capture compounds that affect any step in a targeted metabolic or biochemical signaling pathway. While a natural product discovered by such a screen will itself only rarely become a drug (its potency, selectivity, bioavailability, and/or stability may be inadequate), it may suggest a type of structure that would interact with the target, serving as a point of departure for a medicinal chemistry effort--i.e., it may be a "lead." It is still beyond our capability to design, routinely, such lead structures, based simply upon knowledge of the structure of our target. However, if a drug discovery target contains regions of structure homologous to that in other proteins, structures known to interact with those proteins may prove useful as leads for a medicinal chemistry effort. The specificity of a lead for a target may be optimized by directing structural variation to specificity-determining sites and away from those sites required for interaction with conserved features of the targeted protein structure. Strategies that facilitate recognition and exploration of sites at which variation is most likely to generate a novel function increase the efficiency with which useful molecules can be created.

Protoplast fusion in microtiter plates for expression cloning in mammalian cells: demonstration of feasibility using membrane-bound alkaline phosphatase as a reporter enzyme.

Protoplast fusion is a method for directly transferring cloned DNA from bacteria to mammalian cells at high efficiency. Here, we have used membrane-bound alkaline phosphatase as a reporter enzyme in a miniprotoplast fusion assay. This work demonstrates the principle that large numbers of protoplast fusions can be done simultaneously and successfully, to assay for an activity encoded by an expression vector. The technique described here circumvents key hurdles to expression cloning. This method does not require a highly sensitive assay or a way of separating a rare expressing cell from the mixture of transfected cells containing other transfected genes. With a strong promoter, the protein encoded by the undiluted transfected cDNA should be produced at at least as high a level as it is endogenously produced in the cell from which its activity was first detected. Reference clones are stored, avoiding the need to separate out the cells that are successfully transfected; this also avoids the need to repurify the DNA from the transfected cell. Because of the use of microtiter plates, it is likely that such a method could be partially automated for many types of assays.

Modifications of position 12 in parathyroid hormone and parathyroid hormone related protein: toward the design of highly potent antagonists.

Truncated N-terminal fragments of parathyroid hormone (PTH), [Tyr34]bovine PTH(7-34)NH2, and parathyroid hormone related protein (PTHrP), PTHrP(7-34)NH2, inhibit [Nle8,18,[125I]iodo-Tyr34]-bPTH(1-34)NH2 binding and PTH-stimulated adenylate cyclase in bone and kidney assays. However, the receptor interactions of these peptides are 2-3 orders of magnitude weaker than those of their agonist counterparts. To produce an antagonist with increased receptor-binding affinity but lacking agonist-like properties, structure-function studies were undertaken. Glycine at position 12 (present in all homologues of PTH and in PTHrP), which is predicted in both hormones to participate in a beta-turn, was examined by substituting conformational reporters, such as D- or L-Ala, Pro, and alpha-aminoisobutyric acid (Aib), in both agonist and antagonist analogues. Except for N-substituted amino acids, which substantially diminished potency, substitutions were well tolerated, indicating that this site can accept a wide latitude of modifications. To augment receptor avidity, hydrophobic residues compatible with helical secondary structure were introduced. Incorporation of the nonnatural amino acids D-Trp, D-alpha-naphthylalanine (D-alpha-Nal), or D-beta-Nal into either [Tyr34]bPTH(7-34)NH2 or [Nle8,18,Tyr34]bPTH(7-34)NH2 resulted in antagonists that were about 10-fold more active than their respective 7-34 parent compound. Similarly, [D-Trp12]PTHrP(7-34)NH2 was 6 times more potent than the unsubstituted peptide but retained partial agonistic properties, although markedly reduced, similar to PTHrP(7-34)NH2. The antagonistic potentiating effect was configurationally specific.(ABSTRACT TRUNCATED AT 250 WORDS)

A novel cleavage product of human complement component C3 with structural and functional properties of cobra venom factor.

The generation of two cleavage products of human C3, termed C3o and C3p, by incubation with a C3-cleaving protease isolated from cobra venom (Naja naja siamensis) is described. The venom protease removes the C3p fragment (Mr approximately 33,000) from the C3dg region of the C3 alpha-chain. The major cleavage fragment C3o (Mr approximately 140,000) contains the unaltered beta-chain of C3 and two alpha-chain-derived polypeptides of Mr approximately 29,000 and Mr approximately 38,000, respectively. Amino-terminal amino acids sequence analysis of C3p and the three chains of C3o allowed the identification of the exact location of the two alpha-chain-derived fragments of C3o and the three cleavage sites of the venom protease. The chain structure of C3o resembles those of C3c and cobra venom factor. In contrast to C3c but like cobra venom factor (and C3b), C3o was found to support the activation of the serine protease Factor B by cleavage in the presence of Factor D and Mg2+ into Bb and Ba, generating an enzymatically active complex that is able to cleave a fluorogenic peptide substrate for C3 convertases. Since the only stretch of amino acid residues of C3o not present in C3c is the carboxyl terminus of the Mr approximately 29,000 chain of C3o, it is suggested that this region is important for the interaction with Factor B and convertase formation.

Solid-phase synthesis of melittin: purification and functional characterization.

The main component of the honey bee venom, melittin, is a cationic polypeptide containing 26 amino acids. Exposure of lipid bilayers to this peptide results in the formation of anion-selective channels with a variety of unit conductances. One of the possible causes for this heterogeneity in the conductance could be heterogeneity of the melittin preparation, and indeed, the existence of two prominent forms of naturally occurring melittin, differing only at the N-terminal amino group, has been documented. This paper describes the synthesis of the major form of melittin, using stepwise solid-phase methodology and the demonstration that the synthetic melittin, devoid of the minor component (N-formylmelittin) and other contaminants, interacts with lipid bilayers to form channels which are qualitatively indistinguishable from the ones formed by the naturally occurring toxin. This result indicates that the heterogeneity in the channels produced in bilayers by bee venom is not due to differences in the channel-forming properties of the formyl and non-formyl melittin but rather to differences in the number and orientation of melittin monomers of identical primary structure as they aggregate to form channels in the lipid bilayer.

Immunoprecipitation of the parathyroid hormone receptor.

An 125I-labeled synthetic analog of bovine parathyroid hormone, [8-norleucine,18-norleucine,34-tyrosine]PTH-(1-34) amide ([Nle]PTH-(1-34)-NH2), purified by high-pressure liquid chromatography (HPLC), was employed to label the parathyroid hormone (PTH) receptor in cell lines derived from PTH target tissues: the ROS 17/2.8 rat osteosarcoma of bone and the CV1 and COS monkey kidney lines. After incubation of the radioligand with intact cultured cells, the hormone was covalently attached to receptors by using either a photoaffinity technique or chemical (affinity) cross-linking. In each case, covalent labeling was specific, as evidenced by a reduction of labeling when excess competing nonradioactive ligand was present. After covalent attachment of radioligand, membranes were prepared from the cells and solubilized in the nonionic detergent Nonidet P-40 or octyl glucoside. The soluble membrane fraction present in the supernatant of a 100,000 X g centrifugation was incubated with IgG prepared from anti-PTH antiserum generated to the amino-terminal region, residues 1-34, of PTH. The IgG-PTH-receptor complex was precipitated with staphylococcal protein A-Sepharose. Analysis of the immunoprecipitate on NaDod-SO4/polyacrylamide gel electrophoresis followed by autoradiography revealed the presence of a doublet of apparent molecular mass 69-70 kDa. Specifically labeled bands of approximate molecular mass 95 and 28 kDa were also observed. The anti-PTH IgG was affinity purified by passage over a PTH-Sepharose column and used to make an immunoaffinity column. The 70- and 28-kDa bands were also observed after labeled solubilized membrane preparations were allowed to bind to this column and then were eluted by using a [Nle]PTH-(1-34)-NH2-containing buffer or acetic acid. These studies suggest that the use of an anti-PTH antiserum that binds receptor-bound hormone is likely to be a useful step in the further physiochemical characterization and purification of the PTH receptor.

Is there a higher level genetic code that directs evolution?

Because the genetic code is redundant for most amino acids, different codons can be used in a given position without altering the structure of the protein for which the gene codes. This flexibility permits information encoding structural, and therefore functional, properties of RNA and DNA to be transmitted simultaneously by a protein-coding sequence of DNA. Among the other messages that might be transmitted, it is proposed, is one modulating the evolution of the DNA itself.

An improved fluorogenic substrate for the alternative complement pathway C3/5 converting enzyme CVFBb.

By lengthening the sequence of a previously available tripeptide to a pentapeptide, we were able to increase the specificity of the substrate for the complement enzyme CVFBb (EC 3.4.21.47) over Factor Xa (EC 3.4.21.6). This increase in specificity was achieved by both an increase in the kcat/Km for CVFBb for the longer substrate compared to the original substrate, and a decrease in the kcat/Km for Factor Xa. The new substrate, Boc-Nle-Gln-Leu-Gly-Arg-amino methyl coumarin (AMC) was synthesized by coupling Boc-Nle-Gln-Leu-Gly to Arg-AMC in solution. p-Toluenesulfonic acid was added to the coupling mixture to improve the solubility of the arginine derivative and avoid the need for covalent protection.

A fluorescent assay for complement activation.

We report here a rapid assay for the complement enzymes CVFBb, C4b2a and Cls. This assay involves the use of a peptide substrate that releases a fluorescent coumarin derivative (AMC) upon cleavage by the convertase. The substrate, BocLeuGlyArgAMC, was chosen because its sequence is similar to the carboxyl terminus of C3a, and identical to that of C5a. The Km of this substrate are about 125 microM for the C3/5 convertase CVFBb, 169 microM for C4b2a, and 140 microM for C1s.

The active site of C3a anaphylatoxin.

The essential active site responsible for the inflammatory activities of C3a, an anaphylatoxin derived from the serum complement system, has been elucidated using C3a peptides synthesized by the solid phase method and assayed for their ability to contract guinea pig ileal tissue and to produce a wheal and flare response in human skin. The COOH-terminal C3a pentapeptide (Leu-Gly-Leu-Ala-Arg) common to rat, pig, and man shows vascular and smooth muscle activity as well as specificity similar to natural human C3a. The porcine C3a octapeptide is 3 times more active than the common pentapeptide, but the human octapeptide (Ala(70)-Ser-His-Leu(73)-Gly-Leu(75)-Ala-Arg(77) is 12 times more active than the pentapeptide. Replacement of the serine and histidine by alanine or acetylation of the NH2 terminus provides analogues with the same activity as the octapeptide. Thus, the increased activity of the human C3a octapeptide over the pentapeptide appears to be related to the backbone of residues 70 to 72 and is not due to the presence of the hydroxyl group of serine-71, the imidazole ring of histidine-72, or a positive charge at or near the NH2 terminus. Since the COOH-terminal tetrapeptide is 40 times less active than the pentapeptide, an adequate model of the essential active site of C3a anaphylatoxin is the common COOH-terminal pentapeptide region. A C3a active site analogue containing a COOH-terminal lysyl residue is devoid of ileal activity. In addition, the [alanine-73]pentapeptide is 9 times less active and the [alanine-75]pentapeptide is at least 70 times less active than the active site pentapeptide in the ileal assay. Thus, the hydrophobic side chains of leucine-73 and leucine-75 and the guanidinium group of arginine-77 are important for the contractile activity of the active site COOH-terminal pentapeptide of human C3a anaphylatoxin.

Characterization of colony-stimulating activity produced by human monocytes and phytohemagglutinin-stimulated lymphocytes.

Human colony-stimulating activity (CSA) may support the proliferation of both human and murine granulocyte-macrophage progenitor cells (CFU-C) or, in the case of human urinary CSA, may only stimulate murine bone marrow CFU-C. CSA produced in the culture media of monocytes and macrophages and phytohemagglutinin-stimulated lymphocytes from human peripheral blood was characterized for both human and mouse marrow CFU-C stimulating activities. During the initial phase of a long-term cultures of monocytes, both human- and mouse-active CSA (MnCM-HM) were produced. In later phases of culture, however, only mouse-active CSA (MnCM-M) was produced. Fractionation on Sephadex G-150 revealed two functionally distinct species from MnCM-HM and lymphocytes conditioned medium, a high molecular weight factor (MW greater than 150,000) which stimulated mouse but not human colony formation, and a low molecular weight species (MW 25,000-35,000) which was active against both mouse and human target cells. However, MnCM-M revealed only one high molecular weight species (greater than 150,000), active only on mouse marrow. The possible biologic significance of such an activity is discussed.