Identifying structure-function relationships in four-helix bundle cytokines: towards de novo mimetics design.

Many cytokines (growth-factor proteins) are constructed from a common four-helix bundle structural framework. Rapid advances have been made in relating the structure and function of a growing number of four-helix bundle cytokines. This understanding opens the way to design de novo mimetics through such strategies as cytokine hybrids, structure-excerpted scaffolds and contact residue topology mimics. These may provide leads for agonists and antagonists of cell growth and differentiation.

Onset of neurophysin self-association upon neurophysin/neuropeptide hormone precursor biosynthesis.

The potential of the common biosynthetic precursor of neurophysin and neuropeptide hormones to self-associate has been assessed by quantitative affinity chromatographic analysis. The precursor form, with the hormone sequence in the amino terminal region and assumed able to interact intramolecularly with the hormone binding site of the neurophysin domain of the folded precursor, exhibits an affinity for neurophysin-agarose which is intermediate between those of unliganded neurophysin and non-covalently hormone-liganded neurophysin. The results lead to a prediction that neurophysin self-association is established upon precursor synthesis and prior to limited proteolysis of the precursor to release mature neurophysin and hormone components. Such self-association could play a role in packaging of the precursor into secretory granules and in regulating subsequent precursor processing events within the granules.

Isolation and sequence analysis of oxytocin from the sheep corpus luteum.

Studies have revealed that the corpus luteum (CL) of the sheep releases oxytocin (OT) -like immunoreactivity under normal and physiological conditions. We have now purified and completely characterized the OT-like species from ovine CL and established by Edman degradation and comparative reverse-phase HPLC its identity with hypothalamic oxytocin. On the basis of radioimmunoassay, the characterized oxytocin was the only peptide possessing OT-like immunoreactivity. This study represents the first identification by sequence analysis of oxytocin outside the central nervous system.

Kinetic analysis of a protein antigen-antibody interaction limited by mass transport on an optical biosensor.

Using BIAcore technology, we determined the rate constants for a protein antigen-antibody interaction that was mass transport limited on the optical biosensor. The antigen consisted of a soluble form of the human T-cell receptor CD4 (two amino terminal domains, D1D2) and the antibody was an anti-CD4 monoclonal from monkey engineered with the constant domains from human IgG1. High quality response data were obtained for this interaction by orienting the attachment of the antibody on the sensor surface and correcting for instrument artifacts with control experiments. Using numerical integration and global fitting, we demonstrate that a mass transport limited reaction was the only model of those tested that described well D1D2 binding to three different surface densities of the antibody. Statistical profiling techniques showed that the error space and correlation for the parameters in the non-linear model were essentially linear, but only when the model was simultaneously fitted to data from multiple surface densities. The "on" and "off" rate constants (1.2 x 10(-6) M-1 s-1 and 2.9 x 10(-4) s-1) determined from the kinetic analysis predict an equilibrium dissociation constant (KD = 0.24 +/- 0.01 nM) that agrees with the value measured in solution by titration calorimetry (KD = 0.2 +/- 0.1 nM). The results indicate that, although the D1D2-antibody reaction is partially controlled by mass transport on the optical biosensor, by optimizing the experimental design and analyzing data from multiple surface densities it is possible to determine accurate estimates of the intrinsic equilibrium and kinetic rate constants.

Current trends in molecular recognition and bioseparation.

Molecular recognition guides the selective interaction of macromolecules with each other in essentially all biological processes. Perhaps the most impactful use of biomolecular recognition in separation science has been in affinity chromatography. The results of the last 26 years, since Cuatrecases, Wilchek and Anfinsen first reported the purification of staphylococcal nuclease, have validated the power of biomolecular specificity for purification. This power has stimulated an explosion of solid-phase ligand designs and affinity chromatographic applications. An ongoing case in point is the purification of recombinant proteins, which has been aided by engineering the proteins to contain Affinity-Tag sequences, such as hexa-histidine for metal-chelate separation and epitope sequence for separation by an immobilized monoclonal antibody. Tag technology can be adapted for plate assays and other solid-phase techniques. The advance of affinity chromatography also has stimulated immobilized ligand-based methods to characterize macromolecular recognition, including both chromatographic and optical biosensor methods. And, new methods such as phage display and other diversity library approaches continue to emerge to identify new recognition molecules of potential use as affinity ligands. Overall, it is tantalizing to envision a continued evolution of new affinity technologies which use the selectivity built into biomolecular recognition as a vehicle for purification, analysis, screening and other applications in separation sciences.

Molecular diagnostics using analytical immuno high performance liquid affinity chromatography.

Analytical immuno high performance liquid affinity chromatography (analytical immuno HPLAC) was evaluated as a molecular diagnostic tool. Antibodies raised in rabbits against bovine neurophysin II were immobilized through Protein A crosslinking onto coated silica. Interaction of immobilized antibody with mobile antigen was characterized by zonal and frontal elutions of 14C-labeled bovine neurophysin II under isocratic, nondenaturing conditions. The chromatographic behavior shows that analytical immuno HPLAC with immobilized antibodies can be used to detect the number and functional nature of matrix-interacting antigens in mixtures, thus providing a quantitative chromatographic technology for "antigen mapping."

Use of enzymes in peptide synthesis.

Recent experiments in several laboratories have emphasized the benefits of proteolytic enzymes as effective catalysts for the formation of peptide bonds for synthesis and semisynthesis. This review summarizes successful applications in both stepwise synthesis for small peptides and fragment condensation to produce large polypeptides and proteins.

Interactions and uses of antisense peptides in affinity technology.

Antisense peptides, amino acid sequences encoded in the antisense strand of DNA, can interact with significant affinity and selectivity with their corresponding sensepeptides. Experimentally, sense-antisense peptide recognition has been observed repeatedly. However, skepticism about the biological relevance of this phenomenon has persisted. This is due in part to the unexpected and somewhat couterintutive nature of the interaction as well as to its non-universality as an empirical observation. Nonetheless, antisense peptides in several cases investigated so far have been used as immobilized ligands for the successful affinity chromatographic separation of native (sense) peptides and proteins. For example, immobilized antisense peptides corresponding to Arg8-vasopressin (AVP) have been used to separate vasopressin from oxytocin chromatographically as well as to affinity capture AVP-receptor complex. These results, together with improved understanding of the general features of amino acid sequence which drive antisense-sense peptide interactions as well as new ideas for making antisense peptides chimeras, are beginning to suggest improved ways to make antisense-related peptides as affinity agents for separation as well as for other biotechnology applications.

Revealing and utilizing receptor recognition mechanisms in a high-throughput world.

Recent genomic mapping promises to identify essentially all of the proteins that underpin normal and aberrant biology in humans. What genomics leaves undone is to determine how these proteins interact and integrate into molecular pathways in health and disease. Specific molecular interactions provide the fundamental mechanism for selectivity in virtually every aspect of biological structure and function. The convergence of structural and mutational studies makes it possible to define what parts of a protein are important for recognition. Still, knowing what is important does not necessarily foretell how binding epitopes actually function. We have applied the approach of epitope randomization on phage to explore how structural elements in such receptor recruitment systems as interleukin-5 (IL-5) and HIV-1 function in receptor recognition. This work has led in the IL-5 case to differentiation of recognition and activation epitopes, and this in turn has potential to help in the design of non-activating mimetics that could stimulate development of therapeutic antagonists for allergic inflammations such as asthma. Whether it is possible to differentiate recognition and activation in designing inhibitors in cases such as HIV-1 cell attachment and infection remains a tantalizing, but unsolved goal at present. Overall, these studies portray advances as well as limitations in the effort to decipher protein recognition mechanisms and utilize the wisdom gained for mechanism-based antagonist design in an increasingly high throughput world stimulated by the advent of genomics and proteomics.

Analytical affinity chromatography in studies of molecular recognition in biology: a review.

Measuring macromolecular and cellular interactions remains central to the study of recognition in biology and its application in biotechnology. Analytical affinity chromatography provides a versatile methodology to detect and quantitate such interactions. Both zonal and frontal elution approaches have been developed, essentially in parallel, for analytical affinity chromatography. A close quantitative relatedness of chromatographically obtained equilibrium constants and analogous constants determined fully in solution has been found for a growing number of proteins. This consistently observed correlation has formed the basis for extending theoretical treatments in order to evaluate not only monovalent molecular systems of varying types but also multivalently interacting macromolecules, including those which exhibit cooperativity. The potential to measure chemical rate constants by affinity chromatography also has been recognized, and experimental tests of the available theory are being made. As a micromethod, the quantitative use of affinity chromatography has important applicability for biochemical analysis of an increasing array of biologically active molecules being discovered and isolated but available in only relatively small amounts. Analytical affinity chromatography thus provides a means to use matrix--mobile interactant systems to study mechanisms of biomolecular interactions and therein to attain an understanding of such interactions which often is not easily achieved by solution methods alone.

Bioaffinity chromatography: synergy between interactive chromatography and molecular recognition for the separation and analysis of macromolecules.

Affinity chromatography, commonly regarded as an integral tool in macromolecular separation sciences, also provides an analytical method to study structure-function relationships of macromolecular interaction processes and to design recognition molecules. The latter, as found recently for the case of antisense peptides, may be useful as affinity agents in immobilized forms to effect new types of biomolecular separation.

Semisynthetic peptides and proteins.

Semisynthesis provides a flexible approach for using chemical synthesis to produce large, biologically active polypeptides and analogues. Currently developing improvements in the basic methods used, including polypeptide fragmentation, peptide synthesis, and reconstitution of synthetic and native components, make this overall approach applicable to a variety of species. Sequence modification through semisynthesis thus provides a flexible route to explore the code of rules whereby primary structure directs higher order properties of folded conformation and biological function of large peptides and proteins. The fruits of this endeavor, an understanding of how these macromolecules work, and therein, a basis for design of new structures that ultimately may be produced directly or by recombinant DNA methods, have begun to emerge.

Design and characterization of an intramolecular antiparallel coiled coil peptide.

A 56-residue polypeptide was designed to fold into a stable intramolecular antiparallel coiled coil, referred to as a coiled coil stem loop. The antiparallel orientation of the alpha-helices was dictated by the alignment of hydrophobic and ionic residues in the heptad repeat sequence (a, b, c, d, e, f, g)n. The hydrophobic core at the coiled coil interface was occupied by leucine and valine residues in heptad positions d and a' and positions a and d', respectively. The interface border positions e and g were occupied by glutamic acid in the amino-terminal helix and lysine residues in the carboxy-terminal helix. A loop segment connecting the alpha-helices began and ended with the helix-breaking residues glycine and proline. Alanine and serine residues were placed on the exposed b, c, and f positions of both helices to increase the helical propensity and solubility of the peptide, respectively. Several lines of evidence argued that the synthetic peptide made with this design folded into a stable monomeric coiled coil stem loop conformation: (1) the peptide was highly soluble in 150 mM sodium chloride and 50 mM sodium phosphate, pH 7.4; (2) the circular dichroism spectrum was alpha-helical but with relative ellipticity minima at 222 and 208 nm characteristic of a coiled coil structure: (3) the peptide exhibited an alpha-helical content near 80%, which was independent of peptide concentration and unchanged in the presence of trifluoroethanol; (4) size exclusion chromatography and sedimentation equilibrium ultracentrifuge measurements confirmed that the peptide was monomeric in aqueous solution; (5) the peptide exhibited high helical content over a wide pH range; (6) the apparent Tm for unfolding the alpha-helical structure was greater than 65 degrees C, and 3.0 M urea was required to reduce the helical structure by 50%; (7) a disulfide bond was readily formed in the monomer between the amino- and carboxy-terminal cysteine residues, confirming the antiparallel orientation of the helices; and (8) the peptide competed with fibrinogen for the GPIIbIIIa receptor indicating that the RGD residues present in the loop sequence were available for binding. This work establishes that an antiparallel alignment of alpha-helices can be achieved by designing specific hydrophobic and ionic interactions within the coiled coil. The prototype coiled coil peptide represents a sequence-simplified scaffold into which residues from alpha-helices and loops of native proteins can be inserted to form conformationally constrained mimetic recognition molecules.