Hydropathic Complementarity Research Articles

Intuitive, but not simple: Including explicit water molecules in protein–protein docking simulations improves model quality

Characterizing the nature of interaction between proteins that have not been experimentally cocrystallized requires a computational docking approach that can successfully predict the spatial conformation adopted in the complex. In this work, the Hydropathic INTeractions (HINT) force field model was used for scoring docked models in a data set of 30 high-resolution crystallographically characterized "dry" protein-protein complexes and was shown to reliably identify native-like models. However, most current protein-protein docking algorithms fail to explicitly account for water molecules involved in bridging interactions that mediate and stabilize the association of the protein partners, so we used HINT to illuminate the physical and chemical properties of bridging waters and account for their energetic stabilizing contributions. The HINT water Relevance metric identified the "truly" bridging waters at the 30 protein-protein interfaces and we utilized them in "solvated" docking by manually inserting them into the input files for the rigid body ZDOCK program. By accounting for these interfacial waters, a statistically significant improvement of ∼24% in the average hit-count within the top-10 predictions the protein-protein dataset was seen, compared to standard "dry" docking. The results also show scoring improvement, with medium and high accuracy models ranking much better than incorrect ones. These improvements can be attributed to the physical presence of water molecules that alter surface properties and better represent native shape and hydropathic complementarity between interacting partners, with concomitantly more accurate native-like structure predictions.

Algorithms for the Design of Maximum Hydropathic Complementarity Molecules

In this article, we address the problem of designing a string with optimal complementarity properties with respect to another given string according to a given criterion. The motivation comes from a drug design application, in which the complementarity between two sequences (proteins) is measured according to the values of the hydropathic coefficients associated with the sequence elements (amino acids). We present heuristic and exact optimization algorithms, and we report on some computational experiments on amino peptides taken from Semaphorin and human Interleukin-1β, which have already been investigated in the literature using heuristic algorithms. With our techniques, we proved the optimality of a known solution for Semaphorin-3A, and we discovered several other optimal and near-optimal solutions in a short computing time; we also found in fractions of a second an optimal solution for human interleukin-1β, whose complementary value is one order of magnitude better than previously known ones. The source code of a prototype C++ implementation of our algorithms is freely available for noncommercial use on the web. As a main result, we showed that in this context mathematical programming methods are more successful than heuristics, such as simulated annealing. Our algorithm unfolds its potential, especially when different measures could be used for scoring peptides, and is able to provide not only a single optimal solution, but a ranking of provable good ones; this ranking can then be used by biologists as a starting basis for further refinements, simulations, or in vitro experiments.

Identification of Semaphorin 5A Interacting Protein by Applying Apriori Knowledge and Peptide Complementarity Related to Protein Evolution and Structure

In the post-genomic era, various computational methods that predict protein-protein interactions at the genome level are available; however, each method has its own advantages and disadvantages, resulting in false predictions. Here we developed a unique integrated approach to identify interacting partner(s) of Semaphorin 5A (SEMA5A), beginning with seven proteins sharing similar ligand interacting residues as putative binding partners. The methods include Dwyer and Root-Bernstein/Dillon theories of protein evolution, hydropathic complementarity of protein structure, pattern of protein functions among molecules, information on domain-domain interactions, co-expression of genes and protein evolution. Among the set of seven proteins selected as putative SEMA5A interacting partners, we found the functions of Plexin B3 and Neuropilin-2 to be associated with SEMA5A. We modeled the semaphorin domain structure of Plexin B3 and found that it shares similarity with SEMA5A. Moreover, a virtual expression database search and RT-PCR analysis showed co-expression of SEMA5A and Plexin B3 and these proteins were found to have co-evolved. In addition, we confirmed the interaction of SEMA5A with Plexin B3 in co-immunoprecipitation studies. Overall, these studies demonstrate that an integrated method of prediction can be used at the genome level for discovering many unknown protein binding partners with known ligand binding domains.

Polyclonal anti-idiotypic antibodies which mimic an epitope of the human prion protein

Immunization with anti-idiotypic (anti-Id) antibodies, used as surrogate antigens, has led to promising results, notably in active immunotherapy of cancers, essentially because it breaks immunological tolerance against self-tumor-associated antigens. The aim of the present study was to provide a proof-of-principle that this vaccination approach could be envisaged also in the field of prion diseases, caused by the accumulation of an aggregated pathological isoform of the highly tolerogenic self-prion protein (PrP), and for which no therapy is available. We investigated the possibility of raising anti-Id antibodies mimicking the human PrP (hPrP), using as immunogens either a peptide derived from the paratope of an anti-PrP mAb or the entire antibody. To this end, we cloned and sequenced SAF61 mAb, an anti-PrP antibody already produced in the laboratory, directed against a critical epitope of PrP involved in the aggregation process. A synthetic peptide (denoted CDR3L) was designed from the identification of a 17-amino-acid sequence encompassing the CDR3 region of the light chain whose hydropathic profile was opposed to that of PrP epitope. CDR3L peptide was directly demonstrated to bind hPrP, confirming the role of hydropathic complementarity in antigen–antibody interactions. When injected into rabbits, CDR3L generated anti-SAF61 anti-Id polyclonal antibodies that exclusively recognized SAF61 mAb but were unable to compete with hPrP for antibody binding. By contrast, immunizations with the entire SAF61 mAb generated anti-Id antibodies specifically competing with soluble or membrane-bound hPrP (in EIA or flow cytometry experiments, respectively) for binding not only SAF61 mAb but also other anti-PrP mAbs directed against similar epitopes, i.e. behaving as “internal images” of this disease-related PrP epitope. These results could open the way to raising PrP-like mAbs, which might serve as surrogate antigens in a new active immunotherapeutic approach to prion diseases.

Inhibition of amyloid β‐peptide production by blockage of β‐secretase cleavage site of amyloid precursor protein

Amyloid beta-peptide (Abeta) is implicated as the major causative agent in Alzheimer's disease (AD). Abeta is produced by the processing of the amyloid precursor protein (APP) by BACE1 (beta-secretase) and gamma-secretase. Many inhibitors have been developed for the secretases. However, the inhibitors will interfere with the processing of not only APP but also of other secretase substrates. In this study, we describe the development of inhibitors that prevent production of Abeta by specific binding to the beta-cleavage site of APP. We used the hydropathic complementarity (HC) approach for the design of short peptide inhibitors. Some of the HC peptides were bound to the substrate peptide (Sub W) corresponding to the beta-cleavage site of APP and blocked its cleavage by recombinant human BACE1 (rhBACE1) in vitro. In addition, HC peptides specifically inhibited the cleavage of Sub W, and not affecting other BACE1 substrates. Chemical modification allowed an HC peptide (CIQIHF) to inhibit the processing of APP as well as the production of Abeta in the treated cells. Such novel APP-specific inhibitors will provide opportunity for the development of drugs that can be used for the prevention and treatment of AD with minimal side effects.

A computational tool to optimize ligand selectivity between two similar biomacromolecular targets

Algorithms for a new computer program designed to increase ligand-receptor selectivity between two proteins are described. In this program ligand-receptor selectivity is increased by functional modifications to the ligand so as to increase the calculated binding affinity of it to one protein and/or decrease the calculated binding affinity of it to the other protein. The structure of the ligand is modified by selective replacement of atoms and/or functional groups in silico based on a specific set of steric and/or hydropathic complementarity rules involving atoms and functional groups. Relative binding scores are calculated with simple grid-based steric penalty, hydrogen bond complementarity, and with the HINT score model. Two examples are shown. First, modifying the structure of the ligand CB3717 is illustrated in a number of ways such that the binding selectivity to wild type L. casei thymidylate synthase or its E60Q mutant may be improved. Second, starting with a non-selective lead compound that had been co-crystallized with both plant and mammalian 4-hydroxyphenylpyruvate dioxygenases, new compounds (similar to selective ligands discovered by screening) to improve the selectivity of (herbicidal) inhibitors for the plant enzyme were designed by the program.

Hydropathic Complementarity Determines Interaction of Epitope 869HITDTNNK876 in Manduca sexta Bt-R1 Receptor with Loop 2 of Domain II ofBacillus thuringiensis Cry1A Toxins

In susceptible insects, Cry toxin specificity correlates with receptor recognition. In previous work, we characterized an scFv antibody (scFv73) that inhibits binding of Cry1A toxins to cadherin-like receptor. The CDR3 region of scFv73 shared homology with an 8-amino acid epitope ((869)HITDTNNK(876)) of the Manduca sexta cadherin-like receptor Bt-R(1) (Gomez, I., Oltean, D. I., Gill, S. S., Bravo, A., and Soberón, M. (2001) J. Biol. Chem. 276, 28906-28912). In this work, we show that the previous sequence of scFv73 CDR3 region was obtained from the noncoding DNA strand. However, most importantly, both scFv73 CDR3 amino acid sequences of the coding and noncoding DNA strands have similar binding capabilities to Cry1Ab toxin as Bt-R(1) (869)HITDTNNK(876) epitope, as demonstrated by the competition of scFv73 with binding to Cry1Ab with synthetic peptides with amino acid sequences corresponding to these regions. Using synthetic peptides corresponding to three exposed loop regions of domain II of Cry1Aa and Cry1Ab toxins, we found that loop 2 synthetic peptide competed with binding of scFv73 to Cry1A toxins in Western blot experiments. Also, loop 2 mutations that affect toxicity of Cry1Ab toxin are affected in scFv73 binding. Toxin overlay assays of Cry1A toxins to M. sexta brush border membrane proteins showed that loop 2 synthetic peptides competed with binding of Cry1A toxins to cadherin-like Bt-R(1) receptor. These experiments identified loop 2 in domain II of as the cognate binding partner of Bt-R(1) (869)HITDTNNK(876). Finally, 10 amino acids from beta-6-loop 2 region of Cry1Ab toxin ((363)SSTLYRRPFNI(373)) showed hydropathic pattern complementarity to a 10-amino acid region of Bt-R(1) ((865)NITIHITDTNN(875)), suggesting that binding of Cry1A toxins to Bt-R(1) is determined by hydropathic complementarity and that the binding epitope of Bt-R(1) may be larger than the one identified by amino acid sequence similarity to scFv73.

Design of a Novel Small Peptide Targeted against a Tumor-Specific Receptor

EGFRvIII is the most common deletion variant of the epidermal growth factor receptor and is found in cancers of the brain, breast, ovary, and lung. The complete absence of the receptor in healthy tissues makes it an ideal tumor marker. We sought to design a peptide ligand against EGFRvIII for development as a diagnostic imaging agent. We used the concept of hydropathic complementarity to search for sequences whose amino acid sidechains display a reciprocal pattern of hydropathicity to those of the deletion junction of EGFRvIII. The resulting peptide (PEPHC1) was synthesized and tested for binding to EGFRvIII and EGFR. In in vitro assays, PEPHC1 bound the recombinant EGFRvIII extracellular domain or full-length EGFRvIII solubilized from cell membranes in preference to native EGFR. These results demonstrate the utility of hydropathic complementarity as a basis for the design of highly specific ligands that may prove useful as tumor-targeting agents.

A monoclonal antibody directed against the neurokinin-1 receptor contains a peptide sequence with similar hydropathy and functional properties to substance P, the natural ligand for the receptor

Monoclonal antibody (mAb) PS12, obtained using the complementary peptide methodology, mimics the neuropeptide substance P (SP) in recognizing the SP-binding domain of the neurokinin-1 receptor (NK1R) and eliciting production of polyclonal antibodies cross-reacting with SP with a high affinity (Déry et al., 1997. J. Neuroimmunol. 76, 1–9). The aim of the present study was to investigate which structural features of mAb PS12 might account for this molecular mimicry. Cloning and sequencing of variable regions of both light (VL) and heavy (VH) chains of this ‘SP-like’ antibody did not indicate any primary sequence homology between SP and any antibody region. Instead, they revealed a striking similarity between the hydropathic profile of SP and that of an 11-amino-acid region in the light chain encompassing the second complementarity determining region (CDR2). When applied to CHO cells expressing the human NK1R, a synthetic extended 17-amino-acid peptide (denoted CDR2L) corresponding to this VL region inhibited the high-affinity binding of radiolabeled SP and antagonized the SP-induced inositol phosphate production. Moreover, a re-examination of the sequences of several antibodies that previously served in the design of CDR-derived bioactive peptides indicated that these antibodies also carried the hydropathic image of the respective ligands that they mimic. In agreement with previous observations on artificial synthetic peptides, our data thus suggest that the molecular mimicry between natural proteins (i.e. antibody and hormone, for example) could be understood on a structural level directly related, at least in part, to hydropathic homology. These results could then guide the search for bioactive paratope-derived peptides of potential pharmacological interest. We also observed inverse hydropathy between multiple CDRs of mAb PS12 (including CDR3H and CDR3L) and the peptide epitope, confirming the importance of hydropathic complementarity in antigen–antibody interactions.

A search within the IL-1 type I receptor reveals a peptide with hydropathic complementarity to the IL-1β trigger loop which binds to IL-1 and inhibits in vitro responses

In previous research, we were able to demonstrate that a seven amino acid residue peptide (VITFFSL), designed as an antisense peptide of the β-bulge trigger loop region of interleukin 1β (IL-1β) (QGEESND; residues 48–54 [mature protein sequence]), was able to interact with IL-1 specifically and inhibit the response to IL-1 in an in vitro bioassay. The evidence was consistent with a specific interaction ocurring between antisense peptide and the trigger loop region. On the basis that antisense peptides are able to interact with their corresponding sense peptide sequences as a result of their mutually complementary hydropathic profiles (Fassina G., Verdoliva, A., Cassani, G., Melli, M., 1994. Binding of type I IL-1 receptor fragment 151–162 to IL-1. Growth Factors 10, 99–106; Maier, C.C., Moseley, H.N.B., Zhou, S., Whitaker, J.N., Blalock, J.E., 1994. Indentification of interactive determinants on idiotypic-anti-idiotypic antibodies through comparison of their hydropathic profiles. Immunomethods 5, 107–113), we devised a computer program (FINDH) to search the amino acid residue sequence of interleukin-1 type 1 receptor (IL-1 R1) for peptide motifs possessing hydropathic complementarity to the trigger loop sequence. The most complementary “best-fit peptide” motif (LITVLNI) was located in the third extracellular domain of IL-1 R1. A best-fit peptide corresponding to this motif was synthesised and found to bind to IL-1β as well as inhibit the response to IL-1 in two independent in vitro bioassays (monitoring IL-1 dependent serum amyloid A synthesis and IL-1 dependent alkaline phosphatase activity, respectively). A second peptide motif (VIEFITL) was identified and the corresponding peptide synthesised along with a reordered version (LTILINV) of the best fit peptide. Both failed to bind measurably with IL-1β or inhibit the response to IL-1 in the two bioassays. This best fit peptide behaved very similarly, in terms of IL-1 binding and inhibition behaviour, to the original trigger loop antisense peptide. Reference to the recently released X-ray crystal structure of IL-1β and the IL1-R1 extracellular domain shows that the best fit peptide motif in IL-1 R1 is not apparantly interacting with the IL-1 trigger loop, although both are close in space. The intriguing possibility exists that the best fit peptide motif could represent an alternative site for IL-1β receptor interaction which has not thus far been identified.

Identification in the NK1 tachykinin receptor of a domain involved in recognition of neurokinin A and septide but not of substance P

The three mammalian tachykinins, substance P (SP), neurokinin A (NKA) and neurokinin B (NKB), exert their physiological effects through specific receptors, NK1, NK2 and NK3, respectively. However, homologous binding studies have recently demonstrated that, contrary to the generally accepted belief, NKA could bind NK1 receptor with high affinity (Hastrup and Schwartz, 1996). Using COS-7 cells expressing the human NK1 receptor, we show that two simultaneous point mutations (E193L and V195R) in a restricted five amino acid sequence (the (193–197) region), selected because of its hydropathic complementarity with the common C-terminal extremity of tachykinins, abolish both the high-affinity binding and highly potent biological activity of NKA, without affecting those of SP. In addition, the same mutations also suppressed the high functional activity of septide, a synthetic SP atypical agonist ([pGlu 6-Pro 9] SP 6–11). These results suggest that the (193–197) region, located at the end of the second extracellular loop of the receptor, could be part of a common high-affinity binding domain for both NKA and septide, distinct from the SP binding site.

MIMOTOPES, CONTINUOUS PARATOPES AND HYDROPATHIC COMPLEMENTARITY: NOVEL APPROXIMATIONS IN THE DESCRIPTION OF IMMUNOCHEMICAL SPECIFICITY

ABSTRACT Most antigenic sites of proteins, known as discontinuous epitopes, are made up of residues on different loops that are brought together by the folding of the polypeptide chain. The individual loops are sometimes able, on their own, to bind to the antibody and they are then known as continuous epitopes. The binding sites of antibodies, known as paratopes, are built up from residues on six hypervariable loops known as complementarity determining regions (CDRs). Peptides corresponding to individual CDR loops are often able to bind the antigen and such peptides may be viewed as continuous paratopes. Using random combinatorial peptide libraries, it is possible to obtain peptides that bind to an antiprotein antibody without showing any sequence similarity with any part of the protein. Such epitope mimics are called mimotopes provided they are able also to elicit antibodies that react with the original antigen. The binding activity of mimotopes may partly be due to the phenomenon of hydropathic complementarity between epitope and paratope peptides. Although these concepts are vague in their structural connotation, they are useful for describing the immunological activity of linear peptides.

Importance of hydropathic complementarity for the binding of the neuropeptide substance P to a monoclonal antibody: Equilibrium and kinetic studies

In a previous study (Boquet et al., 1995, Molec. Immunol. 32, 303–308) we observed remarkable inversions of hydropathic profiles between complementarity determining regions (CDRs) of an anti-substance P monoclonal antibody (SP31) and the corresponding 5 amino acid C-terminal peptide epitope. Here we demonstrate the importance this hydropathic complementarity by measuring the immunoreactivity of SP-related peptides which have been modified in their C-terminal parts so that hydropathic profile has been conserved (by substituting amino acids in the epitope) or modified (by mixing the sequence of amino acids in the epitope). Experiments performed in equilibrium conditions using a competitive enzyme immunoassay showed that most of the peptides conserving the hydropathic profile of SP epitope were recognized by mAb SP31 (even if marked variations in affinity were observed), while those for which the hydropathic profile was modified exhibited very low or undetectable affinity. The kinetic parameters ( k a and k d) of peptide-antibody interactions were determined using Surface Plasmon Resonance technology (BIACORE 2000). These measurements showed that all peptides recognized by mAb SP31 had similar association rate constants (close to 2 × 10 5 M −1 s −1), differences in binding affinities essentially resulting from differences in dissociation rate constants (ranging from 1.61 × 10 −4 to 1.15 × 10 −1 s −1). From these results, it was concluded that hydropathic complementarity between the epitope and the paratope could be a necessary but not sufficient condition for establishing high-affinity binding. We hypothesize that hydropathic interactions may play a critical role during the first contacts between antibody CDRs and the peptide, possibly by favouring reorganization of water molecules at the antibody-peptide interface.

Is hydropathic complementarity involved in antigen-antibody binding?

Is hydropathic complementarity involved in antigen-antibody binding?

Identification of Interactive Sites of Proteins and Protein Receptors by Computer-Assisted Searches for Complementary Peptide Sequences

Protein sites important for receptor binding have been identified in several systems by searching for protein/receptor stretches characterized by hydropathic anti-complementarity. A computer-assisted method [SITESEARCH] has been developed to identify protein sites responsible for receptor recognition, once the amino acid sequences of the protein ligand and its receptor are available. The software first determines the hydropathic profiles of the two polypeptide chains under investigation, and then compares profiles of preselected length, determining at the same time the degree of their hydropathic complementarity. The procedure is repeated until all the different segments in the two chains are compared. Fragments characterized by the maximal level of hydropathic complementarity are selected as putative binding sites. This approach has been initially applied to the interleukin-1β (IL-1β)/receptor type I case. SITESEARCH identified residues 88-99 in IL-1β and 151-162 in the receptor as the sequence pair characterized by the maximal level of hydropathic complementarity. These fragments, once produced by chemical synthesis, have displayed specific recognition properties for each other, as detected by solid-phase binding assays. The IL-1β sequence identified corresponds to a highly exposed part of the protein molecule, and substitution of this sequence with another of the same length but with different hydropathic characteristics generated mutants with drastically reduced binding activity to the receptor. Mutations in this sequence did not alter the protein biological activity, thus suggesting the structural integrity of the mutants. Cumulatively, these results validate the SITESEARCH prediction, suggesting that IL-1β sequence 88-99 is involved in at least a portion of the protein/receptor binding site.

Binding of Type I IL-1β Receptor Fragment 151–162 to Interleukin-1β

The relevance of hydropathically complementary sequences in ligand receptor interactions has been evaluated in the interleukin-1 beta/receptor type I case. Computer assisted comparison of the hydropathic profiles of IL-1 beta and its receptor (type I) identified residues 88-99 in IL-1 beta and 151-162 in the receptor as the sequences pair characterized by the highest level of hydropathic complementarity. These fragments, once produced by chemical synthesis and derivatized with biotin, displayed specific recognition properties for each other, as detected by solid phase binding assays. Binding between the two fragments occurred independently from the assay format, was saturable and specifically inhibited by unlabeled peptides. Receptor fragment (151-162) derivatized with biotin recognized also full length recombinant IL-1 beta, and binding was inhibited to 50% in the presence of 3 microM IL-1 beta (88-99) peptide. Interaction specificity was further confirmed by the non competitive effect on the interaction of a sequence scrambled IL-1 beta (88-99) peptide. In a similar way, full length biotinylated IL-1 beta recognized immobilized IL-1 beta receptor fragment (151-162), and this interaction was diminished in the presence of unlabeled receptor fragment or IL-1 beta Results indicate that IL-1 beta receptor fragment (151-162) binds IL-1 beta recognizing the IL-1 beta (88-99) sequence, thus suggesting a possible role of these fragments in the protein/receptor recognition surface.

Sequence-directed recognition peptides: inhibition of endothelin generation via a substrate-depletion mechanism

Sequence-directed recognition peptides (SDRPs) were constructed on the basis of their hydropathic complementarity for big-endothelin (bigET). These peptides can inhibit in vitro the proteolytic cleavage that generates endothelin (ET) from its bigET precursor. Comparison of dissociation constants of the complexes SDRP:bigET with kinetic constants obtained for the cleavage of bigET by α-chymotrypsin (taken as a model proteinase) provides evidence of the potential of SDRPs. This is a novel application of SDRPs used as inhibitors of a proteolytic reaction.

Prediction of homologous binding sites on RB and p107 common for viral oncoproteins and cellular ligands.

Hydropathic anticomplementarity of amino acids specifies that peptides translated from complementary DNA strands may acquire amphiphilic conformations and bind to each other. This concept has been coined 'Molecular Recognition Theory' (MRT) or 'complementary peptide theory'. Inactivation of retinoblastoma protein (RB), a tumor suppressor gene product, has been shown to be involved in the pathogenesis of many tumors and to be due to either mutation of the RB gene, hyperphosphorylation or complex formation with viral oncoproteins. The viral oncoproteins share a common RB binding motif with cellular ligands. The exact site on RB associating with this common RB binding motif of viral oncoproteins and cellular ligands has not been identified yet. This study is the first to predict putative binding sites on RB and p107, a cellular protein with RB sequence homology, respectively, by using the hydropathic complementarity approach. These sites are residues 649-654 of RB and 657-662 of p107. Moreover, this paper proposes a structure for a potential antineoplastic agent based on the amino acid sequence of the predicted RB binding site. The data presented herein should have important implications both for the understanding of cancer pathophysiology and for the drug design of antineoplastic compounds.

Proposed interaction between insulin and retinoblastoma protein.

Retinoblastoma protein (RB) is a tumor suppressor gene product involved in embryogenesis and cell cycle progression. One of the major mechanisms leading to RB dysfunction is complex formation with viral oncoproteins using the common RB binding motif Leu X Cys X Glu (LXCXE) which has also been identified in cellular ligands, e.g., RBP-1 and RBP-2. p107, a cellular protein with RB sequence homology, has been shown to bind to the same viral oncoproteins associating with RB and is therefore thought to contribute to cell cycle regulation. It has recently been suggested that insulin stimulates gene transcription through direct association with an, as yet, unidentified intracellular transcription factor. Due to the central roles of RB and p107 in coupling external growth signals with the progression of the cell cycle clock, we have hypothesized that these two proteins might be candidates for mediating the effects of insulin on DNA. We report here the identification of a region in the B-chain of human insulin that has the sequence LXCXE. Based on this finding we predict that the insulin B-chain may interact with RB and/or p107. Since we have also identified sequences hydropathically related to LXCXE in insulin-like growth factor I (IGF-I) and II (IGF-II), but not in relaxin, nerve growth factor, epidermal growth factor, glucagon or beta-endorphin, we further propose that both IGF-I and -II may assemble with RB and/or p107, too. Moreover, binding sites on RB and p107 identical with those suggested for viral oncoproteins and cellular ligands are predicted for insulin/IGF-I/IGF-II by using the hydropathic complementarity approach.(ABSTRACT TRUNCATED AT 250 WORDS)

A model for hydropathy-based peptide interactions

Two peptides are specified when the noncoding DNA strand is read in the 5′ to 3′, or the 3′ to 5′ direction, and both peptides form strong complexes with the natural peptide, as found by J. E. Blalock and K. L. Bost with ACTH ((1986) Biochem. J. 234, 679–683). We report here that strong hydropathic complementarity (pairing of hydrophobic with hydrophilic residues), the assumed basis of these interactions, is obtained only if the peptide resulting from reading in the 3′ to 5′ direction is aligned parallel to the natural peptide, or if the peptide derived by opposite reading of the DNA is aligned antiparallel to it. Complementary is abolished in other alignments, including all staggered ones. In the appropriate alignments of the constructs the amino acid residues opposite one another are specified by a pair of complementary codons in the DNA; Blalock and Bost have indeed shown that complementary pairs of codons specify amino acids of opposite hydropathy. A model is proposed to explain how hydropathic complementarity can lead to interaction between peptides. We propose that in the interacting peptides hydrophilic residues of both chains are oriented toward the aqueous solvent, while the hydrophobic ones form the interphase between the two chains. Tight packing is made possible by the stipulation that whenever a hydrophilic residue turns toward the aqueous phase, a space is liberated which can accommodate a hydrophobic residue from the opposing chain. This entropy-driven configuration can lead to strong interactions between portions of peptides consisting of hydropathically complementary residues.