Molecular Recognition Theory Research Articles

Role of Solvation in Drug Design as Revealed by the Statistical Mechanics Integral Equation Theory of Liquids.

Recent developments and applications in theoretical methods focusing on drug design and particularly on the solvent effect in molecular recognition based on the three-dimensional reference interaction site model (3D-RISM) theory are reviewed. Molecular recognition, a fundamental molecular process in living systems, is known to be the functional mechanism of most drugs. Solvents play an essential role in molecular recognition processes as well as in ligand-protein interactions. The 3D-RISM theory is derived from the fundamental statistical mechanics theory, which reproduces all solvation thermodynamics naturally and has some advantages over conventional solvation methods, such as molecular simulation and the continuum model. Here, we review the basics of the 3D-RISM theory and methods of molecular recognition in its applications toward drug design.

Molecular recognition theory and sense-antisense interaction therapeutic applications in autoimmunity

Perhaps behind only the understanding of the genetic code in importance is the comprehension of protein sequence and structure in its effect on modern scientific investigation. How proteins are structured and interact dictates a considerable amount of the body's processes in maintaining homeostasis. Unfortunately, in diseases of autoimmunity, these processes are directed against the body itself and most of the current clinical responses are severely lacking. This review addresses current therapeutics involved in the treatment of various autoimmune diseases and details potential future therapeutics designed with a more targeted approach. Detailed in this manuscript is the concept of utilizing peptides possessing an inverse hydropathy to the immunogenic region of proteins to generate anti-idiotypic (anti-Id) and anti-clonotypic T cell receptor (TCR) antibodies (Abs). Theoretically, the anti-Id Abs cross react with Id Abs and negate the powerful machinery of the adaptive immune response with little to no side effects. A series of studies by a number of groups have shown this to be an exciting and intriguing concept that will likely play a role in the future treatment of autoimmune diseases.

Molecular recognition theory and sense-antisense interaction: therapeutic applications in autoimmunity

Perhaps behind only the understanding of the genetic code in importance is the comprehension of protein sequence and structure in its effect on modern scientific investigation. How proteins are structured and interact dictates a considerable amount of the body's processes in maintaining homeostasis. Unfortunately, in diseases of autoimmunity, these processes are directed against the body itself and most of the current clinical responses are severely lacking. This review addresses current therapeutics involved in the treatment of various autoimmune diseases and details potential future therapeutics designed with a more targeted approach. Detailed in this manuscript is the concept of utilizing peptides possessing an inverse hydropathy to the immunogenic region of proteins to generate anti-idiotypic (anti-Id) and anti-clonotypic T cell receptor (TCR) antibodies (Abs). Theoretically, the anti-Id Abs cross react with Id Abs and negate the powerful machinery of the adaptive immune response with little to no side effects. A series of studies by a number of groups have shown this to be an exciting and intriguing concept that will likely play a role in the future treatment of autoimmune diseases.

Silk Protein Assisted<i> Ex Vivo</i> Remineralization of Enamel-Like Microstructure

Based on the basic theory of molecular recognition, we designed an organic molecules model that spontaneously form three-dimensional fibrillar scaffolds to induce the crystallization of hydroxyapatite to synthesized enamel-like calcium phosphate/hydroxyapatite under a controllable way in vitro. Cross-linking of collagen on the dentin surface and silk fibroin with N,N-(3-dimethylaminopropyl)-N'-ethyl-carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) was optimized by varying the NHS/EDC molar ratio at constant EDC concentration. CaCl2 and Na3PO4-12H2O solution was added with Ca: P odd as 1.67:1 after conjugated. The results showed that the dentinal tubule were blocked by neonatal hydroxyapatite layer which has a continuous structure of columns crystal with size of 10-40nm. Furthermore, there were column crystal with parallel direction inside, similar to the crystal array in the top of enamel rod. The results suggest that silk protein monolayer may be useful in the modulation of mineral behavior during in situ dental tissue engineering.

Functions of Biomolecule Revealed by Statistical Mechanics of Molecular Recognition

Recent progress in the theory of molecular recognition in biomolecules is reviewed, which has been made based on the statistical mechanics of liquids or the 3D-RISM/RISM theory. The molecular recognition of a ligand by the protein is realized by the 3D-distribution functions: if one finds some conspicuous peaks in the distribution of a ligand inside protein, then the ligand is regarded as “recognized” by the protein. 3D-distribution functions can be obtained by means of 3D-RISM/RISM theory. Some biochemical processes are investigated, which are intimately related to the molecular recognition of small ligands such as water, ions, and carbon monoxide by a protein.

Biomimetic Synthesis of Tooth-Like Hydroxyapatite under Organic Polymer Monolayer

Based on the basic theory of molecular recognition , we design a organic molecules model to induce the crystallization of hydroxyapatite to synthesized tooth-like calcium phosphate/hydroxyapatite under a controllable way in vitro. The cross-linking of collagen on the dentin surface and extraneous collagen was optimized by varying the molar ratio of N,N-(3-dimethylaminopropyl)- N'-ethyl-carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) at a constant EDC concentration. CaCl2 and Na3PO4-12H2O solutions were added after the crosslinking process. X-ray photoelectron spectroscopic (XPS) and Fourier transform infrared spectroscopy (FTIR) analysis of organic protein monolayer for samples. The obtained composite were characterized by X-ray diffraction (XRD) and scanning electron microscopy (SEM) as well as energy dispersive X-ray (EDX). XPS and FTIR analysis showed the surface organic compositions in experimental group is higher than that of normal dentin and decalcified dentin surface. The results showed that the dentinal tubule were blocked by neonatal hydroxyapatite layer which has a continuous structure of columns crystal with size of 10-40nm. Furthermore, there were column crystal with parallel direction inside, similar to the crystal array in the top of enamel rod. This study showed that the specific organic molecule model can be used as a potential effective crystal growth modifier.

Molecular Recognition in Biomolecules Studied by Statistical-Mechanical Integral-Equation Theory of Liquids

Recent progress in the theory of molecular recognition in biomolecules is reviewed, which has been made based on the statistical mechanics of liquids or the RISM/3D-RISM theory during the last five years in the authors' group. The method requires just the structure of protein and the potential energy parameters for the biomolecules and solutions as inputs. The calculation is carried out in two steps. The first step is to obtain the pair correlation functions for solutions consisting of water and ligands based on the RISM theory. Then, given the pair correlation functions prepared in the first step, we calculate the 3D-distribution functions of water and ligands around and inside protein based on the 3D-RISM theory. The molecular recognition of a ligand by the protein is realized by the 3D-distribution functions: if one finds some conspicuous peaks in the distribution of a ligand inside protein, then the ligand is regarded as "recognized" by the protein. Some biochemical processes are investigated, which are intimately related to the molecular recognition of small ligands including water, noble gases, and ions by a protein.

Controlled Crystallization of Tooth-Like Hydroxyapatite under Gelatin Monolayer

Based on the molecular recognition theory, an organic molecules model was designed to induce the hydroxyapatite crystallization, to build a tooth-like calcium phosphate/hydroxyapatite under a controllable way in vitro. The cross-linking of collagen on the dentin surface and gelatin was optimized by varying the molar ratio of N,N-(3-dimethylaminopropyl)- N'-ethyl-carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) at a constant EDC concentration. CaCl2 and Na3PO4-12H2O solutions were added after the crosslinking process. The whole process requires repeating the crosslinking and mineralization process for five times. The obtained composite were characterized by X-ray diffraction (XRD) and scanning electron microscopy (SEM) as well as energy dispersive X-ray photoelectron spectroscopy (XPS). The results showed that the dentinal tubule were blocked by neonatal hydroxyapatite layer which has a continuous structure of columns crystal with size of 10-40nm. Furthermore, there was column crystal with parallel direction inside, similar to the crystal array in the top of enamel rod. This study showed that the specific organic molecule model can be used as a potential effective crystal growth modifier.

Molecular Recognition Theory of the complementary (antisense) peptide interactions

Molecular Recognition Theory is based on the finding of Blalock et al. (Biochem. Biophys. Res. Commun. 121 (1984) 203–207; Nature Med. 1 (1995) 876–878; Biochem. J. 234 (1986) 679–683) that peptides specified by the complementary RNAs bind to each other with higher specificity and efficacy. This theory is investigated considering the interaction of the sense peptides coded by means of messenger RNA (read in 5′→3′ direction) and antisense peptides coded in 3′→5′ direction. We analysed the hydropathy of the complementary amino acid pairs and their frequencies in 10 peptide–receptor systems with verified ligand–receptor interaction. An optimization procedure aimed to reduce the number of possible antisense peptides derived from the sense peptide has been proposed. Molecular Recognition Theory was also validated by an “in vivo” experiment. It was shown that 3′→5′ peptide antisense of α-MSH abolished its cytoprotective effects on the gastric mucosa in rats. Molecular Recognition Theory could be useful method to simplify experimental procedures, reduce the costs of the peptide synthesis, and improve peptide structure modelling.

Sex-specific effects of dual ET-1/ANG II receptor (Dear) variants in Dahl salt-sensitive/resistant hypertension rat model

Essential (polygenic) hypertension is a complex genetic disorder that remains a major risk factor for cardiovascular disease despite clinical advances, reiterating the need to elucidate molecular genetic mechanisms. Elucidation of susceptibility genes remains a challenge, however. Blood pressure (BP) regulatory pathways through angiotensin II (ANG II) and endothelin-1 (ET-1) receptor systems comprise a priori candidate susceptibility pathways. Here we report that the dual ET-1/ANG II receptor gene (Dear) is structurally and functionally distinct between Dahl salt-sensitive, hypertensive (S) and salt-resistant, normotensive (R) rats. The Dahl S S44/M74 variant is identical to the previously reported Dear cDNA with equivalent affinities for both ET-1 and ANG II, in contrast to Dahl R S44P/M74T variant, which exhibits absent ANG II binding but effective ET-1 binding. The S44P substitution localizes to the ANG II-binding domain predicted by the molecular recognition theory, providing compelling support of this theory. The Dear gene maps to rat chromosome 2 and cosegregates with BP in female F2(RxS) intercross rats with highly significant linkage (LOD 3.61) accounting for 14% of BP variance, but not in male F2(RxS) intercross rats. Altogether, the data suggest the hypothesis that modification of the critical balance between ANG II and ET-1 systems through variant Dear contributes to hypertension susceptibility in female F2(RxS) intercross rats. Further investigations are necessary to corroborate genetic linkage through congenic rat studies, to investigate putative gene interactions, and to show causality by transgenesis and/or intervention. More importantly, the data reiterate the importance of sex-specific factors in hypertension susceptibility.

Identification of a Novel V1-type AVP Receptor Based on the Molecular Recognition Theory

The molecular recognition theory predicts that binding domains of peptide hormones and their corresponding receptor binding domains evolved from complementary strands of genomic DNA, and that a process of selective evolutionary mutational events within these primordial domains gave rise to the high affinity and high specificity of peptide hormone-receptor interactions observed today in different peptide hormone-receptor systems. Moreover, this theory has been broadened as a general hypothesis that could explain the evolution of intermolecular protein-protein and intramolecular peptide interactions. Applying a molecular cloning strategy based on the molecular recognition theory, we screened a rat kidney cDNA library with a vasopressin (AVP) antisense oligonucleotide probe, expecting to isolate potential AVP receptors. We isolated a rat kidney cDNA encoding a functional V1-type vasopressin receptor. Structural analysis identified a 135 amino acid-long polypeptide with a single transmembrane domain, quite distinct from the rhodopsin-based G protein-coupled receptor superfamily. Functional analysis of the expressed V1-type receptor in Cos-1 cells revealed AVP-specific binding, AVP-specific coupling to Ca2+ mobilizing transduction system, and characteristic V1-type antagonist inhibition. This is the second AVP receptor cDNA isolated using AVP antipeptide-based oligonucleotide screening, thus providing compelling evidence in support of the molecular recognition theory as the basis of the evolution of this peptide hormone-receptor system, as well as adds molecular complexity and diversity to AVP receptor systems.

Evolution of the genetic code: the nonsense, antisense, and antinonsense codes make no sense

According to the molecular recognition theory, the complementarity of the sense and nonsense DNA strands is reflected in a complementarity of polypeptides and the corresponding nonsense polypeptides. A comparison of the sense and nonsense code matrices, and of the antisense and antinonsense code matrices, either by visual inspection or by comparing the corresponding hydrophobicity matrices (e.g. by simply adding them together), revealed no complementarity of these pairs of matrices in terms of possible attractive physical forces. Instead, it was evident that the codes divide the amino acids into two major groups: hydrophilic and hydrophobic, a division which is directly correlated with the folding property of proteins. A simple primordial genetic code distinguishing between these two types of amino acids would have been capable of generating three-dimensionally folded peptides, which could stabilize coding RNAs by forming ribonucleoprotein complexes. This evolutionary scheme is reflected in the present organisation of information processing and storage in essentially all organisms. RNAs are processed and translated into proteins by ribonucleoproteins, while other steps in information retrieval and processing, such as DNA replication, transcription, protein folding and posttranslational processing, are catalyzed by proteins. This shows that the evolution of DNA as an information storage medium was a secondary event, unrelated to the evolution of the genetic code. From the primordial hydrophilic/hydrophobic (f.ex. Leu/Arg) code, evolution proceeded by introduction of a catalytic amino acid (Ser). The further evolution of the code has mainly served to increase the number of functional hydrophilic amino acids, since there has not been a great advantage in increasing the number of structural, hydrophobic amino acids. At some stage during the evolution of the genetic code, double-stranded DNA was introduced as a maximally safe genetic copy of RNA. This required the action of highly specific enzymes, and was therefore preceded by the refinement of the genetic code. As a conclusion of this evolutionary scheme, it can be inferred that, in general only the sense strand encodes proteins.

Towards a theory of molecular recognition

Why do we have a continuous conception of the opening of doors? Actually because the rotations around the hinges act as conceptual tools that allow us to “think” of door arrangements as continuously interchangeable states. If our geometrical tooling were reduced to the identity, then our conception of door opening would reduce to the dichotomous alternative closed/non-closed. This example highlights the role of geometry in the conception of physical phenomena. Accordingly, the recently introduced “gauge” geometries result in an original approach to molecular recognition when applied to quantum molecular states. In particular, this theory features a graphical description of molecular recognition between biomolecules. The 2D theory is discussed. The application of 2D gauge geometry to the description of chirality is also briefly presented.

Есть ли место антисенс-пептидам в теории молекулярного узнавания?

Есть ли место антисенс-пептидам в теории молекулярного узнавания?

Molecular Characterization of a Dual Endothelin-1/Angiotensin II Receptor

The molecular recognition theory (MRT) provides a conceptual framework that could explain the evolution of intermolecular and intramolecular interaction of peptides and proteins. As such, it predicts that binding sites of peptide hormones, and its receptor binding sites were originally encoded by and evolved from complementary strands of genomic DNA. On the basis of principles underlying the MRT, we screened a rat brain complementary DNA library using an AngII followed by an endothelin-1 (ET-1) antisense oligonucleotide probe, expecting to isolate potential cognate receptors. An identical cDNA clone was isolated independently from both the AngII and ET-1 oligonucleotide screenings. Structural analysis revealed a receptor polypeptide containing a single predicted transmembrane region with distinct ET-1 and AngII putative binding domains. Functional analysis demonstrated ET-1- and AngII-specific binding as well as ET-1- and AngII-induced coupling to a Ca2+ mobilizing transduction system. Amino acid substitutions within the predicted ET-1 binding domain obliterate ET-1 binding while preserving AngII binding, thus defining the structural determinants of ET-1 binding within the dual ET-1/AngII receptor, as well as corroborating the dual nature of the receptor. Elucidation of the dual ET-1/AngII receptor provides further molecular genetic evidence in support of the molecular recognition theory and identifies for the first time a molecular link between the ET-1 and AngII hormonal systems that could underlie observed similar physiological responses elicited by ET-1 and AngII in different organ systems. The prominent expression of the ET-1/AngII receptor mRNA in brain and heart tissues suggests an important role in cardiovascular function in normal and pathophysiological states.

Identification of a novel dual angiotensin II/vasopressin receptor on the basis of molecular recognition theory.

The molecular recognition theory suggests that binding sites of interacting proteins, for example, peptide hormone and its receptor binding site, were originally encoded by and evolved from complementary strands of genomic DNA. To test this theory, we screened a rat kidney complementary DNA library twice: first with the angiotensin II (AII) followed by the vasopressin (AVP) antisense oligonucleotide probe, expecting to isolate cDNA clones of the respective receptors. Surprisingly, the identical cDNA clone was isolated twice independently. Structural analysis revealed a single receptor polypeptide with seven predicted transmembrane regions, distinct AII and AVP putative binding domains, a Gs protein-activation motif, and an internalization recognition sequence. Functional analysis revealed specific binding to both AII and AVP as well as AII- and AVP-induced coupling to the adenylate cyclase second messenger system. Site-directed mutagenesis of the predicted AII binding domain obliterates AII binding but preserves AVP binding. This corroborates the dual nature of the receptor and provides direct molecular genetic evidence for the molecular recognition theory.

Identification of an idiotypic peptide recognized by autoantibodies in human immunodeficiency virus-1-infected individuals.

Antibodies against HIV-1 proteins in HIV-1-infected individuals share a cross-reactive idiotype defined by the monoclonal antiidiotypic antibody 1F7 (5). Using a computer algorithm based on the molecular recognition theory, regions of inverse hydropathy between the variable sequence of 1F7 and human monoclonal anti-HIV-1 antibodies were identified, which are assumed to be involved in idiotype-antiidiotype contacts. A peptide was designed from the proposed contact in the variable heavy chain framework 3-complementarity determining region 3 (FR3-CDR3) of human antibodies and was synthesized. This peptide is recognized by the antiidiotype 1F7 and inhibits the binding of 1F7 to human anti-HIV-1 antibodies which express the 1F7 idiotype. A survey of normal and HIV-1-infected sera revealed the presence of antibodies in infected sera which bind to the FR3-CDR3 peptide. The biological relevance of autoantibodies against a self idiotope associated with HIV-1 infection is discussed in the context of the regulation of the antibody response to HIV-1.

Complementary Peptides as Antibody Mimetics for Protein Purification and Assay

The possibility of designing sequence-directed recognition peptides (complementary peptides) able to noncovalently associate target peptides or proteins is one of the most important biotechnological applications deriving from the molecular recognition theory [MRT]. Complementary peptides can be used widely as synthetic ligands for the development of affinity purification strategies to isolate target peptides or proteins from crude sources. Generally, the observed affinity and selectivity are sufficient to allow one-step purification of target molecules directly from crude mixtures and the possibility of producing the ligands in enzymatically stable forms greatly enhance their applicability. In addition, the noninterference of nonionic detergents or denaturants on recognition expand their use in the case of poorly soluble targets. The ligand′s synthetic nature overcomes all the problems associated with the use of immunoaffinity columns, since the possibility of biological contaminations is extremely limited. Numerous examples demonstrate the usefulness of this methodology, which allows the creation of a large number of peptidyl ligands tailored to specific purification needs. Recognition properties of complementary peptides can be applied also to the development of solid-phase assays for the identification and quantification of different molecular targets. As antibody mimetics, they can be used on solid phases to capture, and then to detect and consequently quantify, the desired target polypeptide in complex biological mixtures. Even if assay sensitivity cannot be compared with conventional antibody-based assays, the simplicity of complementary peptide design and production makes their use an attractive alternative in various circumstances.

Antisense peptides to the 43-57 region of acylphosphatase and to the 46-60 region of two isoenzymes of a low-M(r) phosphotyrosine protein phosphatase do not interact with the corresponding proteins.

Three peptides complementary to exposed regions of two low-M(r) phosphotyrosine protein phosphatase isoenzymes and of the acylphosphatase muscle isoenzyme have been synthesized. Each peptide was synthesized on two different types of resins; the peptides were anchored to the resins by amide linkages. The peptide resins were checked by amino acid analysis and Edman degradation and directly used for enzyme purification. Despite our attempts, none of the resins was able to bind significant amounts of the corresponding protein, indicating the lack of interaction between the three proteins and the corresponding complementary peptides. This result agrees with many other reports, confirming that the molecular-recognition theory has no general validity.

Nuclear Magnetic Resonance Studies on Complementary Peptides

From the original observation that the codons for the hydrophobic and hydrophilic amino acids on one strand of the DNA may be complemented by the codons for the hydrophilic and hydrophobic amino acids, respectively, on the complementary strand, arose the molecular recognition theory which forms the basis for much of the work involving complementary peptides. A number of examples have been documented where peptides with inverted hydropathic profiles have been shown to form complexes in high-affinity chromatography and solid matrix binding assays. Nevertheless, our current understanding of the molecular forces leading to the formation of these complexes is rather rudimentary, and it is highly desirable to have a detailed three-dimensional structure of a complex of interacting complementary peptides. In this article, we provide a brief review of the solution NMR work done by different laboratories in an attempt to study these interactions.