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2.
Protein Pept Lett ; 14(4): 381-7, 2007.
Article in English | MEDLINE | ID: mdl-17504096

ABSTRACT

Di/oligomerization of G-protein coupled receptors (GPCRs) is well established, however very little is known regarding the interaction details. Current paper presents results of molecular dynamics simulations of theoretical model of rhodopsin tetramer with transducine (Gt) in lipid bilayer. Ligand-protein and receptor-receptor interactions have been proposed.


Subject(s)
Rhodopsin/chemistry , Transducin/chemistry , Computer Simulation , Lipid Bilayers/chemistry , Models, Molecular , Protein Structure, Quaternary
3.
Protein Eng ; 14(10): 747-52, 2001 Oct.
Article in English | MEDLINE | ID: mdl-11739892

ABSTRACT

Molecular simulations able to exactly represent solvated charged proteins are helpful in understanding protein dynamics, structure and function. In the present study we have used two different starting structures of papain (a typical, stable, globular protein of intermediate net charge) and different modeling procedures to evaluate some effects of counterions in simulations. A number of configurations have been generated and relaxed for each system by various combinations of constrained simulated annealing and molecular dynamics procedures, using the AMBER force field. The analysis of trajectories shows that the simulations of solvated proteins are moderately sensitive to the presence of counterions. However, this sensitivity is highly dependent on the starting model and different procedures of equilibration used. The neutralized systems tend to evince smaller root mean square deviations regardless of the system investigated and the simulation procedure used. The results of parameterized fitting of the simulated structures to the crystallographic data, giving quantitative measure of the total charge influence on the stability of various elements of the secondary structure, revealed a clear scatter of different reactions of various systems' secondary structures to counterions addition: some systems apparently were stabilized when neutralized, while the others were not. Thus, one cannot unequivocally state, despite consideration of specific simulation conditions, whether protein secondary structures are more stable when they have neutralized charges. This suggests that caution should be taken when claiming the stabilizing effect of counterions in simulations other than those involving small, unstable polypeptides or highly charged proteins.


Subject(s)
Computer Simulation , Ions/chemistry , Proteins/chemistry , Papain/chemistry , Protein Conformation
4.
Acta Biochim Pol ; 48(1): 1-20, 2001.
Article in English | MEDLINE | ID: mdl-11440158

ABSTRACT

Cysteine proteases (CPs) are responsible for many biochemical processes occurring in living organisms and they have been implicated in the development and progression of several diseases that involve abnormal protein turnover. The activity of CPs is regulated among others by their specific inhibitors: cystatins. The main aim of this review is to discuss the structure-activity relationships of cysteine proteases and cystatins, as well as of some synthetic inhibitors of cysteine proteases structurally based on the binding fragments of cystatins.


Subject(s)
Cysteine Endopeptidases/chemistry , Cysteine Proteinase Inhibitors/chemistry , Amino Acid Motifs , Amino Acid Sequence , Amino Acids/chemistry , Animals , Catalytic Domain , Conserved Sequence , Humans , Models, Molecular , Molecular Sequence Data , Phylogeny , Protein Structure, Tertiary , Sequence Homology, Amino Acid
5.
Acta Biochim Pol ; 48(1): 131-5, 2001.
Article in English | MEDLINE | ID: mdl-11440162

ABSTRACT

Molecular docking simulations are now fast developing area of research. In this work we describe an effective procedure of preparation of the receptor-ligand complexes. The amino-acid residues involved in ligand binding were identified and described.


Subject(s)
Ligands , Receptors, Oxytocin/chemistry , Receptors, Oxytocin/metabolism , Receptors, Vasopressin/chemistry , Receptors, Vasopressin/metabolism , Amino Acids/chemistry , Biophysical Phenomena , Biophysics , Humans , Models, Molecular , Protein Binding , Temperature
6.
Acta Biochim Pol ; 48(1): 35-52, 2001.
Article in English | MEDLINE | ID: mdl-11440182

ABSTRACT

The oligomeric metalloenzymes protein phosphatases dephosphorylate OH groups of Ser/Thr or Tyr residues of proteins whose actions depend on the phosphorus signal. The catalytic units of Ser/Thr protein phosphatases 1, 2A and 2B (PP1c, PP2Ac and PP2Bc, respectively), which exhibit about 45% sequence similarity, have their active centers practically identical. This feature strongly suggests that the unknown structure of PP2Ac could be successfully homology-modeled from the known structures of PP1c and/or PP2Bc. Initially, a theoretical model of PP1c was built, including a phosphate and a metal dication in its catalytic site. The latter was modeled, together with a structural hydroxyl anion, as a triangular pseudo-molecule (Zno or Mno), composed of two metal cations (double Zn2+ or Mn2+, respectively) and the OH- group. To the free PP1c two inhibitor sequences R29RRRPpTPAMLFR40 of DARPP-32 and R30RRRPpTPATLVLT42 of Inhibitor-1, and two putative substrate sequences LRRApSVA and QRRQRKpRRTI were subsequently docked. In the next step, a free PP2Ac model was built via homology re-modeling of the PP1c template and the same four sequences were docked to it. Thus, together, 20 starting model complexes were built, allowing for combination of the Zno and Mno pseudo-molecules, free enzymes and the peptide ligands docked in the catalytic sites of PP1c and PP2Ac. All models were subsequently subjected to 250-300 ps molecular dynamics using the AMBER 5.0 program. The equilibrated trajectories of the final 50 ps were taken for further analyses. The theoretical models of PP1c complexes, irrespective of the dication type, exhibited increased mobilities in the following residue ranges: 195-200, 273-278, 287-209 for the inhibitor sequences and 21-25, 194-200, 222-227, 261, 299-302 for the substrate sequences. Paradoxically, the analogous PP2Ac models appeared much more stable in similar simulations, since only their "prosegment" residues 6-10 and 14-18 exhibited an increased mobility in the inhibitor complexes while no areas of increased mobility were found in the substrate complexes. Another general observation was that the complexes with Mn dications were more stable than those with Zn dications for both PP1c and PP2Ac units.


Subject(s)
Catalytic Domain , Cations , Magnesium/chemistry , Phosphoprotein Phosphatases/chemistry , Zinc/chemistry , Animals , Binding Sites , Catalysis , Computer Simulation , Ligands , Models, Molecular , Phosphates/chemistry , Phosphoserine/chemistry , Phosphothreonine/chemistry , Protein Binding , Protein Phosphatase 1 , Protein Structure, Tertiary , Time Factors
7.
Acta Biochim Pol ; 48(1): 83-93, 2001.
Article in English | MEDLINE | ID: mdl-11440186

ABSTRACT

Cholesterol, an integral component of membranes in Eucaryota, is a modifier of membrane properties. In vivo studies have demonstrated that cholesterol can also modulate activities of some G protein-coupled receptors (GPCRs), which are integral membrane proteins. This can result either from an effect of cholesterol on the membrane fluidity or from specific interactions of the membrane cholesterol with the receptor, as recently demonstrated for the cholecystokinin type beta (CCKRbeta) or the oxytocin receptor (OTR). Using molecular modelling, we studied conformational preferences of cholesterol and several of its analogues. Subsequently, we simulated the distributions of their preferred conformations around the surface of OTR, CCKRbeta and a chimeric oxytocin/cholecystokinin receptor. Consequently, we suggest residues on the surface of OTR which are potentially significant in the OTR/cholesterol interaction.


Subject(s)
Cholesterol/chemistry , Receptors, Oxytocin/chemistry , Amino Acid Sequence , Cholecystokinin/chemistry , Humans , Models, Molecular , Molecular Sequence Data , Mutation , Protein Binding , Protein Conformation , Sequence Homology, Amino Acid , Sterols/chemistry
8.
J Comput Aided Mol Des ; 15(12): 1085-104, 2001 Dec.
Article in English | MEDLINE | ID: mdl-12160092

ABSTRACT

The nonapeptide hormones arginine vasopressin (CYFQNCPRG-NH2, AVP) and oxytocin (CYIQNCPLG-NH2, OT), control many essential functions in mammals. Their main activities include the urine concentration (via stimulation of AVP V2 receptors, V2R, in the kidneys), blood pressure regulation (via stimulation of vascular V1a AVP receptors, V1aR), ACTH control (via stimulation of V1b receptors, V1bR, in the pituitary) and labor and lactation control (via stimulation of OT receptors, OTR, in the uterus and nipples, respectively). All four receptor subtypes belong to the GTP-binding (G) protein-coupled receptor (GPCR) family. This work consists of docking of YM087, a potent non-peptide V1aR and V2R - but not OTR - antagonist, into the receptor models based on relatively new theoretical templates of rhodopsin (RD) and opiate receptors, proposed by Mosberg et al. (Univ. of Michigan, Ann Arbor, USA). It is simultaneously demonstrated that this RD template satisfactorily compares with the first historical GPCR structure of bovine rhodopsin (Palczewski et al., 2000) and that homology-modeling of V2R, V1aR and OTR using opiate receptors as templates is rational, based on relatively high (20-60%) sequence homology among the set of 4 neurophyseal and 4 opiate receptors. YM087 was computer-docked to V1aR, V2R and OTR using the AutoDock (Olson et al., Scripps Research Institute, La Jolla, USA) and subsequently relaxed using restrained simulated annealing and molecular dynamics, as implemented in AMBER program (Kollman et al., University of California, San Francisco, USA). From about 80 diverse configurations, sampled for each of the three ligand/receptor systems, 3 best energy-relaxed complexes were selected for mutual comparisons. Similar docking modes were found for the YM087/V1aR and YM087/V2R complexes, diverse from those of the YM087/OTR complexes, in agreement with the molecular affinity data.


Subject(s)
Antidiuretic Hormone Receptor Antagonists , Benzazepines/chemistry , Receptors, Oxytocin/antagonists & inhibitors , Amino Acid Sequence , Computer Simulation , Computer-Aided Design , Drug Design , Humans , In Vitro Techniques , Models, Molecular , Molecular Sequence Data , Receptors, Oxytocin/chemistry , Receptors, Oxytocin/genetics , Receptors, Vasopressin/chemistry , Receptors, Vasopressin/genetics , Sequence Homology, Amino Acid
9.
Acta Biochim Pol ; 48(4): 1203-7, 2001.
Article in English | MEDLINE | ID: mdl-11995993

ABSTRACT

G protein-coupled receptors (GPCRs) transducing diverse external signals to cells via activation of heterotrimeric GTP-binding (G) proteins, estimated to mediate actions of 60% of drugs, had been resistant to structure determination until summer 2000. The first atomic-resolution experimental structure of a GPCR, that of dark (inactive) rhodopsin, thus provides a trustworthy 3D prototype for antagonist-bound forms of this huge family of proteins. In this work, our former theoretical GPCR models are evaluated against the new experimental template. Subsequently, a working hypothesis regarding the signal transduction mechanism by GPCRs is presented.


Subject(s)
Receptors, Oxytocin/chemistry , Rhodopsin/chemistry , Humans , Ligands , Models, Molecular , Protein Binding , Protein Structure, Tertiary , Receptors, Cell Surface/chemistry , Receptors, Cell Surface/metabolism , Receptors, Vasopressin/chemistry , Signal Transduction
10.
Exp Physiol ; 85 Spec No: 41S-49S, 2000 Mar.
Article in English | MEDLINE | ID: mdl-10795905

ABSTRACT

Cholesterol affects the ligand binding function of the oxytocin receptor in a highly specific manner. While the structurally-related cholecystokinin receptor shows a strong correlation between the membrane fluidity and its binding function, the oxytocin receptor behaves differently. A stringent and unique requirement of the affinity state of the oxytocin receptor for structural features of the sterol molecule has been found. The molecular requirements differ both from those postulated for sterol-phospholipid interactions and from those known to be necessary for the activity of other proteins. Employing a new detergent-free subcellular fractionation protocol, a two-fold enrichment of the oxytocin receptors (10-15% of total receptors) has been detected in the cholesterol-rich, caveolin-containing membrane domains of the plasma membrane. While most of the properties of the oxytocin receptors were indistinguishable in cholesterol-poor versus cholesterol-rich membrane compartments, high-affinity oxytocin receptors localised in caveolin-enriched low-density membranes showed about a 3-fold higher stability against thermal denaturation at 37 degrees C compared with the oxytocin receptors localised in high-density membranes. Moreover, addition of cholesterol to the cholesterol-poor high-density membranes fully protected the oxytocin receptors against thermal denaturation and partially rescued high-affinity oxytocin binding. Although the membrane fluidity of the caveolin-enriched domains was lower than that in the high-density membranes, there was no correlation between the stability of oxytocin receptors and the fluidity level of the membrane domains. Finally, in a molecular modelling approach a putative cholesterol binding motif on the extracellular surface of the oxytocin receptor was found.


Subject(s)
Caveolins , Cell Membrane/metabolism , Cholesterol/metabolism , Receptors, Oxytocin/genetics , Receptors, Oxytocin/metabolism , Binding Sites/drug effects , Binding Sites/physiology , Caveolin 1 , Cell Membrane/chemistry , Cells, Cultured , Cholesterol/pharmacology , Genes, Reporter , Green Fluorescent Proteins , Humans , Indicators and Reagents/metabolism , Kidney/cytology , Luminescent Proteins/genetics , Membrane Fluidity/drug effects , Membrane Fluidity/physiology , Membrane Proteins/metabolism , Models, Molecular , Receptors, Cholecystokinin/metabolism , Receptors, Oxytocin/chemistry , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Steroids/pharmacology , Transfection
11.
Comput Chem ; 24(3-4): 381-90, 2000 May.
Article in English | MEDLINE | ID: mdl-10816008

ABSTRACT

Catalytic domains of the metalloenzymes protein phosphatases (PPP) 1, 2A and 2B (PP1, PP2A and PP2B, respectively) are homologous to approximately 45%, with the residues in the enzymatic centers strictly conserved. PP1, PP2A and PP2B are abundant in cells and they dephosphorylate serine and/or threonine residues in a variety of proteins serving as cellular phospho switches. The active enzymes work as invariant catalytic subunits PP1c, PP2Ac and PP2Bc, respectively, complexed with diverse regulatory subunits, dependent on the enzymes' specific location and biological function. The crystal structures of PP1c and PP2B (calcineurin) heterotetramer calcineurinA x calcineurinB x FKBP x FK506 have been determined. A comparison of the catalytic subunits of both enzymes indicates their significant structural homology and virtual identity within the catalytic centers, each including a set of conservative amino acids, two metal ions and a phosphate; thus confirming a hypothesis on their common enzymatic mechanisms. The elongated substrate cleft at the active centre is kinked by approximately 120 degrees at the active center in its middle and thus divided into a pre-phospho-Ser/Thr (ligand N-terminal) and a post-phospho-Ser/Thr (ligand C-terminal) section. In PP1c the N-terminal section is highly acidic while in PP2Bc is not. This feature is likely pertinent but not sufficient to the enzymes' selectivity, which is also controlled by regulatory subunits, diverse in various tissues. The metalloenzymes in general and PPP in particular are hard to deal with using theoretical simulations due to parameterization problems for the metal cations. In fact, there are only a few PP1c simulations reported, with the metal di-cations treated quite crudely. This is a preliminary work, in which we introduce and test against some experimental evidence a concept of pseudomolecules of proper geometry, composed of double metal (2Zn2+ or 2Mn2+) cation, and the OH- nuclephile incorporated into the PP1c catalytic site. Both models are associated with either the phosphate (a free enzyme) or the phosphorylated dodecapeptide RRRRPpTPAMLFR, an active fragment (residues 29-40) of a regulatory subunit DARPP-32 inhibitor (PP1c-inhibitor complex); four models total. We have parameterized both pseudomolecules within the AMBER force field. Subsequently, using molecular dynamic in water, we have found the free PP1c subunits to be less stable than the complexed ones and we have speculated on possible reasons for this feature.


Subject(s)
Manganese/chemistry , Nerve Tissue Proteins , Phosphoprotein Phosphatases/chemistry , Zinc/chemistry , Binding Sites , Catalysis , Computer Simulation , Dopamine and cAMP-Regulated Phosphoprotein 32 , Models, Molecular , Phosphoproteins/chemistry , Phosphothreonine/chemistry , Protein Phosphatase 1
12.
Acta Biochim Pol ; 47(4): 1061-6, 2000.
Article in English | MEDLINE | ID: mdl-11996096

ABSTRACT

Physiological and pathological roles of cysteine proteases make them important targets for inhibitor development. Although highly potent inhibitors of this group of enzymes are known, their major drawback is a lack of sufficient specificity. Two cysteine protease covalent inhibitors, viz. (i) Z-RL-deoxo-V-peptide-epoxysuccinyl hybrid, and (ii) Z-RLVG-methyl-, have been developed and modeled in the catalytic pocket of papain, an archetypal thiol protease. A number of configurations have been generated and relaxed for each system using the AMBER force field. The catalytic pockets S3 and S4 appear rather elusive in view of the observed inhibitors' flexibility. This suggest rather limited chances for the development of selective structure-based inhibitors of thiol proteases, designed to exploit differences in the structure of catalytic pockets of various members of this family.


Subject(s)
Cysteine Proteinase Inhibitors/pharmacology , Enzyme Inhibitors/pharmacology , Peptides/pharmacology , Binding Sites , Catalytic Domain , Cysteine Proteinase Inhibitors/chemistry , Models, Chemical , Models, Molecular , Papain/chemistry , Peptides/chemistry , Protein Binding , Protein Conformation , Protein Structure, Tertiary , Software , Temperature , Time Factors
13.
Biochim Biophys Acta ; 1431(2): 290-305, 1999 May 18.
Article in English | MEDLINE | ID: mdl-10350606

ABSTRACT

Papain from Carica papaya, an easily available cysteine protease, is the best-studied representative of this family of enzymes. The three dimensional structure of papain is very similar to that of other cysteine proteases of either plant (actinidin, caricain, papaya protease IV) or animal (cathepsins B, K, L, H) origin. As abnormalities in the activities of mammalian cysteine proteases accompany a variety of diseases, there has been a long-lasting interest in the development of potent and selective inhibitors for these enzymes. A covalent inhibitor of cysteine proteases, designed as a combination of epoxysuccinyl and peptide moieties, has been modeled in the catalytic pocket of papain. A number of its configurations have been generated and relaxed by constrained simulated annealing-molecular dynamics in water. A clear conformational variability of this inhibitor is discussed in the context of a conspicuous conformational diversity observed earlier in several solid-state structures of other complexes between cysteine proteases and covalent inhibitors. The catalytic pockets S2 and even more so S3, as defined by the pioneering studies on the papain-ZPACK, papain-E64c and papain-leupeptin complexes, appear elusive in view of the evident flexibility of the present inhibitor and in confrontation with the obvious conformational scatter seen in other examples. This predicts limited chances for the development of selective structure-based inhibitors of thiol proteases, designed to exploit the minute differences in the catalytic pockets of various members of this family. A simultaneous comparison of the three published proenzyme structures suggests the enzyme's prosegment binding loop-prosegment interface as a new potential target for selective inhibitors of papain-related thiol proteases.


Subject(s)
Cysteine Endopeptidases/chemistry , Cysteine Proteinase Inhibitors/chemistry , Epoxy Compounds/chemistry , Oligopeptides/chemistry , Amino Acid Sequence , Binding Sites , Cysteine Proteinase Inhibitors/chemical synthesis , Enzyme Precursors/chemistry , Epoxy Compounds/chemical synthesis , Models, Molecular , Molecular Sequence Data , Oligopeptides/chemical synthesis , Papain/chemistry , Sequence Alignment , Substrate Specificity , Temperature , Water/chemistry
14.
J Comput Aided Mol Des ; 13(1): 21-33, 1999 Jan.
Article in English | MEDLINE | ID: mdl-10087497

ABSTRACT

Subject of this work is the analysis of molecular dynamics (MD) trajectories of neurophysins I (NPI) and II (NPII) and their complexes with the neurophyseal nonapeptide hormones oxytocin (OT) and vasopresssin (VP), respectively, simulated in water. NPs serve in the neurosecretory granules as carrier proteins for the hormones before their release to the blood. The starting data consisted of two pairs of different trajectories for each of the (NPII/VP)2 and (NPI/OT)2 heterotetramers and two more trajectories for the NPII2 and NPI2 homodimers (six trajectories in total). Using essential dynamics which, to our judgement, is equivalent to factor analysis, we found that only about 10 degrees of freedom per trajectory are necessary and sufficient to describe in full the motions relevant for the function of the protein. This is consistent with these motions to explain about 90% of the total variance of the system. These principal degrees of freedom represent slow anharmonic motional modes, clearly pointing at distinguished mobility of the atoms involved in the protein's functionality.


Subject(s)
Neurophysins/chemistry , Amino Acid Sequence , Animals , Biopolymers , Cattle , Models, Molecular , Molecular Sequence Data
15.
J Recept Signal Transduct Res ; 19(1-4): 355-67, 1999.
Article in English | MEDLINE | ID: mdl-10071770

ABSTRACT

Molecular dynamics simulations were carried out for a V2 receptor (V2R) model embedded in a dimyristoylphosphatidylcholine (DMPC) bilayer. Both free and ligand-bound states of V2R were modeled. Our initial V2R model was obtained using a rule-based automated method for GPCR modeling and refined using constrained simulated annealing in vacuo. The docking site of the native vasopressin ligand was selected and justified upon consideration of ligand-receptor interactions and structure-activity data. The primary purpose of this work was to investigate the usefulness of MD simulation of an integral membrane protein like a GPCR receptor, upon inclusion of a carefully parameterized surrounding lipid membrane and water. Physical properties of the system were evaluated and compared with the fully hydrated pure DMPC bilayer membrane. The solvation interactions, individual lipid-protein interaction and fluctuations of the protein, the lipid, and water were analyzed in detail. As expected, the membrane-spanning helices of the protein fluctuate less than the peripheral loops do. The protein appears to disturb the local lipid structure. Simulations were carried out using AMBER 4.1 package upon constant number-pressure-temperature (NPT) conditions on massively parallel computers Cray T3E and IBM SP2.


Subject(s)
Receptors, Vasopressin/chemistry , Animals , Dimyristoylphosphatidylcholine/chemistry , Humans , Lipid Bilayers/chemistry , Models, Molecular , Protein Structure, Secondary , Thermodynamics
16.
Acta Biochim Pol ; 46(3): 581-90, 1999.
Article in English | MEDLINE | ID: mdl-10698266

ABSTRACT

Oxytocin is a nonapeptide hormone (CYIQNCPLG-NH2, OT), controlling labor and lactation in mammalian females, via interactions with specific cellular membrane receptors (OTRs). The native hormone is cyclized via a 1-6 disulfide and its receptor belongs to the GTP-binding (G) protein-coupled receptor (GPCR) family, also known as heptahelical transmembrane (7TM) or serpentine receptors. Using a technique combining multiple sequence alignments with available experimental constraints, a reliable OTR model was built. Subsequently, the OTR complexes with a selective agonist [Thr4,Gly7]OT, a selective cyclohexapeptide antagonist L-366,948 and oxytocin itself were modeled and relaxed using a constrained simulated annealing (CSA) protocol. All three ligands seem to prefer similar modes of binding to the receptor, manifested by repeating receptor residues which directly interact with the ligands. Those involved in the three complexes are putative helices: TM3: R113, K116, Q119, M123; TM4: Q171, and TM5: I201 and T205. Most of them are the equivalent residues/positions to those found in our earlier studies, regarding related vasopressin V2 receptor/bioligand interactions.


Subject(s)
Receptors, Oxytocin/chemistry , Receptors, Oxytocin/metabolism , Amino Acid Sequence , Binding Sites , Female , Hormone Antagonists/chemistry , Humans , In Vitro Techniques , Kinetics , Ligands , Models, Molecular , Molecular Sequence Data , Oxytocin/agonists , Oxytocin/analogs & derivatives , Oxytocin/antagonists & inhibitors , Oxytocin/chemistry , Peptides, Cyclic/chemistry , Pregnancy , Protein Conformation , Receptors, Oxytocin/genetics
17.
J Comput Aided Mol Des ; 12(3): 275-87, 1998 May.
Article in English | MEDLINE | ID: mdl-9749370

ABSTRACT

The V2 vasopressin renal receptor (V2R), which controls antidiuresis in mammals, is a member of the large family of heptahelical transmembrane (7TM) G protein-coupled receptors (GPCRs). Using the automated GPCR modeling facility available via Internet (http:/(/)expasy.hcuge.ch/swissmod/SWISS-MODEL.+ ++html) for construction of the 7TM domain in accord with the bovine rhodopsin (RD) footprint, and the SYBYL software for addition of the intra- and extracellular domains, the human V2R was modeled. The structure was further refined and its conformational variability tested by the use of a version of the Constrained Simulated Annealing (CSA) protocol developed in this laboratory. An inspection of the resulting structure reveals that the V2R (likewise any GPCR modeled this way) is much thicker and accordingly forms a more spacious TM cavity than most of the hitherto modeled GPCR constructs do, typically based on the structure of bacteriorhodopsin (BRD). Moreover, in this model the 7TM helices are arranged differently than they are in any BRD-based model. Thus, the topology and geometry of the TM cavity, potentially capable of receiving ligands, is in this model quite different than it is in the earlier models. In the subsequent step, two ligands, the native [arginine8]vasopressin (AVP) and the selective agonist [D-arginine8]vasopressin (DAVP) were inserted, each in two topologically non-equivalent ways, into the TM cavity and the resulting structures were equilibrated and their conformational variabilities tested using CSA as above. The best docking was selected and justified upon consideration of ligand-receptor interactions and structure-activity data. Finally, the amino acid residues were indicated, mainly in TM helices 3-7, as potentially important in both AVP and DAVP docking. Among those Cys112, Val115-Lys116, Gln119, Met123 in helix 3; Glu174 in helix 4; Val206, Ala210, Val213-Phe214 in helix 5; Trp284, Phe287-Phe288, Gln291 in helix 6; and Phe307, Leu310, Ala314 and Asn317 in helix 7 appeared to be the most important ones. Many of these residues are invariant for either the GPCR superfamily or the neurophyseal (vasopressin V2R, V1aR and V1bR and oxytocin OR) subfamily of receptors. Moreover, some of the equivalent residues in V1aR have already been found critical for the ligand affinity.


Subject(s)
Receptors, Vasopressin/agonists , Receptors, Vasopressin/chemistry , Amino Acid Sequence , Animals , Cattle , Computer Simulation , GTP-Binding Proteins/metabolism , Humans , Ligands , Models, Molecular , Molecular Sequence Data , Receptors, Vasopressin/metabolism
18.
Acta Biochim Pol ; 45(1): 19-26, 1998.
Article in English | MEDLINE | ID: mdl-9701492

ABSTRACT

We predict some essential interactions between the V2 vasopressin renal receptor (V2R) and its selective peptide antagonist desGly9-[Mca1,D-Ile2,Ile4]AVP, and compare these predictions with the earlier ones for the non-peptide OPC-36120 antagonist- and the [Arg8]vasopressin (AVP) agonist-V2 receptor interactions. V2R controls antidiuresis in mammals and belongs to the superfamily of the heptahelical transmembrane (7TM) G protein-coupled receptors (GPCR)s. V2R was built, the ligands docked and the structures relaxed using advanced molecular modeling techniques. Both the agonist and the antagonists (no matter whether of peptide- or non-peptide type) appear to prefer a common V2R compartment for docking. The receptor amino-acid residues, potentially important in ligand binding, are mainly in the TM3-TM7 helices. A few of these residues are invariant for the whole GPCR superfamily while most of them are conserved in the subfamily of neurohypophyseal receptors, to which V2R belongs. Some of the equivalent residues in a related V1a receptor have been earlier reported as critical for the ligand affinity.


Subject(s)
Antidiuretic Hormone Receptor Antagonists , Arginine Vasopressin/analogs & derivatives , Kidney/drug effects , Models, Molecular , Amino Acid Sequence , Arginine Vasopressin/metabolism , Benzazepines/metabolism , Kidney/metabolism , Molecular Sequence Data , Receptors, Vasopressin/metabolism
19.
J Comput Aided Mol Des ; 11(1): 9-20, 1997 Jan.
Article in English | MEDLINE | ID: mdl-9139116

ABSTRACT

Neurophysins I and II (NPI and NPII) act in the neurosecretory granules as carrier proteins for the neurophyseal hormones oxytocin (OT) and vasopressin (VP), respectively. The NPI/OT functional unit, believed to be an (NPI/OT)2 heterotetramer, was modeled using low-resolution structure information, viz. the C alpha carbon atom coordinates of the homologous NPII/dipeptide complex (file 1BN2 in the Brookhaven Protein Databank) as a template. Its all-atom representation was obtained using standard modeling tools available within the INSIGHT/Biopolymer modules supplied by Biosym Technologies Inc. A conformation of the NPI-bound OT, similar to that recently proposed in a transfer NOE experiment, was docked into the ligand-binding site by a superposition of its Cys1-Tyr2 fragment onto the equivalent portion of the dipeptide in the template. The starting complex for the initial refinements was prepared by two alternative strategies, termed Model I and Model II, each ending with a approximately 100 ps molecular dynamics (MD) simulation in water using the AMBER 4.1 force field. The free homodimer NPI2 was obtained by removal of the two OT subunits from their sites, followed by a similar structure refinement. The use of Model I, consisting of a constrained simulated annealing, resulted in a structure remarkably similar to both the NPII/dipeptide complex and a recently published solid-state structure of the NPII/OT complex. Thus, Model I is recommended as the method of choice for the preparation of the starting all-atom data for MD. The MD simulations indicate that, both in the homodimer and in the heterotetramer, the 3(10)-helices demonstrate an increased mobility relative to the remaining body of the protein. Also, the C-terminal domains in the NPI2 homodimer are more mobile than the N-terminal ones. Finally, a distinct intermonomer interaction is identified, concentrated around its most prominent, although not unique, contribution provided by an H-bond from Ser25 O gamma in one NPI unit to Glu81 O epsilon in the other unit. This interaction is present in the heterotetramer (NPI/OT)2 and absent or weak in the NPI2 homodimer. We speculate that this interaction, along with the increased mobility of the 3(10)-helices and the carboxy domains, may contribute to the allosteric communication between ligand binding and NPI dimerization.


Subject(s)
Models, Molecular , Neurophysins/chemistry , Oxytocin/chemistry , Allosteric Regulation , Amino Acid Sequence , Animals , Binding Sites , Cattle , Computer Simulation , Dimerization , Ligands , Macromolecular Substances , Molecular Sequence Data , Neurophysins/genetics , Oxytocin/genetics , Protein Conformation , Thermodynamics
20.
Acta Biochim Pol ; 44(3): 453-66, 1997.
Article in English | MEDLINE | ID: mdl-9511957

ABSTRACT

This is a review of our recent modeling work aimed at: (i) development and assessment of techniques for reliable refinement of low-resolution protein structures and (ii) using these techniques, at solving specific problems pertinent to neurophysin-bioligand interactions. Neurophysins I and II (NPI and NPII) serve in the neurosecretory granules of the posterior pituitary as carrier proteins for the neurophyseal hormones oxytocin (OT) and vasopressin (VP), respectively, until the latter are released into blood. NPs are homologous two-domain, sulphur rich small proteins (93-95 residues, 7 disulphide bridges per monomer), capable of being aggregated. The C2 symmetrical NPI2 and NPII2 homodimers, and the (NPI/OT)2 and (NPII/VP)2 heterotetramers, all believed to be the smallest functional units, were modeled using low-resolution structure information, i.e. the C alpha-carbon coordinates of the homologous NPII/dipeptide complex as a template. The all-atom representations of the models were obtained using the SYBYL suite of programs (by Tripos, Inc.). Subsequently, they were relaxed, using a constrained simulated annealing (CSA) protocol, and submitted to about 100 ps molecular dynamics (MD) in water, using the AMBER 4.1 force field. The (NPI/OT)2 and (NPII/VP)2 structures, averaged after the last 20 ps of MD, were remarkably similar to those recently reported either for NPII/dipeptide or NPII/oxytocin complex in the solid state (Chen et al., 1991, Proc. Natl. Acad. Sci., U.S.A. 88, 4240-4244; Rose et al., 1996, Nature Struct. Biol. 3, 163-169). The results indicate that the 3(10) helices (terminating the amino domains) and the carboxyl domains are more mobile than the remainder of the NP monomers. The hormones become anchored by residues 1-3 and 6 to the host, leaving residues 4-5 and 7-9 exposed on the surface and free to move. A cluster of attractive interactions, extending from the ligand binding site, Tyr-24-Ile-26 of unit 1(2), to the inter-monomer interface Val-36 of unit 1(2), Cys-79 and Ile-72 of unit 2(1), is clearly seen. We suggest that both these interactions as well as the increased mobility of the 3(10) helix and the carboxyl domain may contribute to the allosteric communication between the ligand and the unit1-unit2 interface.


Subject(s)
Neurophysins/metabolism , Oxytocin/metabolism , Vasopressins/metabolism , Amino Acid Sequence , Animals , Cattle , Ligands , Models, Molecular , Molecular Sequence Data , Neurophysins/chemistry
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