@article {293, title = {MSITE: a new computational tool for comparison of homological proteins in holo form}, journal = {The Journal of Steroid Biochemistry and Molecular Biology}, volume = {121}, year = {2010}, month = {2010 Jul}, pages = {34-42}, abstract = {The mechanism by which nuclear receptors respond differentially to structurally distinct agonists is not a well understood process. However, it is now obvious that transcriptional activity of nuclear receptors is a function of their interactions with co-activators. Recently, we released a new computational tool, CCOMP, for comparing side chain conformations in crystal structures of homologous protein complexes. Application of the CCOMP program revealed that 20-epi-1alpha,25-(OH)2D3 changes the side chain conformation of vitamin D receptor amino acids residing mostly far away from the ligand-receptor contacts. This strongly suggests that the ligand-co-activator signaling pathway involves indirect interactions between amino acids lining the binding pocket and outer surface residues that could attract co-activators. To facilitate identification of amino acids transmitting the subtle receptor changes upon ligand/modulator binding we developed another simple tool, MSITE. The program automatically lists the nearest neighbors of a given amino acid (for example neighbors of residues that are in contact with a ligand or reorient their side chains in the presence of a co-factor) in an arbitrary number of compared complexes. Comparison of seven binary vitamin D receptor complexes holding as ligands the analogs of 1alpha,25-(OH)2D3 with inverted configuration at carbon 14 or 20, or with incorporated oxolane ring bridging carbons 20 and 23, is reported.}, keywords = {Algorithms, Amino Acid Sequence, Amino Acids, Animals, Computational Biology, DNA Mutational Analysis, Humans, Ligands, Molecular Sequence Data, Protein Binding, Rats, Receptors, Calcitriol, Sequence Homology, Amino Acid, Software, Zebrafish}, issn = {1879-1220}, doi = {10.1016/j.jsbmb.2010.04.006}, author = {Wanda Sicinska and Mateusz Kurcinski} } @article {Kurcinski2010, title = {Theoretical study of molecular mechanism of binding TRAP220 coactivator to Retinoid X Receptor alpha, activated by 9-cis retinoic acid}, journal = {The Journal of Steroid Biochemistry and Molecular Biology}, volume = {121}, number = {1-2}, year = {2010}, month = {jul}, pages = {124{\textendash}9}, publisher = {Elsevier Ltd}, abstract = {

Study on molecular mechanism of conformational reorientation of RXR-alpha ligand binding domain is presented. We employed CABS{\textendash}a reduced model of protein dynamics to model folding pathways of binding 9-cis retinoic acid to apo-RXR molecule and TRAP220 peptide fragment to the holo form. Based on obtained results we also propose a sequential model of RXR activation by 9-cis retinoic acid and TRAP220 coactivator. Methodology presented here may be used for investigation of binding pathways of other NR/hormone/cofactor sets.

}, keywords = {Binding Sites, Cell Nucleus, Cell Nucleus: metabolism, Computer Simulation, Crystallography, Humans, Ligands, Mediator Complex Subunit 1, Mediator Complex Subunit 1: metabolism, Models, Molecular, Molecular Conformation, Peptides, Peptides: chemistry, Protein Binding, Protein Structure, Retinoid X Receptor alpha, Retinoid X Receptor alpha: metabolism, Tertiary, Theoretical, Tretinoin, Tretinoin: metabolism, X-Ray, X-Ray: methods}, issn = {1879-1220}, doi = {10.1016/j.jsbmb.2010.03.086}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2906686\&tool=pmcentrez\&rendertype=abstract}, author = {Mateusz Kurcinski and Andrzej Koli{\'n}ski} } @article {294, title = {Structural changes of vitamin D receptor induced by 20-epi-1alpha,25-(OH)2D3: an insight from a computational analysis}, journal = {The Journal of Steroid Biochemistry and Molecular Biology}, volume = {113}, year = {2009}, month = {2009 Feb}, pages = {253-8}, abstract = {We employ a new computational tool CCOMP for the comparison of side chain (SC) conformations between crystal structures of homologous protein complexes. The program is applied to the vitamin D receptor (VDR) liganded with 1alpha,25-(OH)(2)D(3) (in 1DB1) or its 20-epi (in 1IE9) analog with an inverted C-20 configuration. This modification yields no detectable changes in the backbone configuration or ligand topology in the receptor binding cavity, yet it dramatically increases transcription, differentiation and antiproliferation activity of the VDR. We applied very stringent criteria during the comparison process. To eliminate errors arising from the different packing of investigated crystals and the thermal flexibility of atoms, we studied complexes belonging to the same space group, having a low R value (0.2) and a B-factor below 40 for compared residues. We find that 20-epi-1alpha,25-(OH)(2)D(3) changes side chain conformation of amino acids residing far away from direct ligand-VDR contacts. We further verify that a number of the reoriented residues were identified in mutational experiments as important for interaction with SRC-1, GRIP, TAFs co-activators and VDR-RXR heterodimerization. Thus, CCOMP analysis of protein complexes may be used for identifying amino acids that could serve as targets for genetic engineering, such as mutagenesis.}, keywords = {Animals, Bone Density Conservation Agents, Calcitriol, Computer Simulation, Crystallography, X-Ray, Drug Design, Humans, Ligands, Molecular Structure, Protein Structure, Tertiary, Receptors, Calcitriol, Reproducibility of Results, Software, Transcription, Genetic}, issn = {1879-1220}, doi = {10.1016/j.jsbmb.2009.01.007}, author = {Wanda Sicinska and Piotr Rotkiewicz} } @article {Kurcinski2007, title = {Steps towards flexible docking: modeling of three-dimensional structures of the nuclear receptors bound with peptide ligands mimicking co-activators{\textquoteright} sequences}, journal = {The Journal of Steroid Biochemistry and Molecular Biology}, volume = {103}, number = {3-5}, year = {2007}, month = {mar}, pages = {357{\textendash}60}, abstract = {We developed a fully flexible docking method that uses a reduced lattice representation of protein molecules, adapted for modeling peptide-protein complexes. The CABS model (Carbon Alpha, Carbon Beta, Side Group) employed here, incorporates three pseudo-atoms per residue-Calpha, Cbeta and the center of the side group instead of full-atomic protein representation. Force field used by CABS was derived from statistical analysis of non-redundant database of protein structures. Application of our method included modeling of the complexes between various nuclear receptors (NRs) and peptide co-activators, for which three-dimensional structures are known. We tried to rebuild the native state of the complexes, starting from separated components. Accuracy of the best obtained models, calculated as coordinate root-mean-square deviation (cRMSD) between the target and the modeled structures, was under 1A, which is competitive with experimental methods, such as crystallography or NMR. Forthcoming modeling study should lead to better understanding of mechanisms of macromolecular assembly and will explain co-activators{\textquoteright} effects on receptors activity, especially on vitamin D receptor and other nuclear receptors.}, keywords = {Amino Acid Sequence, Crystallography, Cytoplasmic and Nuclear, Cytoplasmic and Nuclear: chemistry, Cytoplasmic and Nuclear: metabolism, Ligands, Models, Molecular, Molecular Mimicry, Peptides, Peptides: chemistry, Peptides: metabolism, Protein Binding, Protein Structure, Quaternary, Receptors, X-Ray}, issn = {0960-0760}, doi = {10.1016/j.jsbmb.2006.12.059}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17241780}, author = {Mateusz Kurcinski and Andrzej Koli{\'n}ski} } @article {254, title = {Clustering as a supporting tool for structural drug design}, journal = {Acta Poloniae Pharmaceutica. Drug Research}, volume = {63}, year = {2006}, month = {2006 Sep-Oct}, pages = {436-8}, keywords = {Cluster Analysis, Computer Simulation, Drug Design, Ligands, Models, Molecular, Molecular Structure, Protein Binding}, issn = {0001-6837}, author = {Dominik Gront and Mateusz Kurcinski and Andrzej Koli{\'n}ski} } @article {297, title = {NMR assignments of tryptophan residue in apo and holo LBD-rVDR}, journal = {Proteins}, volume = {61}, year = {2005}, month = {2005 Nov 15}, pages = {461-7}, abstract = {Binding sites in the full-length, ligand-binding domain of rat vitamin D receptor (LBD-rVDR) for an active hormone derived from vitamin D (1alpha,25-dihydroxyvitamin D(3)) and three of its C-2 substituted analogs were compared by nuclear magnetic resonance (NMR) spectroscopy. Specific residue labeled with [UL]-(15)N(2) Trp allowed assignment of the side-chain H(epsilon1) and N(epsilon1) resonances of the single tryptophan residue at position 282 in LBD-rVDR. Comparison of (1)H[(15)N] Heteronuclear Single Quantum Correlation (HSQC) spectra of apo and holo LBD-rVDR revealed that the position of the Trp282 H(epsilon1) and N(epsilon1) signals are sensitive to the presence of the ligand in the receptor cavity. Binding of the ligands to LBD-rVDR results in a shift of both Trp H(epsilon1) and N(epsilon1) resonances to lower frequencies. The results indicate that the interaction between the ligands and Trp282 is not responsible for differences in calcemic activity observed in vitamin D analogs.}, keywords = {Animals, Apoproteins, Binding Sites, Ligands, Magnetic Resonance Spectroscopy, Rats, Receptors, Calcitriol, Tryptophan, Vitamin D}, issn = {1097-0134}, doi = {10.1002/prot.20625}, author = {Wanda Sicinska and William M. Westler and Hector F. DeLuca} } @article {299, title = {2-Methylene analogs of 1alpha-hydroxy-19-norvitamin D3: synthesis, biological activities and docking to the ligand binding domain of the rat vitamin D receptor}, journal = {The Journal of Steroid Biochemistry and Molecular Biology}, volume = {89-90}, year = {2004}, month = {2004 May}, pages = {13-7}, abstract = {In continuing efforts towards the synthesis of biologically active vitamin D compounds of potential therapeutic value, new 2-methylene-1alpha-hydroxy-19-norvitamin D(3) analogs 3 and 4 with modified alkyl side chains have been synthesized. The key synthetic step involved Lythgoe-type Wittig-Horner coupling of Windaus-Grundmann type ketones 9, possessing different 17beta-alkyl substituents, with the phosphine oxide 10 prepared from (-)-quinic acid. The prepared vitamins 3 and 4 were ca. eight times less potent than 1alpha,25-dihydroxyvitamin D(3) (1alpha,25-(OH)(2)D(3)) (1) in binding to the rat intestinal vitamin D receptor (VDR). In comparison with the hormone 1 they exhibited slightly lower cellular HL-60 differentiation activity. When tested in vivo; the analog 3 was characterized by very high bone calcium mobilizing potency and intestinal calcium transport activity. Unexpectedly, the 25-methyl compound 4 showed marked calcemic activity in both assays. Computational docking of the vitamin 3 into the binding pocket of the rat vitamin D receptor is also reported.}, keywords = {Animals, Binding Sites, Calcitriol, Female, HL-60 Cells, Humans, Hydrocarbons, Ligands, Methane, Mice, Models, Molecular, Rats, Receptors, Calcitriol}, issn = {0960-0760}, doi = {10.1016/j.jsbmb.2004.03.103}, author = {Pawel Grzywacz and Lori A. Plum and Wanda Sicinska and Rafal R. Sicinski and Jean M. Prahl and Hector F. DeLuca} } @article {298, title = {Model of three-dimensional structure of VDR bound with Vitamin D3 analogs substituted at carbon-2}, journal = {The Journal of Steroid Biochemistry and Molecular Biology}, volume = {89-90}, year = {2004}, month = {2004 May}, pages = {107-10}, abstract = {All Vitamin D analogs possessing the A ring modified at C-2 and showing calcemic activities nest themselves in the VDR binding pocket, oriented towards Tyr 143. Such topology resembles the position of the Vitamin D hormone in hVDRmt [Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 5491]. Conversely, inactive 2beta-methyl-19-nor-analogs anchor the receptor cavity in a distinguishably different manner, namely by their side chain. Moreover, these inactive vitamins have a different conformation around C(6)-C(7) bond. Topology of modeled complexes suggests that a Vitamin D analog will be biologically active if its intercyclic 5,7-diene moiety assumes parallel position to tryptophan aromatic rings; such orientation allows for creating pi-pi interactions. The broad comparison of calcemic activities of the analogs, and their interactions with VDR, revealed that specific hydrophobic contacts are involved in bone calcium mobilization (BCM). These contacts occur between 21-methyl group and a few amino acids (V296, L305 and L309), conserved in the nuclear receptor superfamily. In the inactive 2beta-methyl-19-nor analogs such contacts do not exist. We speculate that two hydrophobic receptor patches, being in close contact with ligand methyl groups, might influence interaction with co-modulators involved in calcium homeostasis.}, keywords = {Animals, Calcium, Carbon, Cholecalciferol, Ligands, Models, Molecular, Molecular Conformation, Rats, Receptors, Calcitriol}, issn = {0960-0760}, doi = {10.1016/j.jsbmb.2004.03.102}, author = {Wanda Sicinska and Piotr Rotkiewicz and Hector F. DeLuca} } @article {290, title = {2-Ethyl and 2-ethylidene analogues of 1alpha,25-dihydroxy-19-norvitamin D(3): synthesis, conformational analysis, biological activities, and docking to the modeled rVDR ligand binding domain.}, journal = {Journal of Medicinal Chemistry}, volume = {45}, year = {2002}, month = {2002 Aug 1}, pages = {3366-80}, abstract = {Novel 19-nor analogues of 1alpha,25-dihydroxyvitamin D(3) were prepared and substituted at C-2 with an ethylidene group. The synthetic pathway was via Wittig-Horner coupling of the corresponding A-ring phosphine oxides with the protected 25-hydroxy Grundmann{\textquoteright}s ketones. Selective catalytic hydrogenation of 2-ethylidene analogues provided the 2alpha- and 2beta-ethyl compounds. The 2-ethylidene-19-nor compounds with a methyl group from the ethylidene moiety in a trans relationship to the C(6)-C(7) bond (E-isomers) were more potent than the corresponding Z-isomers and the natural hormone in binding to the vitamin D receptor. Both geometrical isomers (E and Z) of (20S)-2-ethylidene-19-norvitamin D(3) and both 2alpha-ethyl-19-norvitamins (in the 20R- and 20S-series) have much higher HL-60 differentiation activity than does 1alpha,25-(OH)(2)D(3). Both E-isomers (20R and 20S) of 2-ethylidene vitamins are characterized by very high calcemic activity in rats. The three-dimensional structure model of the rat vitamin D receptor and the computational docking of four synthesized (20R)-19-norvitamin D(3) analogues into its binding pocket are also reported.}, keywords = {Animals, Binding Sites, Biological Transport, Calcitriol, Calcium, Cell Differentiation, Chromatography, High Pressure Liquid, HL-60 Cells, Humans, Intestinal Mucosa, Ligands, Magnetic Resonance Spectroscopy, Male, Models, Molecular, Molecular Conformation, Rats, Receptors, Calcitriol, Spectrophotometry, Ultraviolet, Structure-Activity Relationship, Swine}, issn = {0022-2623}, author = {Rafal R. Sicinski and Piotr Rotkiewicz and Andrzej Koli{\'n}ski and Wanda Sicinska and Jean M. Prahl and Connie M. Smith and Hector F. DeLuca} } @article {Rotkiewicz2001, title = {Model of three-dimensional structure of vitamin D receptor and its binding mechanism with 1alpha,25-dihydroxyvitamin D(3)}, journal = {Proteins}, volume = {44}, number = {3}, year = {2001}, month = {2001}, pages = {188{\textendash}199}, abstract = {Comparative modeling of the vitamin D receptor three-dimensional structure and computational docking of 1alpha,25-dihydroxyvitamin D(3) into the putative binding pocket of the two deletion mutant receptors: (207-423) and (120-422, Delta [164-207]) are reported and evaluated in the context of extensive mutagenic analysis and crystal structure of holo hVDR deletion protein published recently. The obtained molecular model agrees well with the experimentally determined structure. Six different conformers of 1alpha,25-dihydroxyvitamin D(3) were used to study flexible docking to the receptor. On the basis of values of conformational energy of various complexes and their consistency with functional activity, it appears that 1alpha,25-dihydroxyvitamin D(3) binds the receptor in its 6-s-trans form. The two lowest energy complexes obtained from docking the hormone into the deletion protein (207-423) differ in conformation of ring A and orientation of the ligand molecule in the VDR pocket. 1alpha,25-Dihydroxyvitamin D(3) possessing the A-ring conformation with axially oriented 1alpha-hydroxy group binds receptor with its 25-hydroxy substituent oriented toward the center of the receptor cavity, whereas ligand possessing equatorial conformation of 1alpha-hydroxy enters the pocket with A ring directed inward. The latter conformation and orientation of the ligand is consistent with the crystal structure of hVDR deletion mutant (118-425, Delta [165-215]). The lattice model of rVDR (120-422, Delta [164-207]) shows excellent agreement with the crystal structure of the hVDR mutant. The complex obtained from docking the hormone into the receptor has lower energy than complexes for which homology modeling was used. Thus, a simple model of vitamin D receptor with the first two helices deleted can be potentially useful for designing a general structure of ligand, whereas the advanced lattice model is suitable for examining binding sites in the pocket.}, keywords = {Amino Acid, Amino Acid Sequence, Animals, Binding Sites, Calcitriol, Calcitriol: chemistry, Calcitriol: genetics, Computational Biology, Humans, Ligands, Models, Molecular, Molecular Sequence Data, Point Mutation, Protein Conformation, Protein Structure, Rats, Receptors, Sequence Homology, Tertiary}, issn = {0887-3585}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11455592}, author = {Piotr Rotkiewicz and Wanda Sicinska and Andrzej Koli{\'n}ski and Hector F. DeLuca} }