A fast recursive algorithm for molecular dynamics simulation

165

147

Dopamine neurotransmitter and its receptors play a critical role in the cell signaling process responsible for information transfer in neurons functioning in the nervous system. Development of improved therapeutics for such disorders as Parkinson's disease and schizophrenia would be significantly enhanced with the availability of the 3D structure for the dopamine receptors and of the binding site for dopamine and other agonists and antagonists. We report here the 3D structure of the long isoform of the human D2 dopamine receptor, predicted from primary sequence using firstprinciples theoretical and computational techniques (i.e., we did not use bioinformatic or experimental 3D structural information in predicting structures). The predicted 3D structure is validated by comparison of the predicted binding site and the relative binding affinities of dopamine, three known dopamine agonists (antiparkinsonian), and seven known antagonists (antipsychotic) in the D2 receptor to experimentally determined values. These structures correctly predict the critical residues for binding dopamine and several antagonists, identified by mutation studies, and give relative binding affinities that correlate well with experiments. The predicted binding site for dopamine and agonists is located between transmembrane (TM) helices 3, 4, 5, and 6, whereas the best antagonists bind to a site involving TM helices 2, 3, 4, 6, and 7 with minimal contacts to TM helix 5. We identify characteristic differences between the binding sites of agonists and antagonists.W ith the implication of G protein-coupled receptor (GPCR) in many diseases (1, 2), the need to solve the highresolution 3D structure of this class of integral membrane proteins to enable structure-based drug design is an important problem in structural biology. Despite the importance of solving the structure of the GPCRs, the only experimental 3D structure available for a GPCR is bovine rhodopsin. This lack of structures is because the GPCRs are bound to the membrane, making it difficult to express in sufficient quantities for crystallization.To provide structural and ligand binding information on GPCRs, we have been developing first-principles computational techniques for predicting the 3D structure of GPCRs using only the amino acid sequence (MembStruk) and for predicting binding site and binding energy of various ligands to GPCRs (HierDock). Using these techniques, we have reported the structure of olfactory receptors (3, 4), bovine rhodopsin (4, 5), and other GPCRs (4). Dopamine neurotransmitter plays a critical role in cellular signaling processes responsible for information transfer in neurons functioning in the nervous system (6, 7). Dopamine receptors (DR) belong to the superfamily of GPCRs, and to date there are five reported sequences for the human DR with multiple isoforms for each. The DRs may be subdivided based on their pharmacological behavior into the D1-like and the D2-like subfamilies, and these are ideal targets for treating schizophrenia and Parkinson's disease; th...

Section: Methodsmentioning

confidence: 99%

The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists

Kalani

Vaidehi

Hall

et al. 2004

165

147

“…Besides the addition of the aforementioned new routine for automatic NOE assignments, the presently used, so far unreleased new version of DYANA varies from the original program (20) by a modified implementation of the torsion angle dynamics algorithm (27) and by a different treatment of distance constraints to groups of chemical shift-equivalent protons and pairs of diastereotopic substituents that have not been individually assigned (T. Herrmann, P.G., and K.W., unpublished work). Since the main interest in the structures presented in this paper is focused on quite subtle, local conformational variations relative to the bPrP structures in the preceding paper (7) and the previously published structures of mPrP (2), hPrP (6), and shPrP (5), we reevaluated the input data and repeated the calculations of the previously published PrP structures from our laboratory (hPrP, mPrP) with the new version of DYANA.…”

Section: Methodsmentioning

confidence: 99%

NMR structures of three single-residue variants of the human prion protein

Calzolai¹,

Lysek²,

Güntert³

et al. 2000

The NMR structures of three single-amino acid variants of the C-terminal domain of the human prion protein, hPrP(121-230), are presented. In hPrP(M166V) and hPrP(R220K) the substitution is with the corresponding residue in murine PrP, and in hPrP(S170N) it is with the corresponding Syrian hamster residue. All three substitutions are in the surface region of the structure of the cellular form of PrP (PrP C ) that is formed by the C-terminal part of helix 3, with residues 218 -230, and a loop of residues 166 -172. This molecular region shows high species variability and has been implicated in specific interactions with a so far not further characterized ''protein X,'' and it is related to the species barrier for transmission of prion diseases. As expected, the three variant hPrP(121-230) structures have the same global architecture as the previously determined wild-type bovine, human, murine, and Syrian hamster prion proteins, but with the present study two localized ''conformational markers'' could be related with single amino acid exchanges. These are the length and quality of definition of helix 3, and the NMR-observability of the residues in the loop 166 -172. Poor definition of the C-terminal part of helix 3 is characteristic for murine PrP and has now been observed also for hPrP(R220K), and NMR observation of the complete loop 166 -172 has so far been unique for Syrian hamster PrP and is now also documented for hPrP(S170N).

“…The canonical right-handed ␣-helices were then built with extended side chains and optimized using the NEIMO torsional molecular dynamics (MD) method (31)(32)(33), with fixed bonds and angles. This allows for sequence-specific distortions in the helix, such as for proline, and also the optimization of the side chain conformations.…”

mentioning

confidence: 99%

Prediction of structure and function of G protein-coupled receptors

Vaidehi

Floriano

Trabanino

et al. 2002

278

258

G protein-coupled receptors (GPCRs) mediate our sense of vision, smell, taste, and pain. They are also involved in cell recognition and communication processes, and hence have emerged as a prominent superfamily for drug targets. Unfortunately, the atomic-level structure is available for only one GPCR (bovine rhodopsin), making it difficult to use structure-based methods to design drugs and mutation experiments. We have recently developed first principles methods (MembStruk and HierDock) for predicting structure of GPCRs, and for predicting the ligand binding sites and relative binding affinities. Comparing to the one case with structural data, bovine rhodopsin, we find good accuracy in both the structure of the protein and of the bound ligand. We report here the application of MembStruk and HierDock to ␤1-adrenergic receptor, endothelial differential gene 6, mouse and rat I7 olfactory receptors, and human sweet receptor. We find that the predicted structure of ␤1-adrenergic receptor leads to a binding site for epinephrine that agrees well with the mutation experiments. Similarly the predicted binding sites and affinities for endothelial differential gene 6, mouse and rat I7 olfactory receptors, and human sweet receptor are consistent with the available experimental data. These predicted structures and binding sites allow the design of mutation experiments to validate and improve the structure and function prediction methods. As these structures are validated they can be used as targets for the design of new receptor-selective antagonists or agonists for GPCRs.GPCR ͉ olfactory receptor ͉ ␤-adrenergic receptor ͉ endothelial differentiation gene ͉ taste receptor G protein-coupled receptors (GPCRs) mediate senses such as odor, taste, vision, and pain (1) in mammals. In addition, important cell recognition and communication processes often involve GPCRs. Indeed, many diseases involve malfunction of these receptors (2), making them important targets for drug development. Unfortunately, despite their importance there is insufficient structural information on GPCRs for structure-based drug design. This is because these membrane-bound proteins are difficult to crystallize, and the atomic-level structure has been solved only for bovine rhodopsin (3, 4). Consequently, it is important to develop theoretical methods to predict the structure and function of GPCRs (5, 6).Experimental data relevant to the function of GPCRs is available for ligand activation of GPCRs (7-15) and site-directed mutagenesis (16)(17)(18). This data has led to information about structural features in the ligand-binding regions of GPCRs (refs. 5 and 19, and references therein). Protein sequence analyses on GPCRs reveals a common protein topology consisting of a membrane-spanning seven-helix bundle, which likely accommodates the binding site for low-molecular-weight ligands. Structurally, GPCRs can be classified as (i) GPCRs with short N terminus (5-80 residues) and (ii) GPCRs with a long N-terminal ectodomain (Ϸ80-600 residues). The long N terminus of ...