MOLECULAR MODELING AS A TOOL IN MOLECULAR BIOLOGY OF MEMBRANE-BOUND RECEPTORS
R. Ettrich1, V. Vlachová2, J. Teisinger2, J. Pavlíček3, K. Bezouška3, V. Kopecký Jr.3,4 and D. Štys1
1Laboratory of High Performance Computing, Institute of Physical Biology USB and Institute of Landscape Ecology AS CR, University of South Bohemia, Zámek 136, CZ-373 33 Nové Hrady, Czech Republic, email: firstname.lastname@example.org
2Institute of Physiology, Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
3Department of Biochemistry, Faculty of Sciences, Charles University, Albertov 2030, CZ-128 40 Prague 2, Czech Republic
4Institute of Physics, Charles University, Ke Karlovu 5, CZ- 121 16 Prague 2, Czech Republic
Protein function is strongly connected to the structure. For that we need to explore the three-dimensional structure if we want to understand the enzymatic or structural function of a protein. Although today there are existing several experimental techniques to determine the three-dimensional structure of proteins, as are NMR-spectroscopy or X-ray diffraction, these methods have their shortcomings, especially in the case of membrane proteins, which shows the low number of known structures in the Brookhaven Protein Database. And even if one structure is known it is often difficult to understand the complete function, due to a lack of information with respect to different conformational states of the membrane protein. For that reason can be useful tool in understanding the protein function a combination of homology and energetic modeling with vibrational spectroscopy. We confront the model already in the process of homology modeling (restraint-based method) with data gained by Raman and infrared spectroscopy, to have a continuous feedback. Although these spectroscopic methods do not give such complex information, in combination with the molecular modeling they give often enough information to understand important functional features of the protein or help to identify binding sites. Molecular dynamics then can explain certain dynamical features related to the function in contrast to a static model. Thus gained models are an important help in site-directed mutagenesis, truncation, binding-studies and even in crystallography.
An example for a successful application of the method was achieved in the study of the vanilloid receptor, a member of the transient receptor channel family. Our constructed model for the first time described a folding motif for the C-terminal tail of the channel, and according to this prediction, truncations were constructed for electrophysiological studies. Thus the function not only of the C-tail but also of several secondary structure elements in it could be described in detail. Vanilloid receptor 1 (TRPV1, formerly VR1) has been suggested to function as a multimodal signal transducer of noxious stimuli in the mammalian somatosensory system . Noxious thermal stimuli (> 43°C), acidic pH (< 6.8) or the alkaloid irritant capsaicin are required to open the TRPV1 channel. At room temperature and pH 7.3, TRPV1 behaves as a voltage-gated outwardly rectifying non-selective cation channel since it can be activated strongly by depolarizing voltage steps in the absence of any agonist . Although some knowledge of the structure and function of the TRPV channel subfamily has accumulated recently, the critical structural domains and the mechanisms by which various external stimuli translate into channel gating remain poorly understood. How the C-terminal domain contributes to the conformational stability of TRPV1 channel and the extent to which it influences its function, however, still remained to be determined. In our recently published study , we demonstrate that the cytosolic C-terminal region of TRPV1 channel contains domain(s) responsible for a steep temperature dependence of the TRPV1 heat-evoked responses. We hypothesize that this region is also important for regulation of the capsaicin-, low pH- and voltage-induced channel activity. To explain and predict the involvement of the C-terminal domain in TRPV1 channel function, the sequence of the TRPV1 C terminus from Ala 690 to Lys 838 was used for homology modeling. This section of the TRPV1 receptor shows a high sequence homology (44%) to the fragile histidine triad protein FHIT, whose tertiary structure has been solved at 1.85 Å resolution. The overall predicted structure of the TRPV1 C-tail can be described as a general alpha+beta type and can be further subclassed as an alpha+beta meander fold. The C-tail contains two helices, H1 and H2, and seven beta strands (Fig. 1). The strands three to seven form a five-stranded antiparallel sheet. The antiparallel strands one and two form a beta-hairpin across from and at an angle to the other sheet. Helix H1 packs on one side of the five-stranded antiparallel beta-sheet, and helix H2 packs on the same side and primarily interacts with strand three and the loop connecting strands two and three. The template structure shows a disordered gap from residue 107 to residue 127. Therefore, the structure of the large loop between beta-strand 7 and the second helix was generated only from a loop database and is not based on homology. Probably this loop is highly flexible in reality and the shown structure must be thus taken as only one speculative possibility for its conformation.
Predicted structure of the complete C terminus of TRPV1 and the truncated mutants. WT, Ribbon diagram of the wild type C terminus (residues A690-K838). Homology modeling predicts two alpha-helices H1, H2 and seven beta-strands 1-7. Antiparallel strands 1 and 2 form a beta-hairpin, strands 3-7 form a five-stranded antiparallel sheet. CD31, This mutant (residues A690-T807) lacks the alpha-helix H2. CD72, In this construct (A690-C766) secondary structural elements H2 and beta-strands 6 and 7 are missing. CD104, The predicted structure of the truncated construct (A690-G734) consists only of beta-strands 1-5.
In the molecular model based on homology with the fragile histidine triad protein presented here, the most distal 31 amino acid residues of the TRPV1 carboxyl terminus (Gln 808– Lys 838) correspond to the alpha helical structure H2 and the large flexible loop connecting it with beta-sheet 7 (Fig. 1). Removal of this region is sufficient to shift the thermal threshold for activation from 42°C to 39°C. This structural part seems also to modulate the sensitivity to capsaicin as the mutant CD31 exhibits increased agonist efficacy. Deletion of the remaining short part of the connecting loop (Arg 797–Lys 838) markedly decreased the thermal threshold (to 33°C) for receptor activation. The large loop seems to be anchored between helix H2 and beta-strand 7 to form itself a highly flexible structure that regulates steric accessibility to the core beta-sheet. The effects of the deletion of the remaining 11 loop amino acids in the mutant CD42 suggest the importance of beta-sheets 6 and 7 in channel activation. This view is supported also by construct CD72 which lacks beta-strands 6 and 7 (Glu 767–Lys 838) and displays profound changes in channel function. The thermal threshold dropped from 41.5 to 28.6°C, Q10 decreased from 25.6 to 4.7 and the currents induced by capsaicin, pH 5, heat and voltage decreased significantly suggesting a distinct role of these two beta-strands in the C-terminus of TRPV1. The experimental results for the mutant CD104 presented above indicate a disturbed multimerization of protein subunits. The helix H1 is lost in the model of this mutant. Therefore there is a high probability that this helix plays a role in either the tetrameric organization of the channel or in an interaction with another receptor region, e.g. of the N-terminal. The beta-hairpin formed by he first two antiparallel strands does not seem to exhibit any functional role; however, it could stabilize the proper position of the C-tail towards the membrane. In conclusion, our results provide evidence that the structural basis of the thermal sensitivity of the TRPV1 channel resides in the distal half of the C-terminus and that this terminal region contributes to the regulation of chemically, thermally and voltage induced activity of the TRPV1 channel.
As a second example, using the same technique, may serve the research done on the melatonin receptor type 1B. Melatonin receptors are a subfamily of G protein-coupled receptors for the pineal hormone melatonin, dubbed „the hormone of darkness“. A molecular model of the melatonin receptor was constructed by homology modeling from the structure of rhodopsin. The refined model at this stage contains 194 amino acids and shows five transmembrane segment. About 100 amino acids, which means two transmembrane segments are still missing. At this stage it nicely shows two intracellular loops between the first and the second and the third and fourth transmembrane segment. While the first intracellular loop can be described as just a simple turn between the transmembrane segments, the second from Cys 109–Ser 122 contains 14 amino acids. This loop is an important candidate for playing a crucial role in the channel function. It includes three tyrosines and two lysines. The three aromatic residues are potential candidates for vibrational spectroscopy while the lysine residues can be used for fluorescence labeling. Thus our model can already serve as a tool for predicting proper candidates for site-directed mutagenesis with respect to the role of the second intracellular loop. The next step in our modeling research will be to model the complete sequence containing also the third intracellular loop by the restraint-based method. To examine various possible conformations of the two loops it will be necessary to perform molecular dynamics and to verify and improve the model by means of various spectroscopic methods. The thus confirmed model will then serve as the workhorse for computational ligand docking as well as for experimental studies by means of site-directed mutagenesis, truncation, binding-essays and further. This combination of modeling and recombinant melatonin receptor provides new tools for investigating fundamental mechanisms of melatonin action.
The last example shall show that crystallisation and X-ray diffraction are not always able to answer important physiological questions and that computer modeling can be a useful and even necessary addition.
CD69 is the earliest leukocyte activation antigen playing a pivotal role in cellular signaling. In humans, the CD69 gene is located in chromosome 12 at bands p13-p12 in a region known as natural killer complex in association with other C-type lectin genes that control NK cell activity. CD69 is a disulfide-linked homodimer with two constitutively phosphorylated and variously glycosylated chains. It belongs to the type II integral membrane protein possessing an extracellular C-terminal protein motif related to C-type animal lectins. Since the ligand domain of CD69 has been defined in the recent domain swap experiments , we prepared constructs limited to the C-terminal portion including residues 100–199. This construct is a minimal size monomeric protein known to contain all amino acid residues responsible for potential binding of calcium and carbohydrates .
In order to determine if CD69 binds calcium, we saturated the purified protein with Ca2+ ions, and performed direct determinations of calcium in the samples of protein subjected to various dialysis procedures. More precise parameters for binding of calcium ion to CD69 were obtained from equilibrium dialysis studies using 45Ca2+. In order to identify the amino acids in CD69 involved in calcium binding more precisely, a Conolly-type surface with the electrostatic potential as surface property was generated for the published structure of this antigen. On this surface it was possible to identify a highly negative charged region, which corresponded to a potential calcium-binding site. Calcium was then docked into this single site formed by aspartic acid Asp 171, and the two adjacent glutamic acids Glu 185 and Glu 187. Remarkably, the insertion of calcium into this site resulted in no significant changes in the overall three-dimensional structure of CD69. Binding of calcium to the wild-type protein proceeded with a dissociation constant of approximately 54 mM. In order to prove the role of the specific amino acids in the binding of calcium, mutant proteins have been produced in which the above amino acids, i.e. Asp 171, Glu 185 and Glu 187, have been individually replaced by alanine. Mutation of any of the anticipated carboxyl group of Asp 171, Glu 185, or Glu 187 resulted in considerable reduction of the affinity of calcium binding (Kd of 0.5 mM, 0.1 mM, 0.5 mM has been estimated for the respective mutant proteins), although the effect observed for Glu 185 has been somewhat less profound. The double mutant with Glu 185 and Glu 187 replaced by alanin exhibited totally no binding of calcium. The question why Ca2+ ion was not observed in the published crystal structures is explained by the fact that the proteins used for crystallization were perhaps prepared in the calcium-free form. We believe that the atomic structure of CD69 was then obtained under artificial, non-physiological conditions.
Molecular details of the three GlcNAc molecules docked
into the calcium form of CD69. The potential high-affinity binding site (site 2) is
localized close to the calcium-binding site. One low affinity binding site (site 1) is also close to the calcium ion, while the second low affinity binding site (site 3) is in the more distal part of the molecule.
Since our recently published data  provide clear evidence that calcium is an integral component of CD69 protein under physiological conditions, and since there have been no changes in the overall structure of the protein except in the spatial position of specific amino acid residues, we were interested to investigate the effects of calcium binding by CD69 on the interaction with the carbohydrate ligands. Since the most precise and correct method to address these issues would be a direct binding assay, we decided to perform equilibrium dialysis experiments with the labeled carbohydrates. In order to reveal the structural details of GlcNAc binding to CD69, we have used the structure of the calcium-ligating form of the protein, and performed molecular docking of the carbohydrate into the receptor structure (Fig. 2). According to this model, GlcNAc bound into three sites, designated 1, 2 and 3, The identification of binding sites for N-acetylated hexosamines (3 for GlcNAc and 2 for GalNAc) confirmed by site-directed mutagenesis (together with the elucidation of the role of calcium in the binding process) sheds a light onto the current controversy about the carbohydrate-binding specificity of this protein . The high-affinity binding site for GlcNAc has moreover certain unique features not observed in other C-type animal lectins. The unknown electron density in the Natarajan’s crystal  of hexagonal, pyranose-like shape is localised directly in the position of the carbohydrate-binding site 1 described in our work. Moreover, the arrangement all three carbohydrate-binding sites detected here is in a good agreement with the suggestion of Llera’s ligand-binding surface. (site 1 and 3 are directly in this area, the site 2 is in a close proximity) . Altogether, identification of binding sites for calcium and for monosaccharides now open the way for searching of complex oligosaccharides as the potential physiological ligands for CD69.
The support by the Grant Nos. 309/02/1479, 305/03/0802 and 203/01/1018 of the Grant Agency of the Czech Republic and the Ministry of Education of the Czech Republic (No. MSM113100001, No. MSM123100001, No. MSM113200001) is acknowledged.
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