(b) Faculty of Chemistry, N. Copernicus University,
ul. Gagarina 7, 87-100 Torun, Poland
While bound in TTR, the thyroxine core in a skewed conformation is positioned between aliphatic side chains of Ala and Leu. Its phenolic hydroxyl interacts with the Ser side chains from two TTR subunits, and the alanyl moiety of the hormone forms the pair of salt bridges to Glu and Lys near the binding site entrance [1,2]. The protein crystal structures of TTR complexes have revealed the alternative modes of thyroxine analogues binding [2-4]. The halogen-like substituents are positioned in the hydrophobic pockets between anti-parallel beta strands of TTR. T4 iodine substituents form the alternative interactions to nucleophilic carbonyl oxygen atoms of the surrounding strands. Resulting alternative positions differ by almost 1 A, and in some cases the presence of additional water molecule mediating the binding interactions is suggested [3,5]. The position of the hormone analogue is affected by the tyrosyl ring substitution and the ether bridge flexibility. In this way the mode of the hormone substitution affects the ability to form polar interactions to Glu and Lys, differentiating the binding affinity.
The genetic disorders causing abnormalities in the hormone binding to these proteins result in hypo- or hyperthyroxinemia and severe disfunction of the organisms of affected patients. The molecular level understanding of ligand recognition and binding specificity is a prerequisite condition for an effective treatment.
Our research on the binding of thyroxine and its analogues to TTR had also indicated the possibility of multiple ligand binding modes [2]. In order to understand the molecular basis for ligand recognition in transthyretin, we have initiated a molecular modelling of ligands and TTR. Firstly, we have examined the rigidity of the thyroxine ether bridge using the molecular dynamics technique with the CHARM force field [6]. Secondly, the minimized structures and molecular electrostatic potentials of T4, 3,5,3',5'-tetraiodothyroacetic acid (T4Ac), 3,3',5'-triiodothyronine (rT3), 3,3'-diiodothyronine (T2), 3',5'-dinitro-N-acetyl-thyronine (DNNAT), 3',5'-dibromo-3-methyl-6,4'-dihydroxyflavone (EMD21388) have been calculated using standard quantum-chemical methods (mainly AM1 as implemented in the InsightII package [7]). Results for both X-ray and minimized structures were compared and the effects of conformations on the electrical properties of molecules studied. These data are compared with those of the AMBER force field obtained by the Kollman's group [8,9]. Our results will be used in simulations of the alternative binding modes of T4 in transthyretin tetramers.
All initial structures obtained from the scratch (Builder module of InsightII) or crystal data (ligands of TTR) were subject to a complete energy minimization using the EF method of the MOPAC6 package [13] as implemented in InsightII v.3.5 software [7]. In all cases the PRECISE option was used and the frequencies in the minimized structures were calculated to exclude transition states.
T4 was also subject to the classical CHARMM forcefield minimization using the XPLOR package [14]. Additionaly, the DFT DMOL code [7] was used for calculations of the electrostatic potential of the T4 molecule in the AM1 optimized conformation. The molecules were also subject to geometry optimization using the PM3 method [15].
Unless otherwise indicated all partial charges were calculated using Mulliken population analysis. The ESP charges were obtained using Merz-Kollman method of fitting electrostatic potential on Williams surfaces of studied molecules.
The XMOL software allows for interactive studies of details of the geometry. These structures are also shown in Figs. 9-14, together with the calculated AM1 charge distributions.
The values of torsional degrees of freedom which are most important for the general shape of hormones are presented in Tab. 1. Standard definitions of angles are shown in Fig. 8:
Selected geometry parameters obtained from theoretical calculations are compared with X-ray and literature data in Tab.1.
THYROXINE T4 | rT3 | T4Ac | T2 | DNNAT | Parameter | AM1 | PM3 | XPL | crystal [1] | protein 2.0A res. [2] |
AMB [8] | AM1 * | AM1 * | AM1 | protein 2.0A res. [4] |
AM1 | protein 2.2A res. [2] |
---|---|---|---|---|---|---|---|---|---|---|---|---|
phi | 77.5 | 83.5 | 86.5 | 108.3 | 102.9 | 90.0 | 83.3 | 105.0 | 22.6 | 93.8 | 39.1 | 94.8 |
phi' | 25.2 | 13.0 | 14.1 | -29.2 | -13.7 | 0.0 | 25.7 | -19.9 | 59.5 | 19.2 | 43.0 | 65.3 |
chi1 | 48.6 | 43.9 | 29.8 | -50.0 | -144.7 | -- | 47.0 | -61.9 | -57.2 | -20.6 | 52.3 | -49.8 |
chi2 | 74.8 | 76.7 | 82.6 | 162.2 | 97.9 | -- | 73.7 | 50.9 | 107.4 | 115.8 | 96.9 | 96.0 |
psi | -162.3 | -174.3 | 158.8 | -159.3 | 93.8 | -- | -162.6 | -- | 172.6 | 171.0 | 165.4 | 124.1 |
C-I phe | 2.02 | 1.97 | 2.09 | 2.10 | 2.10 | 2.08 | 2.02 | 2.02 | 2.02 | 2.20** | - | - |
C-I tyr | 2.02 | 1.97 | 2.09 | 2.09 | 2.08 | 2.08 | 2.02 | 2.02 | 2.02 | 2.07 | - | - |
C4O4C1' | 116.2 | 117.1 | 121.3 | 120.4 | 123.6 | 125.0 | 115.9 | 116.2 | 116.5 | 127.0** | 116.2 | 118.2 |
* Crystal structures in TTR or molecular crystals unknown
** Deformation in the crystallographic refinement of 2.0A resolution
AM1 = AM1 minimized structure ,
XPL = X-PLOR minimized structure [14], CHARMM force field,
AMB = AMBER minimized structure.
Torsion angles: phi' = C4-O4-C1'-C2', phi = C3-C4-O4-C1', chi2 = C8-C7-C1-C2, chi1 = N8-C8-C7-C1, psi = N8-C8-C9-O10, bonds C-I phe = phenolic ring C-I, C-I tyr = tyrosyl ring C-I, angle C4O4C1' = C4-O4-C1' (see also Fig. 8)
The AM1 geometry of EMD analog is shown in Fig.9 (bond lengths) and in Fig. 10 (bond angles):
There are numerous ways of obtaining the charge distribution in organic molecules using quantum chemical methods. In Figs. 11-16 we present selected charges calculated within the AM1 method for the minimized structures. All AM1 charges for each compound may be extracted from the MOPAC *.arc files (for example T4). The charges related to the most important atoms and groups of analogues are presented in the Table 2. In this table the DFT charges obtained with BLYP functional (DMOL code [7]) and those used by J.M.Blaney et.al. in their AMBER modelling for T4 are also shown. Below the AM1 charge distribution calculated for the EMD molecule is presented as an example:
Fig.11. Charge distribution in T4.
Fig.12. Charge distribution in T4Ac.
Fig.13. Charge distribution in rT3.
Fig.14. Charge distribution in T2.
Fig.15. Charge distribution in DNNAT.
atom (group) | T4 AM1 | T4 PM3 (a) | T4 DFT (b) | T4 DFT (c) | T4 AMBER - (d) | T4Ac | rT3 | T2 | DNNAT | EMD |
---|---|---|---|---|---|---|---|---|---|---|
O4 (ether) | -0.152 | -0.109 | -0.104 | -0.496 | -0.24 | -0.149 | -0.158 | -0.144 | -0.145 | -- |
O4 (phenol) | -0.230 | -0.195 | -0.173 | -0.636 | -0.40 | -0.231 | -0.231 | -0.233 | -0.199 | -0.223 |
H (phenol) | 0.234 | 0.203 | 0.121 | 0.503 | 0.40 | 0.234 | 0.234 | 0.227 | 0.277 | 0.239 |
I3' (phenol) | 0.162 | 0.058 | 0.060 | 0.037 | -0.07 | 0.160 | 0.161 | 0.183 | -0.125 (a) | 0.095 (Br) |
I5' (phenol) | 0.185 | 0.082 | 0.091 | 0.058 | -0.07 | 0.184 | 0.184 | -- | ?? | 0.075 (Br) |
I3 (tyrosyl) | 0.179 | 0.084 | 0.066 | 0.056 | -0.07 | 0.182 | 0.192 | 0.185 | -- | -- |
I5 (tyrosyl) | 0.200 | 0.116 | 0.103 | 0.081 | -0.07 | 0.188 | -- | -- | -- | -- |
O10 (carboxy) | -0.454 | -0.460 | -0.310 | -0.474 | -0.543 | -0.357(b) | -0.453 | -0.443 | -- | -- |
O11 (carboxy) | -0.526 | -0.577 | -0.331 | -0.494 | -0.543 | -0.311(c) | -0.528 | -0.535 | -- | -- |
N8 (amino) | -0.060 | 0.675 | -0.006 | -1.119 | -0.364 | -- | -0.061 | -0.062 | -- | -- |
H (amino) | 0.203 | -0.011 | 0.153 | 0.491 | 0.332 | -- | 0.231 | 0.282 | -- | -- |
H (amino) | 0.283 | 0.013 | 0.173 | 0.574 | 0.332 | -- | 0.284 | 0.280 | -- | -- |
H (amino) | 0.230 | 0.115 | 0.138 | 0.503 | 0.332 | -- | 0.232 | 0.224 | -- | -- |
(a) PM3 optimized geometry
(b) AM1 geometry used, Hirshfeld partition method
(c) AM1 geometry used, Mulliken partition method
(d) AMBER parameters used, data from [8]
coordinate | AM1 (in A or deg.) | X-ray (in A or deg.) |
---|---|---|
C4-Br5 | 1.873 | 1.887 |
C9-Br10 | 1.875 | 1.901 |
C1-C27 | 1.467 | 1.497 |
C19-O20 | 1.239 | 1.234 |
C6-O7 | 1.367 | 1.350 |
C15-O13 | 1.377 | 1.360 |
C21-O22 | 1.385 | 1.378 |
C27-O22 | 1.388 | 1.378 |
C27-C28 | 1.358 | 1.331 |
C28-C29 | 1.480 | 1.500 |
O22-C27-C1-C2 | 43.93 | 45.31 |
C21-O22-C27 | 117.35 | 118.92 |
O22-C27-C1 | 109.54 | 107.90 |
The specific electrostatic interactions may be responsible for the negative cooperativity observed in the TTR tetramers. Therefore it is very important to study the effects of different structures and conformations of the "tail" tyrosyl group or its equivalents on the charge distribution in the "head" phenol ring moiety. The most important partial charges are collected in Tab.2. In all iodinated analogues the AM1 charges on I3' and I5' are similar (+0.16 and +0.18) and do not depend on details of the tyrosyl group stucture. A slight asymmetry between I3' and I5' results from the interaction of I5' with the hydrogen atom of the hydroxyl group. The charges of O4' (hydroxyl) and the corresponding H atom are also very similar in all derivatives including EMD. A slightly higher charges of H in DNNAT indicate on a greater acidity of the -OH group in this analogue. The PM3 method gives lower positive charges on iodine atoms (+0.05, +0.08) but very similar to the AM1 on the hydroxyl group. The AM1 charges on bromine atoms in EMD are smaller (0.095 and 0.075) than those of iodines so we expect that the halogene interactions of EMD with protein nucleofilic groups should be smaller than the interactions of iodinated compounds. Since in the first modelling of T4 interactions with proteins AMBER parameters with the negative values of charges located on all iodines have been used (see Tab.2), perhaps the electrostatic interactions were not correctly represented in that model.
The DFT partial charges obtained for T4 using the Mulliken population analysis are quite different from those based on the Hirshfeld method, the later beeing more consistent with semiempirical calculations.
It is worthwhile to note that in all zwitterionic molecules ( T4, T2 and rT3) we observe a clear asymmetry of the AM1/PM3 charge distribution on oxygens in the carboxy group. This observation indicates that O10 and O11 are not equivalent with respect to their H-bonding abilities since the "cis" orientation of the COO- and NH3+ groups leads to the preferential interaction of one of the oxygens with the amino group.
The total charges calculated for the NH3+ group are identical in all charged compounds but the PM3 and AM1 methods give different distributions of the charges on N and H atoms.
The sum of partial charges of atoms belonging to the nitro group of DNNAT is negative (-0.125) while all calculated partial charges for iodine atoms are positive. Since sizes of the iodine substituent and the nitro group are similar (in terms of Van der Waals radius) the detailed differences in electron density distribution must be responsible for the different binding properties of T4 (T2) and DNNAT. Indeed, electron density contoured at the same level reveals relatively lower values on iodines compared to the nitro group substituent (see Fig. 19 below). This confirms the role of protein nucleophilic group interactions with ligand halogenes for the ligand recognition and effective binding in transthyretin.
The calculated distribution of the electron density is consistent with the observation based on the protein crystal structures that iodines of T4 interact with nucelofilic carbonyl groups of polypeptide main chains while similarly positioned nitro substituents of DNNAT H-bond to the serine side chain hydroxyles.
The electrostatic potential derived charges, based on the AM1 electron density distribution gave reasonable results only for DNNAT e.g. the only analogue without iodine or bromine substituents. The selected ESP charges are presented in Fig.20 and all values may be obtained from the modified MOPAC archive file dnnatesp.arc
In the other cases the ESP InsightII option led to very high (1.5-3.5) values of point charges located on the phenol ring carbon atoms. In our opinion these results of the fitting procedure indicate on the deficiency of the standard point charge model of electrostatics in iodinated hormones. Perhaps, higher moments should be included or dummy potential sites should be introduced to describe correctly lone pairs of iodine and bromine atoms [18]. The high asymmetry of electrostatic potential in the vicinity of the phenol ring is demonstrated in Fig. 21.
There is also a possibility that we have encountered a case in which a standard least squares fitting procedure is inadequate (see for example [19] ). Thus the problem of ESP charges in iodinated derivatives requires further studies.
A support from the Polish State Commitee for Scientific Research grant no. 6 P04A 032 11, project BiMol (FNP) and UMK grants no. 328-F and 389-F is acknowledged. Authors thanks also Mr K.Wejer for this assistance in HTML editing and Mr G. Bakalarski for DFT calculations.