10 A niversary of IIMCB
10 A niversary of IIMCB
10 A niversary of IIMCB
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• Jozwiak K, Krzysko KA, Bojarski L, Gacia M, Filipek S.<br />
Molecular models <strong>of</strong> the interface between anterior<br />
pharynx-defective protein 1 (APH-1) and presenilin<br />
involving GxxxG motifs. ChemMedChem, 2008; 3:627-634<br />
• Majewski T, Lee S, Jeong J, Yoon DS, Kram A, Kim MS,<br />
Tuziak T, Bondaruk J, Lee S, Park WS, Tang KS, Chung W,<br />
Shen L, Ahmed SS, Johnston DA, Grossman HB, Dinney<br />
CP, Zhou JH, Harris RA, Snyder C, Filipek S, Narod SA,<br />
Watson P, Lynch HT, Gazdar A, Bar-Eli M, Wu XF, McConkey<br />
DJ, Baggerly K, Issa JP, Benedict WF, Scherer SE, Czerniak<br />
B. Understanding the development <strong>of</strong> human bladder<br />
cancer by using a whole-organ genomic mapping<br />
strategy. Lab Invest, 2008; 88:694-721<br />
Current Research<br />
1. Studies <strong>of</strong> activation switches in opioid receptors<br />
G protein coupled receptors (GPCRs) interact with very<br />
diverse sets <strong>of</strong> ligands which bind to the transmembrane<br />
(TM) segments and sometimes also to the receptor<br />
extracellular domains. Each receptor subfamily undergoes<br />
a series <strong>of</strong> conformational rearrangements leading to<br />
the binding <strong>of</strong> a G protein during the activation process.<br />
All GPCRs preserved the 7-TM scaffold during evolution<br />
but adapted it to different sets <strong>of</strong> ligands by structure<br />
customization. Binding <strong>of</strong> structurally different agonists<br />
requires the disruption <strong>of</strong> different intramolecular<br />
interactions, leading to different receptor conformations and<br />
differential effects on downstream signaling proteins. The<br />
dynamic character <strong>of</strong> GPCRs is likely to be essential for their<br />
physiological functions, and a better understanding <strong>of</strong> this<br />
molecular plasticity could be important for drug discovery.<br />
Experiments suggest that agonist binding and receptor<br />
activation occur through a series <strong>of</strong> conformational<br />
intermediates. Transition between these intermediate states<br />
involves the disruption <strong>of</strong> intramolecular interactions that<br />
stabilize the basal state <strong>of</strong> a receptor. Such pr<strong>of</strong>ound changes<br />
are evoked by the action <strong>of</strong> molecular switches. The switches<br />
proposed so far for different GPCRs include the “rotamer<br />
toggle switch” involving the CWxPxF sequence on helix TM6,<br />
the switch based on the NPxxY(x)(5,6)F sequence linking<br />
helices TM7 and H8, the “3-7 lock” interaction connecting<br />
TM3 and TM7 (involving the Schiff base-counterion<br />
interaction in rhodopsin), and the “ion lock” linking<br />
transmembrane helices TM3 and TM6 and employing the<br />
E/DRY motif on TM3. Although, in the rhodopsin structure,<br />
all these switches are closed (inactive state), in recent crystal<br />
structures <strong>of</strong> b 1 - and b 2 -adrenergic receptor complexes with<br />
antagonists and inverse agonists the “ion lock” is open while<br />
the “rotamer toggle switch” remains closed.<br />
Opioid receptors belong to the family <strong>of</strong> GPCRs. They<br />
are located in the membranes <strong>of</strong> neurons <strong>of</strong> the central<br />
nervous system and <strong>of</strong> some types <strong>of</strong> smooth muscle cells.<br />
Due to the important role they play in the human body in<br />
controlling pain and stress, modulating immune responses<br />
and developing addiction, opioid receptors have been the<br />
subject <strong>of</strong> numerous investigations. There are four types <strong>of</strong><br />
opioid receptors: µOR, δOR, κOR and the nociceptin/opioid<br />
receptor-like 1. There are also additional, pharmacologically<br />
classified, subtypes <strong>of</strong> opioid receptors, though it is<br />
believed that they may, at least partly, originate from<br />
homodimerization <strong>of</strong> the four main opioid receptor types<br />
and their heterodimerization with other GPCRs. Knowledge<br />
<strong>of</strong> the structural details <strong>of</strong> receptor activation is absolutely<br />
necessary in order to design new drugs with precise action<br />
and negligible side effects.<br />
Opioid receptors, like other GPCRs, undergo specific<br />
structural rearrangements upon activation by agonists.<br />
Such processes proceed via several steps ruled by different<br />
molecular switches. The first event in opioid receptor<br />
activation includes sensing <strong>of</strong> agonists and antagonists.<br />
Agonist binding is the first step in ligand-induced receptor<br />
activation. To investigate the relationship between the<br />
final movements <strong>of</strong> a ligand in a receptor binding site and<br />
the first steps <strong>of</strong> the activation process in opioid receptors,<br />
we chose a set <strong>of</strong> rigid ligands with the structural motif<br />
<strong>of</strong> tyramine (p-hydroxyphenethylamine) so that the two<br />
parts - the “message” (tyramine) and the “address” - are<br />
well distinguished. We used antagonists - naltrexone and<br />
b-FNA, and two closely related agonists - morphine and<br />
N-methyl-morphine.<br />
Using homology modeling, simulated annealing and<br />
molecular dynamics <strong>of</strong> the µ opioid receptor complexes,<br />
we proposed distinct binding modes <strong>of</strong> opioids carrying<br />
the same structural motif – tyramine. Although they<br />
bind to the same binding pocket and the protonated<br />
amine interacts with D3.32, the antagonist’s phenolic OH<br />
group tends to bind Y3.33 whereas the agonist’s phenolic<br />
OH group tends to bind H6.52 (numbers according to<br />
the Ballesteros-Weinstein numbering scheme). All the<br />
studied agonists broke the “3-7 lock” (the hydrogen<br />
bond D3.32-Y7.43 between TM3 and TM7). Moreover, the<br />
antagonist naltrexone, when restrained to bind H6.52,<br />
was also able to break this connection (Fig. 1a,b) and,<br />
Fig. 1. The structure <strong>of</strong><br />
naltrexone-µOR complex<br />
from unrestrained (ligand<br />
in green) and restrained<br />
(ligand in orange) MD<br />
simulations. During the<br />
restrained simulation<br />
(a bond between the<br />
phenolic OH group <strong>of</strong> the<br />
ligand and H6.52 was fixed) the “3-7 lock” (a hydrogen bond D3.32-Y7.43<br />
between TM3 and TM7) is breaking. (a) view from the extracellular side.<br />
(b) a side view <strong>of</strong> the same structure (author: Sławomir Filipek).<br />
Laboratory <strong>of</strong> Biomodelling 49