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Modeling transmembrane domain dimers/trimers of plexin receptors: implications for mechanisms of signal transmission across the membrane.

Zhang L, Polyansky A, Buck M - PLoS ONE (2015)

Bottom Line: Plexin-B2 does not form stable dimers due to the presence of TM prolines.The structure and dynamics of the JM region and TM-JM junction provide determinants for the distance and distribution of the intracellular domains, and for their binding partners relative to the membrane.The structures suggest experimental tests and will be useful for the interpretation of future studies.

View Article: PubMed Central - PubMed

Affiliation: Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio, 44106, United States of America.

ABSTRACT
Single-pass transmembrane (TM) receptors transmit signals across lipid bilayers by helix association or by configurational changes within preformed dimers. The structure determination for such TM regions is challenging and has mostly been accomplished by NMR spectroscopy. Recently, the computational prediction of TM dimer structures is becoming recognized for providing models, including alternate conformational states, which are important for receptor regulation. Here we pursued a strategy to predict helix oligomers that is based on packing considerations (using the PREDDIMER webserver) and is followed by a refinement of structures, utilizing microsecond all-atom molecular dynamics simulations. We applied this method to plexin TM receptors, a family of 9 human proteins, involved in the regulation of cell guidance and motility. The predicted models show that, overall, the preferences identified by PREDDIMER are preserved in the unrestrained simulations and that TM structures are likely to be diverse across the plexin family. Plexin-B1 and -B3 TM helices are regular and tend to associate, whereas plexin-A1, -A2, -A3, -A4, -C1 and -D1 contain sequence elements, such as poly-Glycine or aromatic residues that distort helix conformation and association. Plexin-B2 does not form stable dimers due to the presence of TM prolines. No experimental structural information on the TM region is available for these proteins, except for plexin-C1 dimeric and plexin-B1 - trimeric structures inferred from X-ray crystal structures of the intracellular regions. Plexin-B1 TM trimers utilize Ser and Thr sidechains for interhelical contacts. We also modeled the juxta-membrane (JM) region of plexin-C1 and plexin-B1 and show that it synergizes with the TM structures. The structure and dynamics of the JM region and TM-JM junction provide determinants for the distance and distribution of the intracellular domains, and for their binding partners relative to the membrane. The structures suggest experimental tests and will be useful for the interpretation of future studies.

No MeSH data available.


RMSD for initial and MD refined structures.a) RMSD values between initial (PREDDIMER predicted) structures across the subfamily of plexins chosen for further simulation. b) RMSD values between the structures (TM+extensions) after MD simulations, showing that the difference between the different subfamilies is essentially preserved.
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pone.0121513.g003: RMSD for initial and MD refined structures.a) RMSD values between initial (PREDDIMER predicted) structures across the subfamily of plexins chosen for further simulation. b) RMSD values between the structures (TM+extensions) after MD simulations, showing that the difference between the different subfamilies is essentially preserved.

Mentions: Since regions immediately outside the hydrophobic TM segment can influence the helix dimer configuration (e.g. [5]), we extended the TM helix peptides by addition of up to 10 residues from the native human plexin sequences, both at the N- and C-termini (Fig. 1b,c). The structures were prepared as explained in the Methods section and simulated for 1.0 μs on Anton. One structure, b2.1, dissociated, while another structure, b2.3, showed a separation of the helices but contacts involving the both N- and C-terminal regions (the added residues) still holding the dimer loosely together. In order to verify the convergence of the simulations, plots of the evolution of the geometric parameters (RMSD to starting structure, helix crossing and rotation angles) were carefully examined for drift. While some of the structures fluctuate, drift was only apparent for crossing angles in Plexin-B1 model1, b1.1 and this simulation was continued to 2.0 μs (Fig. 2, also showing results for b1.2 and b1.3). We averaged the geometric parameters of the TM central regions for the last 250 ns of the simulations (see Methods). These values and the fluctuations around them are given in Table 2. Except for the b2.1 and b2.3 simulations the helix crossing and rotation angles are relatively well preserved from the PREDDIMER initial structures; however, the Fscor value is mostly decreased and becomes < 2.5 in 8 out of 13 simulations. By contrast, in 3 simulations b1.3, b1.6, d1.1, the packing is slight, and the packing in d1.1 is significantly improved over the initial structures. Large changes in packing coincide with larger changes in crossing angles (> ± 30o in case of b1.7, b2.1, b2.3, d1.1, d1.2). Details of the final structures are given in Table 2, incl. the RMSD from the initial structures. Again, in correspondence with the geometric parameters, RMSD values are between 3.0–4.4 Å except for b1.7, b2.1 (which dissociated), and for d1.1 and d1.2. RMSD values less than 4.5 Å suggest that the structures are similar to those predicted ab initio, however there are slight adjustments in helix rotational angles (typically less than ±45o). Importantly, the relationship between the different plexin subfamilies identified in the ab initio predicted structures is largely preserved in the final, all-atom equilibrated structures of the helix dimers with N- and C-terminal extensions. Fig. 3a) gives the scaled pairwise RMSD values between the initial 13 plexin structures chosen for further refinement. Fig. 3b) gives the RMSD values between the final 13 plexin structures; reflecting that only b2.1 (which dissociates) changes with respect to the others.


Modeling transmembrane domain dimers/trimers of plexin receptors: implications for mechanisms of signal transmission across the membrane.

Zhang L, Polyansky A, Buck M - PLoS ONE (2015)

RMSD for initial and MD refined structures.a) RMSD values between initial (PREDDIMER predicted) structures across the subfamily of plexins chosen for further simulation. b) RMSD values between the structures (TM+extensions) after MD simulations, showing that the difference between the different subfamilies is essentially preserved.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383379&req=5

pone.0121513.g003: RMSD for initial and MD refined structures.a) RMSD values between initial (PREDDIMER predicted) structures across the subfamily of plexins chosen for further simulation. b) RMSD values between the structures (TM+extensions) after MD simulations, showing that the difference between the different subfamilies is essentially preserved.
Mentions: Since regions immediately outside the hydrophobic TM segment can influence the helix dimer configuration (e.g. [5]), we extended the TM helix peptides by addition of up to 10 residues from the native human plexin sequences, both at the N- and C-termini (Fig. 1b,c). The structures were prepared as explained in the Methods section and simulated for 1.0 μs on Anton. One structure, b2.1, dissociated, while another structure, b2.3, showed a separation of the helices but contacts involving the both N- and C-terminal regions (the added residues) still holding the dimer loosely together. In order to verify the convergence of the simulations, plots of the evolution of the geometric parameters (RMSD to starting structure, helix crossing and rotation angles) were carefully examined for drift. While some of the structures fluctuate, drift was only apparent for crossing angles in Plexin-B1 model1, b1.1 and this simulation was continued to 2.0 μs (Fig. 2, also showing results for b1.2 and b1.3). We averaged the geometric parameters of the TM central regions for the last 250 ns of the simulations (see Methods). These values and the fluctuations around them are given in Table 2. Except for the b2.1 and b2.3 simulations the helix crossing and rotation angles are relatively well preserved from the PREDDIMER initial structures; however, the Fscor value is mostly decreased and becomes < 2.5 in 8 out of 13 simulations. By contrast, in 3 simulations b1.3, b1.6, d1.1, the packing is slight, and the packing in d1.1 is significantly improved over the initial structures. Large changes in packing coincide with larger changes in crossing angles (> ± 30o in case of b1.7, b2.1, b2.3, d1.1, d1.2). Details of the final structures are given in Table 2, incl. the RMSD from the initial structures. Again, in correspondence with the geometric parameters, RMSD values are between 3.0–4.4 Å except for b1.7, b2.1 (which dissociated), and for d1.1 and d1.2. RMSD values less than 4.5 Å suggest that the structures are similar to those predicted ab initio, however there are slight adjustments in helix rotational angles (typically less than ±45o). Importantly, the relationship between the different plexin subfamilies identified in the ab initio predicted structures is largely preserved in the final, all-atom equilibrated structures of the helix dimers with N- and C-terminal extensions. Fig. 3a) gives the scaled pairwise RMSD values between the initial 13 plexin structures chosen for further refinement. Fig. 3b) gives the RMSD values between the final 13 plexin structures; reflecting that only b2.1 (which dissociates) changes with respect to the others.

Bottom Line: Plexin-B2 does not form stable dimers due to the presence of TM prolines.The structure and dynamics of the JM region and TM-JM junction provide determinants for the distance and distribution of the intracellular domains, and for their binding partners relative to the membrane.The structures suggest experimental tests and will be useful for the interpretation of future studies.

View Article: PubMed Central - PubMed

Affiliation: Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio, 44106, United States of America.

ABSTRACT
Single-pass transmembrane (TM) receptors transmit signals across lipid bilayers by helix association or by configurational changes within preformed dimers. The structure determination for such TM regions is challenging and has mostly been accomplished by NMR spectroscopy. Recently, the computational prediction of TM dimer structures is becoming recognized for providing models, including alternate conformational states, which are important for receptor regulation. Here we pursued a strategy to predict helix oligomers that is based on packing considerations (using the PREDDIMER webserver) and is followed by a refinement of structures, utilizing microsecond all-atom molecular dynamics simulations. We applied this method to plexin TM receptors, a family of 9 human proteins, involved in the regulation of cell guidance and motility. The predicted models show that, overall, the preferences identified by PREDDIMER are preserved in the unrestrained simulations and that TM structures are likely to be diverse across the plexin family. Plexin-B1 and -B3 TM helices are regular and tend to associate, whereas plexin-A1, -A2, -A3, -A4, -C1 and -D1 contain sequence elements, such as poly-Glycine or aromatic residues that distort helix conformation and association. Plexin-B2 does not form stable dimers due to the presence of TM prolines. No experimental structural information on the TM region is available for these proteins, except for plexin-C1 dimeric and plexin-B1 - trimeric structures inferred from X-ray crystal structures of the intracellular regions. Plexin-B1 TM trimers utilize Ser and Thr sidechains for interhelical contacts. We also modeled the juxta-membrane (JM) region of plexin-C1 and plexin-B1 and show that it synergizes with the TM structures. The structure and dynamics of the JM region and TM-JM junction provide determinants for the distance and distribution of the intracellular domains, and for their binding partners relative to the membrane. The structures suggest experimental tests and will be useful for the interpretation of future studies.

No MeSH data available.