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Dimeric interactions and complex formation using direct coevolutionary couplings.

dos Santos RN, Morcos F, Jana B, Andricopulo AD, Onuchic JN - Sci Rep (2015)

Bottom Line: Therefore a systematic way to extract dimerization signals has been elusive.For the most accurate conformations of the structurally diverse dimeric complexes studied the mean and interfacial RMSDs are 1.95Å and 1.44Å, respectively.This methodology is also able to identify distinct dimerization conformations as for the case of the family of response regulators, which dimerize upon activation.

View Article: PubMed Central - PubMed

Affiliation: Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827.

ABSTRACT
We develop a procedure to characterize the association of protein structures into homodimers using coevolutionary couplings extracted from Direct Coupling Analysis (DCA) in combination with Structure Based Models (SBM). Identification of dimerization contacts using DCA is more challenging than intradomain contacts since direct couplings are mixed with monomeric contacts. Therefore a systematic way to extract dimerization signals has been elusive. We provide evidence that the prediction of homodimeric complexes is possible with high accuracy for all the cases we studied which have rich sequence information. For the most accurate conformations of the structurally diverse dimeric complexes studied the mean and interfacial RMSDs are 1.95Å and 1.44Å, respectively. This methodology is also able to identify distinct dimerization conformations as for the case of the family of response regulators, which dimerize upon activation. The identification of dimeric complexes can provide interesting molecular insights in the construction of large oligomeric complexes and be useful in the study of aggregation related diseases like Alzheimer's or Parkinson's.

No MeSH data available.


Related in: MedlinePlus

DCA/SBM for interfaces can infer multiple dimer conformations.(A) Coevolving contacts for the active state of the PhoB response regulator dimer in E. coli shown in black circles overlap well with the dimeric interface (orange). The predicted complex has a resolution of RMSD = 0.89 Å (iRMSD = 0.83 Å). (B) An alternative configuration of the activated dimer in protein regx3 upon phosphorylation is also predicted with an RMSD = 2 Å (iRMSD = 1.3 Å). This configuration involves domain swapping of helix α4 and α5 and sheet β5 and a second interacting region (dashed box) that is also captured by DCA. This structure also includes the effector domain (shown in white) that is a member of the transcriptional regulatory protein, Trans_reg_C (PF00486). Domain swapping is possible because of the contacts formed between the effector domain and the receiver domain in regx3 that allow this helical region to be exposed for binding.
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f4: DCA/SBM for interfaces can infer multiple dimer conformations.(A) Coevolving contacts for the active state of the PhoB response regulator dimer in E. coli shown in black circles overlap well with the dimeric interface (orange). The predicted complex has a resolution of RMSD = 0.89 Å (iRMSD = 0.83 Å). (B) An alternative configuration of the activated dimer in protein regx3 upon phosphorylation is also predicted with an RMSD = 2 Å (iRMSD = 1.3 Å). This configuration involves domain swapping of helix α4 and α5 and sheet β5 and a second interacting region (dashed box) that is also captured by DCA. This structure also includes the effector domain (shown in white) that is a member of the transcriptional regulatory protein, Trans_reg_C (PF00486). Domain swapping is possible because of the contacts formed between the effector domain and the receiver domain in regx3 that allow this helical region to be exposed for binding.

Mentions: Response regulators are members of a very large family of primarily prokaryotic proteins with more than a hundred thousand members. They are involved in signaling pathways where their receiver domain (Pfam PF00072) is typically phosphorylated by a histidine kinase (Pfam PF00512). This event triggers a conformational change and promotes dimerization of the phosphorylated protein, activating its function as a transcription factor that binds to DNA and continues a cascade of events in response to its original input sensed by the kinase474849. Homodimerization of the receiver domain (REC) is fundamental to achieve an active state conformation50. We studied the phosphate regulon transcriptional regulatory protein PhoB in E. coli, which upon activation dimerizes in its typical configuration (α4-β5-α5). Figure 4A shows the result of applying the SBM + DCA methodology to the complex formed by the REC domain of PhoB upon activation. A series of dimeric contacts among residues in the region 90–120 (orange) are detected by DCA (black circles). The complex was predicted with an RMSD accuracy of 0.89 Å with respect to the crystal structure (PDB 1ZES) for the best case and an average of 1.57 Å for the last stabilized simulation stage. This suggests the presence of a clear coevolutionary signal for the active state complex formation. It has also been suggested that the active state dimers for the REC domain of the response regulator can take alternative conformations. One of such conformations involves domain swapping of helices α4 and α5 and sheet β5, as well as the formation of distinct dimeric contacts51. We applied our methodology to the monomeric structures of the sensory transduction protein regx3 of M. bovis (PDB 2OQR) that binds using this alternative active interface. The contact map in Fig. 4B shows that some of the monomeric contacts in Fig. 4A become dimeric for regx3 and are highly coupled. Additionally, another region of contacts involving residues 10–20 interacting with residues 100–110 is also captured using coevolutionary analysis (see Fig. 4B, dashed box). These two contact regions drive the formation of this alternative complex with a resolution of RMSD of 2 Å (iRMSD = 1.33 Å). Regx3 is a multidomain protein containing an effector domain. If we compute the RMSD only for the response regulator domain, as in the case of PhoB, then the best RMSD = 1.13 Å. This implies that coevolutionary signals for multiple dimeric conformations are present and can be used to characterize multiple physiologically relevant configurations. Although the dimeric state of the receiver domain is mainly observed for the activated state, some studies suggest that an inactive state can also form homodimers and some symmetric units supporting this view5052. Nonetheless, it is not known if these inactive homodimers are formed in vivo or if they have any physiological relevance. Furthermore these inactive state complexes are arranged in such a way that the aspartate residue that is phosphorylated upon activation is not accessible to the kinase making this configuration less physiologically viable. Although some of the contacts in the inactive state dimer are captured by DCA, they do not appear to be sufficient to reach the same resolutions as for the active states. Supplementary Fig. S5 shows the predicted structure for such system, which has no resemblance to the inactive state dimeric interface observed in PDB 1B00. One interpretation of this result is that our methodology is not able to capture this alternative dimer correctly. The other view is that the evolutionary signal for this dimeric inactive state is weak and therefore not functional.


Dimeric interactions and complex formation using direct coevolutionary couplings.

dos Santos RN, Morcos F, Jana B, Andricopulo AD, Onuchic JN - Sci Rep (2015)

DCA/SBM for interfaces can infer multiple dimer conformations.(A) Coevolving contacts for the active state of the PhoB response regulator dimer in E. coli shown in black circles overlap well with the dimeric interface (orange). The predicted complex has a resolution of RMSD = 0.89 Å (iRMSD = 0.83 Å). (B) An alternative configuration of the activated dimer in protein regx3 upon phosphorylation is also predicted with an RMSD = 2 Å (iRMSD = 1.3 Å). This configuration involves domain swapping of helix α4 and α5 and sheet β5 and a second interacting region (dashed box) that is also captured by DCA. This structure also includes the effector domain (shown in white) that is a member of the transcriptional regulatory protein, Trans_reg_C (PF00486). Domain swapping is possible because of the contacts formed between the effector domain and the receiver domain in regx3 that allow this helical region to be exposed for binding.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4559900&req=5

f4: DCA/SBM for interfaces can infer multiple dimer conformations.(A) Coevolving contacts for the active state of the PhoB response regulator dimer in E. coli shown in black circles overlap well with the dimeric interface (orange). The predicted complex has a resolution of RMSD = 0.89 Å (iRMSD = 0.83 Å). (B) An alternative configuration of the activated dimer in protein regx3 upon phosphorylation is also predicted with an RMSD = 2 Å (iRMSD = 1.3 Å). This configuration involves domain swapping of helix α4 and α5 and sheet β5 and a second interacting region (dashed box) that is also captured by DCA. This structure also includes the effector domain (shown in white) that is a member of the transcriptional regulatory protein, Trans_reg_C (PF00486). Domain swapping is possible because of the contacts formed between the effector domain and the receiver domain in regx3 that allow this helical region to be exposed for binding.
Mentions: Response regulators are members of a very large family of primarily prokaryotic proteins with more than a hundred thousand members. They are involved in signaling pathways where their receiver domain (Pfam PF00072) is typically phosphorylated by a histidine kinase (Pfam PF00512). This event triggers a conformational change and promotes dimerization of the phosphorylated protein, activating its function as a transcription factor that binds to DNA and continues a cascade of events in response to its original input sensed by the kinase474849. Homodimerization of the receiver domain (REC) is fundamental to achieve an active state conformation50. We studied the phosphate regulon transcriptional regulatory protein PhoB in E. coli, which upon activation dimerizes in its typical configuration (α4-β5-α5). Figure 4A shows the result of applying the SBM + DCA methodology to the complex formed by the REC domain of PhoB upon activation. A series of dimeric contacts among residues in the region 90–120 (orange) are detected by DCA (black circles). The complex was predicted with an RMSD accuracy of 0.89 Å with respect to the crystal structure (PDB 1ZES) for the best case and an average of 1.57 Å for the last stabilized simulation stage. This suggests the presence of a clear coevolutionary signal for the active state complex formation. It has also been suggested that the active state dimers for the REC domain of the response regulator can take alternative conformations. One of such conformations involves domain swapping of helices α4 and α5 and sheet β5, as well as the formation of distinct dimeric contacts51. We applied our methodology to the monomeric structures of the sensory transduction protein regx3 of M. bovis (PDB 2OQR) that binds using this alternative active interface. The contact map in Fig. 4B shows that some of the monomeric contacts in Fig. 4A become dimeric for regx3 and are highly coupled. Additionally, another region of contacts involving residues 10–20 interacting with residues 100–110 is also captured using coevolutionary analysis (see Fig. 4B, dashed box). These two contact regions drive the formation of this alternative complex with a resolution of RMSD of 2 Å (iRMSD = 1.33 Å). Regx3 is a multidomain protein containing an effector domain. If we compute the RMSD only for the response regulator domain, as in the case of PhoB, then the best RMSD = 1.13 Å. This implies that coevolutionary signals for multiple dimeric conformations are present and can be used to characterize multiple physiologically relevant configurations. Although the dimeric state of the receiver domain is mainly observed for the activated state, some studies suggest that an inactive state can also form homodimers and some symmetric units supporting this view5052. Nonetheless, it is not known if these inactive homodimers are formed in vivo or if they have any physiological relevance. Furthermore these inactive state complexes are arranged in such a way that the aspartate residue that is phosphorylated upon activation is not accessible to the kinase making this configuration less physiologically viable. Although some of the contacts in the inactive state dimer are captured by DCA, they do not appear to be sufficient to reach the same resolutions as for the active states. Supplementary Fig. S5 shows the predicted structure for such system, which has no resemblance to the inactive state dimeric interface observed in PDB 1B00. One interpretation of this result is that our methodology is not able to capture this alternative dimer correctly. The other view is that the evolutionary signal for this dimeric inactive state is weak and therefore not functional.

Bottom Line: Therefore a systematic way to extract dimerization signals has been elusive.For the most accurate conformations of the structurally diverse dimeric complexes studied the mean and interfacial RMSDs are 1.95Å and 1.44Å, respectively.This methodology is also able to identify distinct dimerization conformations as for the case of the family of response regulators, which dimerize upon activation.

View Article: PubMed Central - PubMed

Affiliation: Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827.

ABSTRACT
We develop a procedure to characterize the association of protein structures into homodimers using coevolutionary couplings extracted from Direct Coupling Analysis (DCA) in combination with Structure Based Models (SBM). Identification of dimerization contacts using DCA is more challenging than intradomain contacts since direct couplings are mixed with monomeric contacts. Therefore a systematic way to extract dimerization signals has been elusive. We provide evidence that the prediction of homodimeric complexes is possible with high accuracy for all the cases we studied which have rich sequence information. For the most accurate conformations of the structurally diverse dimeric complexes studied the mean and interfacial RMSDs are 1.95Å and 1.44Å, respectively. This methodology is also able to identify distinct dimerization conformations as for the case of the family of response regulators, which dimerize upon activation. The identification of dimeric complexes can provide interesting molecular insights in the construction of large oligomeric complexes and be useful in the study of aggregation related diseases like Alzheimer's or Parkinson's.

No MeSH data available.


Related in: MedlinePlus