Understanding VPAC receptor family peptide binding and selectivity

Sarah J. Piper; Giuseppe Deganutti; Jessica Lu; Peishen Zhao; Yi Lynn Liang; Yao Lu; Madeleine M. Fletcher; Mohammed Akhter Hossain; Arthur Christopoulos; Christopher A. Reynolds; Radostin Danev; Patrick M. Sexton; Denise Wootten

doi:10.1038/s41467-022-34629-3

Understanding VPAC receptor family peptide binding and selectivity

Sarah J. Piper, Giuseppe Deganutti, Jessica Lu, Peishen Zhao, Yi Lynn Liang, Yao Lu, Madeleine M. Fletcher, Mohammed Akhter Hossain, Arthur Christopoulos, Christopher A. Reynolds, Radostin Danev, Patrick M. Sexton, Denise Wootten

Drug Discovery Biology

Research output: Contribution to journal › Article › Research › peer-review

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Abstract

The vasoactive intestinal peptide (VIP) and pituitary adenylate cyclase-activating polypeptide (PACAP) receptors are key regulators of neurological processes. Despite recent structural data, a comprehensive understanding of peptide binding and selectivity among different subfamily receptors is lacking. Here, we determine structures of active, Gs-coupled, VIP-VPAC1R, PACAP27-VPAC1R, and PACAP27-PAC1R complexes. Cryo-EM structural analyses and molecular dynamics simulations (MDSs) reveal fewer stable interactions between VPAC1R and VIP than for PACAP27, more extensive dynamics of VIP interaction with extracellular loop 3, and receptor-dependent differences in interactions of conserved N-terminal peptide residues with the receptor core. MD of VIP modelled into PAC1R predicts more transient VIP-PAC1R interactions in the receptor core, compared to VIP-VPAC1R, which may underlie the selectivity of VIP for VPAC1R over PAC1R. Collectively, our work improves molecular understanding of peptide engagement with the PAC1R and VPAC1R that may benefit the development of novel selective agonists.

Original language	English
Article number	7013
Number of pages	20
Journal	Nature Communications
Volume	13
Issue number	1
DOIs	https://doi.org/10.1038/s41467-022-34629-3
Publication status	Published - Dec 2022

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10.1038/s41467-022-34629-3Licence: CC BY

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@article{d4dc2ad886d349ebaea92bdb3143c543,

title = "Understanding VPAC receptor family peptide binding and selectivity",

abstract = "The vasoactive intestinal peptide (VIP) and pituitary adenylate cyclase-activating polypeptide (PACAP) receptors are key regulators of neurological processes. Despite recent structural data, a comprehensive understanding of peptide binding and selectivity among different subfamily receptors is lacking. Here, we determine structures of active, Gs-coupled, VIP-VPAC1R, PACAP27-VPAC1R, and PACAP27-PAC1R complexes. Cryo-EM structural analyses and molecular dynamics simulations (MDSs) reveal fewer stable interactions between VPAC1R and VIP than for PACAP27, more extensive dynamics of VIP interaction with extracellular loop 3, and receptor-dependent differences in interactions of conserved N-terminal peptide residues with the receptor core. MD of VIP modelled into PAC1R predicts more transient VIP-PAC1R interactions in the receptor core, compared to VIP-VPAC1R, which may underlie the selectivity of VIP for VPAC1R over PAC1R. Collectively, our work improves molecular understanding of peptide engagement with the PAC1R and VPAC1R that may benefit the development of novel selective agonists.",

author = "Piper, {Sarah J.} and Giuseppe Deganutti and Jessica Lu and Peishen Zhao and Liang, {Yi Lynn} and Yao Lu and Fletcher, {Madeleine M.} and Hossain, {Mohammed Akhter} and Arthur Christopoulos and Reynolds, {Christopher A.} and Radostin Danev and Sexton, {Patrick M.} and Denise Wootten",

note = "Funding Information: This work was supported by the National Health and Medical Research Council of Australia (NHMRC) (program grant 1150083, P.M.S./A.C.; Senior Research Fellowship 1155302, D.W.; Senior Principal Research Fellowship 1154434, P.M.S.). R.D. was supported by Takeda Science Foundation 2019 Medical Research Grant and Japan Science and Technology Agency PRESTO (18069571). C.A.R is grateful for a Royal Society Industry Fellowship. This work was supported by the Monash University Ramaciotti Centre for cryo-electron microscopy (negative staining TEM) and the Monash University MASSIVE high-performance computing facility (cryo-EM data processing). The authors would like to thank Yan Zhang, H. Eric Xu and Yi Jiang for providing access to their structural data for VPAC1R prior to publication, George Christopoulos and Villy Julita for generating the expression constructs and alanine mutants of the PAC1R and VPAC1R, as well as Rachel M. Johnson and Matthew J. Belousoff for assisting with map and model refinements and validation. Funding Information: Interactions between chains were analyzed using the “Dimplot” module within the Ligplot+ program (v2.2) (, Supplementary Fig. ). Hydrogen bonds were also assessed using the UCSF ChimeraX package, with relaxed distance and angle criteria (0.4 {\AA} and 20-degree tolerance, respectively; Table , Fig. , Supplementary Figs. , ). Visualization of structures and production of images was performed using the UCSF Chimera package (v1.14) from the Computer Graphics Laboratory, University of California, San Francisco (supported by NIH P41 RR-01081) and ChimeraX (support from National Institutes of Health R01-GM129325). For comparison of complex structures, unless otherwise stated, complexes were aligned by receptor chains using the matchmaker command in Chimera/ChimeraX. Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = dec,

doi = "10.1038/s41467-022-34629-3",

language = "English",

volume = "13",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Publishing Group",

number = "1",

}

TY - JOUR

T1 - Understanding VPAC receptor family peptide binding and selectivity

AU - Piper, Sarah J.

AU - Deganutti, Giuseppe

AU - Lu, Jessica

AU - Zhao, Peishen

AU - Liang, Yi Lynn

AU - Lu, Yao

AU - Fletcher, Madeleine M.

AU - Hossain, Mohammed Akhter

AU - Christopoulos, Arthur

AU - Reynolds, Christopher A.

AU - Danev, Radostin

AU - Sexton, Patrick M.

AU - Wootten, Denise

N1 - Funding Information: This work was supported by the National Health and Medical Research Council of Australia (NHMRC) (program grant 1150083, P.M.S./A.C.; Senior Research Fellowship 1155302, D.W.; Senior Principal Research Fellowship 1154434, P.M.S.). R.D. was supported by Takeda Science Foundation 2019 Medical Research Grant and Japan Science and Technology Agency PRESTO (18069571). C.A.R is grateful for a Royal Society Industry Fellowship. This work was supported by the Monash University Ramaciotti Centre for cryo-electron microscopy (negative staining TEM) and the Monash University MASSIVE high-performance computing facility (cryo-EM data processing). The authors would like to thank Yan Zhang, H. Eric Xu and Yi Jiang for providing access to their structural data for VPAC1R prior to publication, George Christopoulos and Villy Julita for generating the expression constructs and alanine mutants of the PAC1R and VPAC1R, as well as Rachel M. Johnson and Matthew J. Belousoff for assisting with map and model refinements and validation. Funding Information: Interactions between chains were analyzed using the “Dimplot” module within the Ligplot+ program (v2.2) (, Supplementary Fig. ). Hydrogen bonds were also assessed using the UCSF ChimeraX package, with relaxed distance and angle criteria (0.4 Å and 20-degree tolerance, respectively; Table , Fig. , Supplementary Figs. , ). Visualization of structures and production of images was performed using the UCSF Chimera package (v1.14) from the Computer Graphics Laboratory, University of California, San Francisco (supported by NIH P41 RR-01081) and ChimeraX (support from National Institutes of Health R01-GM129325). For comparison of complex structures, unless otherwise stated, complexes were aligned by receptor chains using the matchmaker command in Chimera/ChimeraX. Publisher Copyright: © 2022, The Author(s).

PY - 2022/12

Y1 - 2022/12

N2 - The vasoactive intestinal peptide (VIP) and pituitary adenylate cyclase-activating polypeptide (PACAP) receptors are key regulators of neurological processes. Despite recent structural data, a comprehensive understanding of peptide binding and selectivity among different subfamily receptors is lacking. Here, we determine structures of active, Gs-coupled, VIP-VPAC1R, PACAP27-VPAC1R, and PACAP27-PAC1R complexes. Cryo-EM structural analyses and molecular dynamics simulations (MDSs) reveal fewer stable interactions between VPAC1R and VIP than for PACAP27, more extensive dynamics of VIP interaction with extracellular loop 3, and receptor-dependent differences in interactions of conserved N-terminal peptide residues with the receptor core. MD of VIP modelled into PAC1R predicts more transient VIP-PAC1R interactions in the receptor core, compared to VIP-VPAC1R, which may underlie the selectivity of VIP for VPAC1R over PAC1R. Collectively, our work improves molecular understanding of peptide engagement with the PAC1R and VPAC1R that may benefit the development of novel selective agonists.

AB - The vasoactive intestinal peptide (VIP) and pituitary adenylate cyclase-activating polypeptide (PACAP) receptors are key regulators of neurological processes. Despite recent structural data, a comprehensive understanding of peptide binding and selectivity among different subfamily receptors is lacking. Here, we determine structures of active, Gs-coupled, VIP-VPAC1R, PACAP27-VPAC1R, and PACAP27-PAC1R complexes. Cryo-EM structural analyses and molecular dynamics simulations (MDSs) reveal fewer stable interactions between VPAC1R and VIP than for PACAP27, more extensive dynamics of VIP interaction with extracellular loop 3, and receptor-dependent differences in interactions of conserved N-terminal peptide residues with the receptor core. MD of VIP modelled into PAC1R predicts more transient VIP-PAC1R interactions in the receptor core, compared to VIP-VPAC1R, which may underlie the selectivity of VIP for VPAC1R over PAC1R. Collectively, our work improves molecular understanding of peptide engagement with the PAC1R and VPAC1R that may benefit the development of novel selective agonists.

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U2 - 10.1038/s41467-022-34629-3

DO - 10.1038/s41467-022-34629-3

M3 - Article

C2 - 36385145

AN - SCOPUS:85142194508

SN - 2041-1723

VL - 13

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 7013

ER -

Understanding VPAC receptor family peptide binding and selectivity

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ARC Industrial Transformation Training Centre for Cryo-Electron Microscopy of Membrane Proteins for Drug Discovery

NHMRC Research Fellowship

Novel targeting of the glucagon family of G protein coupled receptors

MASSIVE

Ramaciotti Centre for Cryo-Electron Microscopy

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Understanding VPAC receptor family peptide binding and selectivity

Abstract

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Projects

ARC Industrial Transformation Training Centre for Cryo-Electron Microscopy of Membrane Proteins for Drug Discovery

NHMRC Research Fellowship

Novel targeting of the glucagon family of G protein coupled receptors

Equipment

MASSIVE

Ramaciotti Centre for Cryo-Electron Microscopy

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