The following list are results that have been calculated and made publicly available to everyone to view. Currently, these results are from projects with the Centre for Molecular Simulation at the University of Calgary, but we welcome the interst of others who may want to share their results here. We will happily host your data free of charge. To keep this list curated and of value to others, the data has to have undergone prior peer review before we make it available here.
Please note that for some proteins, during system setup, residues have been renumbered, meaning the residue ID present here will not correspond to what you find in the input PDB. We'll fix and update this very soon.
| Title | Protein | Lipids | Description | Resolution | Authors | DOI | Contact |
|---|---|---|---|---|---|---|---|
|
GIRK - lipid interactions |
GIRK | CHOL, PE, PS lipids | Interaction of GIRK with the surrounding lipid environment. Data are unpublished and will be deleted soon. They are here to highlight the use of ProLint webserver to analyze systems containing 1 protein copy in a trinary lipid mixture. |
CG (martini 2.2) | Corradi et al. | Unpublished Sample Data - shown here only as an example. | tieleman@ucalgary.ca |
|
Serotonin Receptor - Lipid Interactions |
Serotonin (5HT1B) | PC, CHOL, DAG, GM, PIP ... + 7 other lipids. | Lipid interactions with the Serotonin Receptor. A complex bilayer composition of more than 60 lipid species is used to study interactions with 4 copies of the receptor embedded in the membrane. |
CG (martini 2.2) | Sejdiu & Tieleman, Biophys. J., 2020 | https://doi.org/10.1016/j.bpj.2020.03.008 | tieleman@ucalgary.ca |
|
SMO - Lipid Interactions |
Smoothened | POPX, DOPC, PIPX, PEPC, PAPC ... + 60 other lipids. | Smoothened interactions with their surrounding lipid environment. Every lipid (60+) is displayed and calculated individually and each one can be visualized separately. |
CG (martini 2.2) | Sejdiu & Tieleman, Biophys. J., 2020 | https://doi.org/10.1016/j.bpj.2020.03.008 | tieleman@ucalgary.ca |
|
SMO - Lipid Interactions |
Smoothened | CHOL, PC, PE, PIP, PI ... + 7 other lipids. | Smoothened interactions with their surrounding lipid environment. Lipids are grouped according to their headgroup type, instead of showing each one individually. |
CG (martini 2.2) | Sejdiu & Tieleman, Biophys. J., 2020 | https://doi.org/10.1016/j.bpj.2020.03.008 | tieleman@ucalgary.ca |
|
SMO - Lipid Interactions: excluding GM lipids |
Smoothened | POPX, DOPC, PIPX, PEPC, PAPC ... + 43 other lipids. | Smoothened interactions with their surrounding lipid environment. Lipids are grouped according to their headgroup type, instead of showing each one individually. Additionally, GM lipids, which are sticky in martini model, have been excluded from the analysis. |
CG (martini 2.2) | Sejdiu & Tieleman, Biophys. J., 2020 | https://doi.org/10.1016/j.bpj.2020.03.008 | tieleman@ucalgary.ca |
|
COX1 - Lipid Interactions |
COX-1 | CHL1, POPC lipids | Interactions of cyclooxygenase 1 (COX1) with POPC and cholesterol from a 400 ns MD trajectory. COX1 is a homodimer and for this calculation, they have been grouped so that the results are averages over the individual chains. |
AT (charmm36) | Sejdiu & Tieleman, bioRxiv, 2020 | https://doi.org/10.1101/2020.05.21.109363 | tieleman@ucalgary.ca |
|
Rhodopsin Inactive State - Lipid Interactions |
Rhodopsin (inactive) | PC, CHOL, DAG, GM, PIP ... + 7 other lipids. | Lipid interactions with the Rhodopsin Receptor in its inactive state. A complex bilayer composition of more than 60 lipid species is used to study interactions with 4 copies of the receptor embedded in the membrane. |
CG (martini 2.2) | Sejdiu & Tieleman, Biophys. J., 2020 | https://doi.org/10.1016/j.bpj.2020.03.008 | tieleman@ucalgary.ca |
|
Rhodopsin Active State - Lipid Interactions |
Rhodopsin (active) | PC, CHOL, DAG, GM, PIP ... + 7 other lipids. | Lipid interactions with the Rhodopsin Receptor in its active state. |
CG (martini 2.2) | Sejdiu & Tieleman, Biophys. J., 2020 | https://doi.org/10.1016/j.bpj.2020.03.008 | tieleman@ucalgary.ca |
|
Metabotropic glutamate receptor 5 - lipid interactions |
mGlu5 | PC, CHOL, DAG, GM, PIP ... + 7 other lipids. | mGlu5 interactions with their surrounding lipid environment. Lipids are grouped according to their headgroup type. |
CG (martini 2.2) | Sejdiu & Tieleman, Biophys. J., 2020 | https://doi.org/10.1016/j.bpj.2020.03.008 | tieleman@ucalgary.ca |
|
Chemokine Receptor - Lipid Interactions |
CXCR1 (2LNL) | PC, CHOL, DAG, GM, PIP ... + 7 other lipids. | CXCR1 interactions with their surrounding lipid environment. Lipids are grouped according to their headgroup type. Proteins have not been grouped. |
CG (martini 2.2) | Sejdiu & Tieleman, Biophys. J., 2020 | https://doi.org/10.1016/j.bpj.2020.03.008 | tieleman@ucalgary.ca |
|
Adenosine A2A Receptor - Lipid Interactions |
A2AR inactive state | PC, CHOL, DAG, GM, PIP ... + 7 other lipids. | Inactive state A2AR interactions with their surrounding lipid environment. Lipids are grouped according to their headgroup type. Proteins have not been grouped. |
CG (martini 2.2) | Sejdiu & Tieleman, Biophys. J., 2020 | https://doi.org/10.1016/j.bpj.2020.03.008 | tieleman@ucalgary.ca |
|
Adenosine A2A Receptor - Lipid Interactions |
A2AR active state | PC, CHOL, DAG, GM, PIP ... + 7 other lipids. | Active state A2AR interactions with their surrounding lipid environment. Lipids are grouped according to their headgroup type. Proteins have not been grouped. |
CG (martini 2.2) | Sejdiu & Tieleman, Biophys. J., 2020 | https://doi.org/10.1016/j.bpj.2020.03.008 | tieleman@ucalgary.ca |
|
beta2 Adrenergic Receptor - Lipid Interactions |
beta2AR inactive state | PC, CHOL, DAG, GM, PIP ... + 7 other lipids. | Inctive state b2AR interactions with their surrounding lipid environment. Lipids are grouped according to their headgroup type. Proteins have not been grouped. |
CG (martini 2.2) | Sejdiu & Tieleman, Biophys. J., 2020 | https://doi.org/10.1016/j.bpj.2020.03.008 | tieleman@ucalgary.ca |
|
beta2 Adrenergic Receptor - Lipid Interactions |
beta2AR active state | PC, CHOL, DAG, GM, PIP ... + 7 other lipids. | Active state b2AR interactions with their surrounding lipid environment. Lipids are grouped according to their headgroup type. Proteins have not been grouped. |
CG (martini 2.2) | Sejdiu & Tieleman, Biophys. J., 2020 | https://doi.org/10.1016/j.bpj.2020.03.008 | tieleman@ucalgary.ca |
|
mu Opioid Receptor - Lipid Interactions |
muOR inactive state | PC, CHOL, DAG, GM, PIP ... + 7 other lipids. | Inactive state muOR interactions with their surrounding lipid environment. Lipids are grouped according to their headgroup type. Proteins have not been grouped. |
CG (martini 2.2) | Sejdiu & Tieleman, Biophys. J., 2020 | https://doi.org/10.1016/j.bpj.2020.03.008 | tieleman@ucalgary.ca |
|
mu Opioid Receptor - Lipid Interactions |
muOR active state | PC, CHOL, DAG, GM, PIP ... + 7 other lipids. | Active state muOR interactions with their surrounding lipid environment. Lipids are grouped according to their headgroup type. Proteins have not been grouped. |
CG (martini 2.2) | Sejdiu & Tieleman, Biophys. J., 2020 | https://doi.org/10.1016/j.bpj.2020.03.008 | tieleman@ucalgary.ca |
|
AE1(OF-OF) |
SLC4 | CHOL, PC, PE, PIP, PS ... + 1 other lipids. | TBA |
CG (martini 2.2) | Zhekova et al. (TBA) | TBA | tieleman@ucalgary.ca |
|
NBCe1 |
SLC4 | CHOL, PC, PE, PIP, PS ... + 1 other lipids. | TBA |
CG (martini 2.2) | Zhekova et al. (TBA) | TBA | tieleman@ucalgary.ca |
|
NDCBE |
SLC4 | CHOL, PC, PE, PIP, PS ... + 1 other lipids. | TBA |
CG (martini 2.2) | Zhekova et al. (TBA) | TBA | tieleman@ucalgary.ca |
|
AE1(IF-IF) |
SLC4 | CHOL, PC, PE, PIP, PS ... + 1 other lipids. | TBA |
CG (martini 2.2) | Zhekova et al. (TBA) | TBA | tieleman@ucalgary.ca |