Abstract
The M1 and M17 aminopeptidases are metallo-exopeptidases that rely on the presence of divalent cations, usually zinc, in their active site for proteolytic activity. They are from separate protease superfamilies, however, members often have overlapping substrate specificity. Inhibitors of one or both enzymes can be used to modulate hypertension, reduce proliferation of certain types of cancers and control malaria parasites. Current inhibitors act to chelate the zinc ions in the active site, locking the enzymes in an inactive transition state. We were interested in using a computational approach to understand the structure and dynamics of the M1 and M17 aminopeptidases, however, the presence of the essential metal ions in the proteases presents a challenge to classical molecular dynamics (MD) simulation. The zinc amber force field does not contain applicable descriptions of the zinc coordination environment present in either of these two protease families. To provide tools for the study of these two enzymes, we have used the metal centre parameter builder to generate new hybrid bonded/nonbonded force field (FF) parameters to correctly describe the active site architecture for each enzyme. The new parameters were evaluated by fitting the normal mode frequencies of molecular mechanics to the quantum mechanics frequencies and validated by performing short MD simulations. The new FF parameters now enable more accurate and reliable MD simulations for any member of the M1 or M17 aminopeptidase superfamilies.
| Original language | English |
|---|---|
| Pages (from-to) | 2595-2604 |
| Number of pages | 10 |
| Journal | Journal of Biomolecular Structure and Dynamics |
| Volume | 36 |
| Issue number | 10 |
| DOIs | |
| Publication status | Published - 28 Aug 2017 |
Keywords
- force field parameterisation
- molecular dynamics, metallo-exopeptidases
- molecular mechanisms
- quantum mechanisms
Cite this
}
Generation of AMBER force field parameters for zinc centres of M1 and M17 family aminopeptidases. / Yang, Wei; Riley, Blake T.; Lei, Xiangyun; Porebski, Benjamin T.; Kass, Itamar; Buckle, Ashley M.; McGowan, Sheena.
In: Journal of Biomolecular Structure and Dynamics, Vol. 36, No. 10, 28.08.2017, p. 2595-2604.Research output: Contribution to journal › Article › Research › peer-review
TY - JOUR
T1 - Generation of AMBER force field parameters for zinc centres of M1 and M17 family aminopeptidases
AU - Yang, Wei
AU - Riley, Blake T.
AU - Lei, Xiangyun
AU - Porebski, Benjamin T.
AU - Kass, Itamar
AU - Buckle, Ashley M.
AU - McGowan, Sheena
PY - 2017/8/28
Y1 - 2017/8/28
N2 - The M1 and M17 aminopeptidases are metallo-exopeptidases that rely on the presence of divalent cations, usually zinc, in their active site for proteolytic activity. They are from separate protease superfamilies, however, members often have overlapping substrate specificity. Inhibitors of one or both enzymes can be used to modulate hypertension, reduce proliferation of certain types of cancers and control malaria parasites. Current inhibitors act to chelate the zinc ions in the active site, locking the enzymes in an inactive transition state. We were interested in using a computational approach to understand the structure and dynamics of the M1 and M17 aminopeptidases, however, the presence of the essential metal ions in the proteases presents a challenge to classical molecular dynamics (MD) simulation. The zinc amber force field does not contain applicable descriptions of the zinc coordination environment present in either of these two protease families. To provide tools for the study of these two enzymes, we have used the metal centre parameter builder to generate new hybrid bonded/nonbonded force field (FF) parameters to correctly describe the active site architecture for each enzyme. The new parameters were evaluated by fitting the normal mode frequencies of molecular mechanics to the quantum mechanics frequencies and validated by performing short MD simulations. The new FF parameters now enable more accurate and reliable MD simulations for any member of the M1 or M17 aminopeptidase superfamilies.
AB - The M1 and M17 aminopeptidases are metallo-exopeptidases that rely on the presence of divalent cations, usually zinc, in their active site for proteolytic activity. They are from separate protease superfamilies, however, members often have overlapping substrate specificity. Inhibitors of one or both enzymes can be used to modulate hypertension, reduce proliferation of certain types of cancers and control malaria parasites. Current inhibitors act to chelate the zinc ions in the active site, locking the enzymes in an inactive transition state. We were interested in using a computational approach to understand the structure and dynamics of the M1 and M17 aminopeptidases, however, the presence of the essential metal ions in the proteases presents a challenge to classical molecular dynamics (MD) simulation. The zinc amber force field does not contain applicable descriptions of the zinc coordination environment present in either of these two protease families. To provide tools for the study of these two enzymes, we have used the metal centre parameter builder to generate new hybrid bonded/nonbonded force field (FF) parameters to correctly describe the active site architecture for each enzyme. The new parameters were evaluated by fitting the normal mode frequencies of molecular mechanics to the quantum mechanics frequencies and validated by performing short MD simulations. The new FF parameters now enable more accurate and reliable MD simulations for any member of the M1 or M17 aminopeptidase superfamilies.
KW - force field parameterisation
KW - molecular dynamics, metallo-exopeptidases
KW - molecular mechanisms
KW - quantum mechanisms
UR - http://www.scopus.com/inward/record.url?scp=85028551643&partnerID=8YFLogxK
U2 - 10.1080/07391102.2017.1364669
DO - 10.1080/07391102.2017.1364669
M3 - Article
VL - 36
SP - 2595
EP - 2604
JO - Journal of Biomolecular Structure and Dynamics
JF - Journal of Biomolecular Structure and Dynamics
SN - 0739-1102
IS - 10
ER -