TY - JOUR
T1 - Conformational stability of the bacterial adhesin, FimH, with an inactivating mutation
AU - Liu, Jenny
AU - Amaral, Luis A.Nunes
AU - Keten, Sinan
N1 - Funding Information:
We are extremely grateful to Kerim Dansuk for his helpful discussions and to Martha Dunbar for her help with the MD simulations. Jenny Liu thanks the Paul and Daisy Soros Fellowship, the Achievement Rewards for College Scientists (ARCS) Illinois chapter, the Northwestern Quest High Performance Computing Cluster, and the National Institute of General Medical Sciences T32GM008152. This project was also supported by the Office of Naval Research N00014163175 and N000141512701 (Sinan Keten), as well as by the National Science Foundation 1764421‐01 and the Simons Foundation 597491‐01 (Luis Amaral).
PY - 2020
Y1 - 2020
N2 - Allostery governing two conformational states is one of the proposed mechanisms for catch-bond behavior in adhesive proteins. In FimH, a catch-bond protein expressed by pathogenic bacteria, separation of two domains disrupts inhibition by the pilin domain. Thus, tensile force can induce a conformational change in the lectin domain, from an inactive state to an active state with high affinity. To better understand allosteric inhibition in two-domain FimH (H2 inactive), we use molecular dynamics simulations to study the lectin domain alone, which has high affinity (HL active), and also the lectin domain stabilized in the low-affinity conformation by an Arg-60-Pro mutation (HL mutant). Because ligand-binding induces an allostery-like conformational change in HL mutant, this more experimentally tractable version has been proposed as a “minimal model” for FimH. We find that HL mutant has larger backbone fluctuations than both H2 inactive and HL active, at the binding pocket and allosteric interdomain region. We use an internal coordinate system of dihedral angles to identify protein regions with differences in backbone and side chain dynamics beyond the putative allosteric pathway sites. By characterizing HL mutant dynamics for the first time, we provide additional insight into the transmission of allosteric information across the lectin domain and build upon structural and thermodynamic data in the literature to further support the use of HL mutant as a “minimal model.” Understanding how to alter protein dynamics to prevent the allosteric conformational change may guide drug development to prevent infection by blocking FimH adhesion.
AB - Allostery governing two conformational states is one of the proposed mechanisms for catch-bond behavior in adhesive proteins. In FimH, a catch-bond protein expressed by pathogenic bacteria, separation of two domains disrupts inhibition by the pilin domain. Thus, tensile force can induce a conformational change in the lectin domain, from an inactive state to an active state with high affinity. To better understand allosteric inhibition in two-domain FimH (H2 inactive), we use molecular dynamics simulations to study the lectin domain alone, which has high affinity (HL active), and also the lectin domain stabilized in the low-affinity conformation by an Arg-60-Pro mutation (HL mutant). Because ligand-binding induces an allostery-like conformational change in HL mutant, this more experimentally tractable version has been proposed as a “minimal model” for FimH. We find that HL mutant has larger backbone fluctuations than both H2 inactive and HL active, at the binding pocket and allosteric interdomain region. We use an internal coordinate system of dihedral angles to identify protein regions with differences in backbone and side chain dynamics beyond the putative allosteric pathway sites. By characterizing HL mutant dynamics for the first time, we provide additional insight into the transmission of allosteric information across the lectin domain and build upon structural and thermodynamic data in the literature to further support the use of HL mutant as a “minimal model.” Understanding how to alter protein dynamics to prevent the allosteric conformational change may guide drug development to prevent infection by blocking FimH adhesion.
KW - Escherichia coli
KW - adhesins
KW - allosteric regulation
KW - infections
KW - molecular dynamics simulation
KW - protein conformation
KW - protein domains
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U2 - 10.1002/prot.26013
DO - 10.1002/prot.26013
M3 - Article
C2 - 32989832
AN - SCOPUS:85094137914
JO - Proteins: Structure, Function and Genetics
JF - Proteins: Structure, Function and Genetics
SN - 0887-3585
ER -