Hydration and DNA recognition by homeodomains.
A 2-nanosecond molecular dynamics (MD) simulation of an Antennapedia homeodomain-DNA complex in explicit solvent water at ambient temperature and pressure was performed to supplement experimental nuclear magnetic resonance (NMR) data on the structure and dynamics of this complex. In addition to direct protein-DNA contacts, the MD trajectory attributes an essential role for specific DNA recognition to hydration water molecules that mediate intermolecular contacts. The simulation provides a detailed description of the pathways of hydration water molecules exchanging in and out of the protein-DNA interface and indicates that the residence times of these "interior" waters are on the nanosecond time scale, near the lower end of the range determined by NMR.
Billeter
M
M
Institut für Molekularbiologie und Biophysik, Eidgenöss ische Techische Hochschule-Hönggerberg, Zürich, Switzerland.
Güntert
P
P
Luginbühl
P
P
Wüthrich
K
K
D000596:Amino Acids / Q000737:chemistry; D051943:Antennapedia Homeodomain Protein; D001483:Base Sequence; D004247:DNA / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry*; D018398:Homeodomain Proteins / Q000737:chemistry*; D006801:Humans; D007091:Image Processing, Computer-Assisted; D008875:Middle Aged; D008969:Molecular Sequence Data; D009687:Nuclear Proteins; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D013997:Time Factors; D014157:Transcription Factors / Q000737:chemistry; D014867:Water / Q000737:chemistry*
D000596:Amino Acids; D051943:Antennapedia Homeodomain Protein; D004268:DNA-Binding Proteins; D018398:Homeodomain Proteins; D009687:Nuclear Proteins; D014157:Transcription Factors; D014867:Water; D004247:DNA