Trans-cis isomerization of proline 22 in bovine prothrombin fragment 1: a surprising result of structural characterization.
The calcium ion-mediated interaction of bovine prothrombin (BF1) with negatively charged phospholipid membranes is assumed to be largely via the Gla domain of BF1 with the fold of the Gla domain essential for binding. It has been reported that Pro22 undergoes classical trans to cis isomerization in the presence of calcium ions with the cis conformation of Pro22 of BF1 responsible for membrane binding [Evans, T. C., Jr., and Nelsestuen, G. L. (1996) Biochemistry 35, 8210-8215]. However, Pro22 was found to be in the trans conformation in the crystal structure of BF1. In the present work, we have used molecular dynamics simulations to investigate the relative importance of the two conformations of Pro22 to the structural and dynamical properties of BF1. The initial trans conformation of Pro22 in BF1 was slowly converted to cis-Pro22 using constrained dynamics. The second-generation AMBER force field in conjunction with the particle mesh Ewald method to accommodate long-range interaction was employed in the trajectory calculations. Comparison of the BF1(trans-Pro22) and BF1(cis-Pro22) equilibrated structures reveals surprisingly that the overall structural changes associated with the trans-cis isomerization is minimal and only minor modifications to the hydrogen bond network and the network of N-terminus Ala1 take place. The calculated electrostatic potential energy surfaces of the two protein structures also appear to be very similar, indicating the near equality of the local interaction site environments in the protein prior to lipid binding.
Perera
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Department of Chemistry, University of North Carolina, Chapel Hill 27599-3290, USA.
Darden
T A
TA
Pedersen
L G
LG
D015055:1-Carboxyglutamic Acid / Q000737:chemistry; D000409:Alanine / Q000737:chemistry; D000595:Amino Acid Sequence; D000818:Animals; D002118:Calcium / Q000737:chemistry; D002417:Cattle; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry* / Q000378:metabolism; D010743:Phospholipids / Q000378:metabolism; D011392:Proline / Q000737:chemistry*; D011485:Protein Binding; D011498:Protein Precursors / Q000737:chemistry* / Q000378:metabolism; D017434:Protein Structure, Tertiary; D011516:Prothrombin / Q000737:chemistry* / Q000378:metabolism; D013237:Stereoisomerism; D013816:Thermodynamics
D010446:Peptide Fragments; D010743:Phospholipids; D011498:Protein Precursors; D015055:1-Carboxyglutamic Acid; C029733:prothrombin fragment 1; D011516:Prothrombin; D011392:Proline; D000409:Alanine; D002118:Calcium