title: Molecular Modeling of Fluorescent SERCA Biosensors.
abstract: Molecular modeling and simulation are useful tools in structural biology, allowing the formulation of functional hypotheses and interpretation of spectroscopy experiments. Here, we describe a method to construct in silico models of a fluorescent fusion protein construct, where a cyan fluorescent protein (CFP) is linked to the actuator domain of the Sarco/Endoplasmic Reticulum Ca(2+)-ATPase (SERCA). This CFP-SERCA construct is a biosensor that can report on structural dynamics in the cytosolic headpiece of SERCA. Molecular modeling and FRET experiments allow us to generate new structural and mechanistic models that better describe the conformational landscape and regulation of SERCA. The methods described here can be applied to the creation of models for any fusion protein constructs and also describe the steps needed to simulate FRET results using molecular models.
authors.affiliation: Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St., Minneapolis, MN, 55455, USA. svens005@umn.edu.
authors.forename: Bengt
authors.initials: B
authors.lastname: Svensson
authors.affiliation: Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St., Minneapolis, MN, 55455, USA.
authors.forename: Joseph M
authors.initials: JM
authors.lastname: Autry
authors.affiliation: Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St., Minneapolis, MN, 55455, USA.
authors.forename: David D
authors.initials: DD
authors.lastname: Thomas
mesh_terms: D000595:Amino Acid Sequence; D004353:Drug Evaluation, Preclinical; D020536:Enzyme Activators / Q000494:pharmacology; D004791:Enzyme Inhibitors / Q000494:pharmacology; D005456:Fluorescent Dyes / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011993:Recombinant Fusion Proteins / Q000737:chemistry / Q000378:metabolism; D053498:Sarcoplasmic Reticulum Calcium-Transporting ATPases / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism*; D016415:Sequence Alignment
chemical_list: D020536:Enzyme Activators; D004791:Enzyme Inhibitors; D005456:Fluorescent Dyes; D011993:Recombinant Fusion Proteins; D053498:Sarcoplasmic Reticulum Calcium-Transporting ATPases
keywords: Biosensor; Fluorescence resonance energy transfer; Fluorescent protein s; Molecular modeling; SERCA