Silva JR, Pan H, Wu D, Nekouzadeh A, Decker KF, Cui J, Baker NA, Sept D, Rudy Y. A multiscale model linking ion-channel molecular dynamics and electrostatics to the cardiac action potential. Proc Natl Acad Sci USA, 106, 11102-6, 2009.
Ion-channel function is determined by its gating movement. Yet, molecular dynamics and electrophysiological simulations were never combined to link molecular structure to function. We performed multiscale molecular dynamics and continuum electrostatics calculations to simulate a cardiac K+ channel (IKs) gating and its alteration by mutations that cause arrhythmias and sudden death. An all-atom model of the IKs α-subunit KCNQ1, based on the recent Kv1.2 structure, is used to calculate electrostatic energies during gating. Simulations are compared with experiments where varying degrees of positive charge—added via point mutation—progressively reduce current. Whole-cell simulations show that mutations cause action potential and ECG QT interval prolongation, consistent with clinical phenotypes. This framework allows integration of multiscale observations to study the molecular basis of excitation and its alteration by disease.
Wong CJ, Rice RL, Baker NA, Ju T, Lohman TM. Probing 3′-ssDNA loop formation in E. coli RecBCD/RecBC-DNA complexes using non-natural DNA: a model for “Chi” recognition complexes. J Mol Biol, 362, 26-43, 2006.
The equilibrium binding of E. coli RecBC and RecBCD helicases to duplex DNA ends containing varying lengths of polyethylene glycol (PEG) spacers within pre-formed 3′-single-stranded (ss) DNA ((dT)_n) tails were studied. These studies were designed to test a previous proposal that the 3′-(dT)_n tail can be looped out upon binding RecBC and RecBCD for 3′-ssDNA tails with n \geq 6 nucleotides. Equilibrium binding of protein to unlabeled DNA substrates with ends containing PEG-substituted 3′-ssDNA tails was examined by competition with a Cy3-labeled reference DNA which undergoes a Cy3 fluorescence enhancement upon protein binding. We find that the binding affinities of both RecBC and RecBCD for a DNA end are unaffected upon substituting PEG for the ssDNA between the sixth and the final two nucleotides of the 3′-(dT)_n tail. However, placing PEG at the end of the 3′-(dT)_n tail increases the binding affinities to their maximum values (i.e. the same as binding constants for RecBC or RecBCD to a DNA end with only a 3′-(dT)_6 tail). Equilibrium binding studies of a RecBC mutant containing a nuclease domain deletion, RecB^{\Delta nuc}C^1 suggest that looping of the 3′-tail (when n \geq 6 nucleotides) occurs even in the absence of the RecB nuclease domain, the nuclease domain stabilizes such loop formation. Computer modeling of the RecBCD-DNA complexes suggests that the loop in the 3′-ssDNA tail may form at the RecB/RecC interface. Based on these results we suggest a model for how a loop in the 3′-ssDNA tail might form upon encounter of a “Chi” recognition sequence during unwinding of DNA by the RecBCD helicase.
Dolinsky TJ, Karplus K, Burgers PMJ, Baker NA. SPrCY: comparison of structural predictions in the S. cerevisiae genome. Bioinformatics, 20, 2312-4, 2004.
SPrCY is a web-accessible database which provides comparison of structure prediction results for the Saccharomyces cerevisiae genome. This web service offers the ability to search, analyze and compare the yeast structural predictions from sequence-only (Superfamily, PDBAA BLAST and Pfam) and sequence-structure-based (SAM-T02, 3D-PSSM, mGenTHREADER) methods.
Silva JR, Pan H, Wu D, Nekouzadeh A, Decker KF, Cui J, Baker NA, Sept D, Rudy Y. A multiscale model linking ion-channel molecular dynamics and electrostatics to the cardiac action potential. Proc Natl Acad Sci USA, 106, 11102-6, 2009.
