http://spudlab.stanford.edu/contact daily 0.75 2015-09-25 https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1439421816915-X9A294W8T4G0RT9VHLNS/image-asset.jpeg Contact http://spudlab.stanford.edu/key-approaches daily 0.75 2015-09-21 https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1442800659723-N8QUBQ62JWUWN4UD9DF5/image-asset.jpeg Key Approaches https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1442800669336-LU2AVJGXLI9XK3EPIRRR/image-asset.jpeg Key Approaches https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1442800647592-1XI1KF64JB77NOVFV258/image-asset.jpeg Key Approaches http://spudlab.stanford.edu/the-entire-collection-methods daily 0.75 2015-09-21 http://spudlab.stanford.edu/lab-alumni daily 0.75 2024-05-16 http://spudlab.stanford.edu/selected-historical-publications daily 0.75 2015-09-29 http://spudlab.stanford.edu/ncbsinstem-colleagues daily 0.75 2015-09-27 https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1443390098034-LN117HK6WR848EW9LV40/inStem+bldg.jpg Center for Cardiovascular Biology and Disease, inStem, Bangalore http://spudlab.stanford.edu/the-entire-collection-publications daily 0.75 2015-09-29 http://spudlab.stanford.edu/recent-publications daily 0.75 2017-05-06 http://spudlab.stanford.edu/the-entire-collection-reviews daily 0.75 2015-09-29 http://spudlab.stanford.edu/current-focus daily 0.75 2017-05-06 https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1439422615044-BVX1F807AQ738RMI0YHO/image-asset.jpeg Current Focus https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1439422592790-MB4ZM4G1T5LHW81XL8E7/image-asset.jpeg Current Focus https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1439422317075-6DJX61K3K51BCBY790A6/image-asset.jpeg Current Focus http://spudlab.stanford.edu/home-1 daily 1.0 2017-10-12 https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1492558635632-VIGGXTSI3FJQ5ARV6RM4/image-asset.jpeg Home Regulation of the number of functionally accessible cardiac myosin heads for interaction with actin https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1447444752661-J2ICCX1NE8DQ32DBWBND/image-asset.png Home https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1442805283644-IXZUVNGSSO3MWCV87UZJ/image-asset.jpeg Home http://spudlab.stanford.edu/fast-for-automatic-motility-measurements daily 0.75 2020-02-27 https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1443284548200-S61E61GMJJMIMB1XJVRL/image-asset.jpeg FAST for automatic motility measurements http://spudlab.stanford.edu/lab-related-websites daily 0.75 2017-05-06 http://spudlab.stanford.edu/current-members daily 0.75 2024-05-31 https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1494373587410-HKY5MXKJ2FL5SE7IZMY0/image-asset.jpeg Current Members https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/205ac03d-803b-47a2-ac92-281fda8659eb/Untitlxf3ed-1.jpg Current Members - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/444d2659-ab8e-4c78-900b-5aa12d78d9dc/photocache.312443.jpg Current Members - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/622f9ff8-ee3b-4360-89e7-37d04bcd5182/1653359214210.jpeg Current Members - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1494373258863-D2PDZ6ILNEPS9VW05MFR/image-asset.jpeg Current Members https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/329447af-7607-4fed-b1e4-fe39adb1264b/Untitlesdf3d-1.jpg Current Members - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/b13cb672-3d8c-42f9-be98-147be8a5cbfa/IMG_7398+2+copy.jpg Current Members - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/70949f90-0578-40a1-94dc-257fff0afb66/masataka-kawana_profilephoto.jpg Current Members - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/be7db962-2c64-4571-86b9-92112dcd01b5/Rama_Photo+%281%29.jpg Current Members - Make it stand out Whatever it is, the way you tell your story online can make all the difference. http://spudlab.stanford.edu/lab-movies daily 0.75 2017-05-06 https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1443737254210-9OJ56QLH414GF2LC7E2I/image-asset.png Lab Movies https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1442800971244-6IFDYB0KERWGYAQX0XFV/image-asset.jpeg Lab Movies https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1442801005583-FTLKJI1KNCGM62UTRFLQ/image-asset.jpeg Lab Movies https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1442801076533-03N1EUAT7H0MJV869VLI/image-asset.jpeg Lab Movies https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1442801094735-RGY0GPQVUO5DWC6JC38R/image-asset.jpeg Lab Movies https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1442801052916-8MSTGNA3OW2TUXF2MKG7/image-asset.jpeg Lab Movies http://spudlab.stanford.edu/homology-models daily 0.75 2017-06-30 https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1498858447401-MNFHC4T41ZR416XA095V/MS03_5TBY+ELCs+Jun2017.png Homology models same as above ELCs only https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1498858357800-KDNYW4ZE9CNGL0S3MD05/MS03_5TBY+RLCs+Jun2017.png Homology models Same as above RLCs only https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1498061449605-XRGKKX1WF2APO0DJBOCD/prestroke+poststroke+eval+metrics.jpeg Homology models The models were evaluated using ModEval [1] methodology. Evaluation metrics are tabulated for the two models that were developed. The TSVMod predicted Cα root-mean-square deviation (RMSD) shows the Cα-RMSD of the model from the template structure and predicted native overlap provides the fraction of Cα atoms in the model within 3.5 Å of the corresponding atoms in the template structure after rigid-body superposition [2]. zDOPE is a normalized Discrete Optimized Protein Energy (DOPE), an atomic distance-dependent statistical score. Negative values indicate better models [3]. GA341 model score is derived from residue-level statistical potential that was optimized, including distance-dependent, contact, Phi/Psi dihedral angle, and accessible surface statistical potentials. A value > 0.7 generally indicates a reliable model, defined as ≥ 95% probability of correct fold [4]. 1. Pieper U et al, ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res (2011). 2. Eramian et al, How well can the accuracy of comparative protein structure models be predicted? Protein Sci (2008). 3. Shen MY et al, Statistical potential for assessment and prediction of protein structures. Protein Sci (2006) 4. Melo F et al, Statistical potentials for fold assessment. Protein Sci (2002). https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1494023480824-5IH0GK2WFOX15N1MR1F0/image-asset.jpeg Homology models The first homology model of full-length human beta-cardiac myosin S1 was described in Spudich, J.A. (2015). The myosin mesa and a possible unifying hypothesis for the molecular basis of human hypertrophic cardiomyopathy. Biochem Soc Trans. 43:64–72. Also see, Homburger, J.R. et al. Multidimensional structure-function relationships in human β-cardiac myosin from population-scale genetic variation. Proc Natl Acad Sci USA 113, 6701–6706 (2016). Image from Adhikari, A.S., Kooiker, K.B., Sarkar, S.S., Liu, C., Bernstein, D., Spudich, J.A. and Ruppel, K.M. (2016). Early Onset HCM Mutations H251N and D239N Significantly Increase the Velocity, Force, and Actin-activated ATPase activity of human β-cardiac Myosin. Cell Rep. 17:2857-2864. https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1492612443094-LCKA2YYSRBN7Z809RT8A/image-asset.jpeg Homology models MS01C0C2 MS01C0C10 https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1494092606192-9W9KH7MH4RGEL0V013JR/Slide2.jpg Homology models MS03C0C2 MS03C0C10v3 https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1494092834574-VNUPQF0OIFWWTT6DQ3MI/image-asset.jpeg Homology models MS01C0C10 MS03C0C10v2 Ms03C0C10v3 https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1498858924417-HWVCJH13BEZORWWU0CH7/MS03_5TBY+complete+Jun2017.png Homology models MS03: HC white, ELCs brown, RLCs green 5TBY: HC black, ELCs yellow, RLCs blue https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1498858058509-1EXNXJ9FDGENJ4ERHWG8/image-asset.png Homology models MS03: yellow 5TBY: red From left to right, mesa residues Arg453, Arg249, Arg663 Note different orientations of side chains for MS03 and 5TBY https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1494024908973-BF4TYWPTWNLPAR35BKCH/PDB+MS01%3A+A+complete+folded-back+model+of+human+beta-cardiac+myosin Homology models MS01: A complete folded-back model of human beta-cardiac myosin with human cardiac light chains. The first homology model of the human beta-cardiac myosin in its folded back off-state (IHM motif) was described in Adhikari, A.S., Kooiker, K.B., Sarkar, S.S., Liu, C., Bernstein, D., Spudich, J.A. and Ruppel, K.M. (2016). Early Onset HCM Mutations H251N and D239N Significantly Increase the Velocity, Force, and Actin-activated ATPase activity of human β-cardiac Myosin. Cell Rep. 17:2857-2864. Image from Nag, S., Trivedi, D.V., Sarkar, S.S., Adhikari, A.S., Sunitha, M.S., Sutton, S., Ruppel, K.M. and Spudich, J.A. The myosin mesa and the basis of hypercontractility caused by hypertrophic cardiomyopathy mutations. Nat. Struct. Mol. Biol., Advance Online Publication. DOI: 10.1038/nsmb.3408 (2017). https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1494024625381-4TG0AZZIA888FPWHQMHI/image-asset.png Homology models MS03 showing the location of a number of Arg residues that cause HCM when mutated. https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1497558164023-DDREY887ET52K4DM9JKR/image-asset.jpeg Homology models The models were evaluated using ModEval [1] methodology. Evaluation metrics are tabulated for the three models that were developed. The TSVMod predicted Cα root-mean-square deviation (RMSD) shows the Cα-RMSD of the model from the template structure and predicted native overlap provides the fraction of Cα atoms in the model within 3.5 Å of the corresponding atoms in the template structure after rigid-body superposition [2]. zDOPE is a normalized Discrete Optimized Protein Energy (DOPE), an atomic distance-dependent statistical score. Negative values indicate better models [3]. GA341 model score is derived from residue-level statistical potential that was optimized, including distance-dependent, contact, Phi/Psi dihedral angle, and accessible surface statistical potentials. A value > 0.7 generally indicates a reliable model, defined as ≥ 95% probability of correct fold [4]. 1. Pieper U et al, ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res (2011). 2. Eramian et al, How well can the accuracy of comparative protein structure models be predicted? Protein Sci (2008). 3. Shen MY et al, Statistical potential for assessment and prediction of protein structures. Protein Sci (2006) 4. Melo F et al, Statistical potentials for fold assessment. Protein Sci (2002). https://images.squarespace-cdn.com/content/v1/55cbcdf4e4b0fe0a5d68c8fa/1498858979280-XXFYONR2MM6SOVLRZTMT/MS03_5TBY+wo+LCs+Jun2017.png Homology models Same as above without LCs