Gerstein Lab Publications
Structure: Large-scale Studies of Macromolecular Motions
We were amongst the first groups to study macromolecular motions statistically, on a large-scale. In particular, we have set up a publicly accessible Database of Macromolecular Motions and coupled it with simulation tools to interpolate between structural conformations; the database also has associated tools to predict likely motions based on simple models, such as normal modes and localized hinges connecting rigid domains. These allowed us to classify motions based on the interdigitating packing at internal interfaces: motions are identified as shear or hinge, based on whether or not a well-packed interface is maintained between the dynamic elements throughout the motion. This classification scheme is motivated by the fact that protein interiors are packed exceedingly tightly and that tight packing greatly constrains a protein's mobility. We have developed tools for measuring and comparing the packing efficiency at different interfaces and locations throughout macromolecules (e.g. inter-domain, protein surface, helix-helix, protein vs. RNA) using specialized geometric constructions. For this we have generated new protein packing parameters, including self-consistent radii and standard volumes for each atom type.
D Clarke, A Sethi, S Li, S Kumar, RW Chang, J Chen, M Gerstein (2016). Structure 24: 826-37.
SC Flores, MB Gerstein (2011). BMC Bioinformatics 12: 417.
N Bhardwaj, A Abyzov, D Clarke, C Shou, MB Gerstein (2011). Protein Sci 20: 1745-54.
NR Voss, M Gerstein (2010). Nucleic Acids Res 38: W555-62.
A Abyzov, R Bjornson, M Felipe, M Gerstein (2010). Proteins 78: 309-24.
R Tonikian, X Xin, CP Toret, D Gfeller, C Landgraf, S Panni, S Paoluzi, L Castagnoli, B Currell, S Seshagiri, H Yu, B Winsor, M Vidal, MB Gerstein, GD Bader, R Volkmer, G Cesareni, DG Drubin, PM Kim, SS Sidhu, C Boone (2009). PLoS Biol 7: e1000218.
N Bhardwaj, M Gerstein (2009). Protein Sci 18: 1230-40.
KS Keating, SC Flores, MB Gerstein, LA Kuhn (2009). Protein Sci 18: 359-71.
SC Flores, KS Keating, J Painter, F Morcos, K Nguyen, EA Merritt, LA Kuhn, MB Gerstein (2008). Proteins 73: 299-319.
SC Flores, MB Gerstein (2007). BMC Bioinformatics 8: 215.
SC Flores, LJ Lu, J Yang, N Carriero, MB Gerstein (2007). BMC Bioinformatics 8: 167.
S Flores, N Echols, D Milburn, B Hespenheide, K Keating, J Lu, S Wells, EZ Yu, M Thorpe, M Gerstein (2006). Nucleic Acids Res 34: D296-301.
V Alexandrov, U Lehnert, N Echols, D Milburn, D Engelman, M Gerstein (2005). Protein Sci 14: 633-43.
CS Goh, D Milburn, M Gerstein (2004). Curr Opin Struct Biol 14: 104-9.
M Gerstein, N Echols (2004). Curr Opin Chem Biol 8: 14-9.
V Alexandrov, M Gerstein (2004). BMC Bioinformatics 5: 2.
WG Krebs, J Tsai, V Alexandrov, J Junker, R Jansen, M Gerstein (2003). Methods Enzymol 374: 544-84.
N Echols, D Milburn, M Gerstein (2003). Nucleic Acids Res 31: 478-82.
WG Krebs, V Alexandrov, CA Wilson, N Echols, H Yu, M Gerstein (2002). Proteins 48: 682-95.
WG Krebs, M Gerstein (2000). Nucleic Acids Res 28: 1665-75.
M Gerstein, C Chothia (1999). Science 285: 1682-3.
M Gerstein, W Krebs (1998). Nucleic Acids Res 26: 4280-90.
M Gerstein, AM Lesk, C Chothia (1994). Biochemistry 33: 6739-49.
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