Matthew L Baker

Summary

Affiliation: Baylor College of Medicine
Country: USA

Publications

  1. doi request reprint Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps
    Matthew L Baker
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA
    Biopolymers 97:655-68. 2012
  2. pmc Modeling protein structure at near atomic resolutions with Gorgon
    Matthew L Baker
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    J Struct Biol 174:360-73. 2011
  3. ncbi request reprint Automated segmentation of molecular subunits in electron cryomicroscopy density maps
    Matthew L Baker
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    J Struct Biol 156:432-41. 2006
  4. pmc Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus
    Dong Hua Chen
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 108:1355-60. 2011
  5. ncbi request reprint Architecture of the herpes simplex virus major capsid protein derived from structural bioinformatics
    Matthew L Baker
    National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA
    J Mol Biol 331:447-56. 2003
  6. pmc Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling
    Matthew L Baker
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 110:12301-6. 2013
  7. pmc Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel
    Irina I Serysheva
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 105:9610-5. 2008
  8. pmc Constructing and validating initial Cα models from subnanometer resolution density maps with pathwalking
    Mariah R Baker
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Structure 20:450-63. 2012
  9. pmc 4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus
    Rui Zhang
    Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, USA
    EMBO J 30:3854-63. 2011
  10. pmc Cryo-EM of macromolecular assemblies at near-atomic resolution
    Matthew L Baker
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
    Nat Protoc 5:1697-708. 2010

Collaborators

Detail Information

Publications34

  1. doi request reprint Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps
    Matthew L Baker
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA
    Biopolymers 97:655-68. 2012
    ..In the end, the utilities that we present here offer users a robust toolkit for analyzing and modeling protein structure in macromolecular assemblies at non-atomic resolutions...
  2. pmc Modeling protein structure at near atomic resolutions with Gorgon
    Matthew L Baker
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    J Struct Biol 174:360-73. 2011
    ..Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure...
  3. ncbi request reprint Automated segmentation of molecular subunits in electron cryomicroscopy density maps
    Matthew L Baker
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    J Struct Biol 156:432-41. 2006
    ..As such, automated segmentation could become a useful tool for the analysis of the ever-increasing number of structures of macromolecular machines derived from cryoEM...
  4. pmc Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus
    Dong Hua Chen
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 108:1355-60. 2011
    ....
  5. ncbi request reprint Architecture of the herpes simplex virus major capsid protein derived from structural bioinformatics
    Matthew L Baker
    National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA
    J Mol Biol 331:447-56. 2003
    ..The combined structural and sequence-based informatics has led to an architectural model of VP5. This model placed in the context of the capsid provides insights into the strategies used to achieve viral capsid stability...
  6. pmc Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling
    Matthew L Baker
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 110:12301-6. 2013
    ..The presence of the canonical phage and jellyroll viral protein folds, gp7 and gp10, respectively, in the same virus suggests that epsilon15 may have emerged more recently relative to other bacteriophages. ..
  7. pmc Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel
    Irina I Serysheva
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 105:9610-5. 2008
    ..Taken together, these results provide a structural context for both channel gating and the consequences of certain malignant hyperthermia and central core disease-associated mutations in RyR1...
  8. pmc Constructing and validating initial Cα models from subnanometer resolution density maps with pathwalking
    Mariah R Baker
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Structure 20:450-63. 2012
    ..With the growing number of near-atomic resolution density maps from cryo-EM and X-ray crystallography, pathwalking can become an important tool in modeling protein structures...
  9. pmc 4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus
    Rui Zhang
    Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, USA
    EMBO J 30:3854-63. 2011
    ..Our structural results suggest a mechanism for the initial stage of nucleocapsid core formation, and shed light on the virulence attenuation, host recognition and neutralizing activities of VEEV and other alphavirus pathogens...
  10. pmc Cryo-EM of macromolecular assemblies at near-atomic resolution
    Matthew L Baker
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
    Nat Protoc 5:1697-708. 2010
    ..Additionally, the feature recognition and computational modeling tools can be applied to any near-atomic resolution density maps, including those from X-ray crystallography...
  11. pmc Mechanism of folding chamber closure in a group II chaperonin
    Junjie Zhang
    Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
    Nature 463:379-83. 2010
    ....
  12. pmc Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density
    Matthew L Baker
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS Comput Biol 2:e146. 2006
    ..While this new model provides for a better understanding of the assembly and interactions of VP26 in HSV-1, the approach itself may have broader applications in modeling the components of large macromolecular assemblies...
  13. doi request reprint Reconstructing virus structures from nanometer to near-atomic resolutions with cryo-electron microscopy and tomography
    Juan Chang
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Adv Exp Med Biol 726:49-90. 2012
    ..Here we present the common techniques used to acquire and process cryo-EM and cryo-ET data and discuss their implications for structural virology both now and in the future...
  14. ncbi request reprint Applications of a bilateral denoising filter in biological electron microscopy
    Wen Jiang
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    J Struct Biol 144:114-22. 2003
    ..In as much, we have applied this technique to individual micrographs, entire 3D reconstructions, segmented proteins, and tomographic reconstructions...
  15. ncbi request reprint Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions
    Wen Jiang
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nat Struct Biol 10:131-5. 2003
    ..The cryo-EM shows that a large conformational change of the P22 capsid during maturation transition involves not only the domain movement of individual subunits, but also refolding of the capsid protein...
  16. pmc Tracing conformational changes in proteins
    Nurit Haspel
    Department of Computer Science, Rice University, Houston, TX 77005, USA
    BMC Struct Biol 10:S1. 2010
    ..Traditional biophysics-based conformational search methods require a large number of calculations and are hard to apply to large-scale conformational motions...
  17. doi request reprint De novo backbone trace of GroEL from single particle electron cryomicroscopy
    Steven J Ludtke
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Structure 16:441-8. 2008
    ..This asymmetric conformation is different from previous asymmetric structures, including GroES-bound GroEL, and may represent a "primed state" in the chaperonin pathway...
  18. ncbi request reprint A 9 angstroms single particle reconstruction from CCD captured images on a 200 kV electron cryomicroscope
    Christopher R Booth
    Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
    J Struct Biol 147:116-27. 2004
    ....
  19. pmc Identification of secondary structure elements in intermediate-resolution density maps
    Matthew L Baker
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Structure 15:7-19. 2007
    ....
  20. ncbi request reprint Structural biology of cellular machines
    Wah Chiu
    National Center for Macromolecular Imaging and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Trends Cell Biol 16:144-50. 2006
    ..The establishment of a database describing the structural and dynamic properties of protein assemblies will provide novel opportunities to define the molecular and atomic mechanisms controlling overall cell physiology...
  21. pmc Analyses of subnanometer resolution cryo-EM density maps
    Matthew L Baker
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
    Methods Enzymol 483:1-29. 2010
    ..A general protocol for analyzing subnanometer resolution density maps is presented along with a full description of steps used in analyzing the 4.3Å resolution structure of Mm-cpn...
  22. pmc 4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement
    Yao Cong
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemsitry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
    Proc Natl Acad Sci U S A 107:4967-72. 2010
    ..These interior surface chemical properties likely play an important role in TRiC's cellular substrate specificity...
  23. pmc Cryoelectron microscopy of protein IX-modified adenoviruses suggests a new position for the C terminus of protein IX
    Michael P Marsh
    Program in Structural and Computational Biology and Molecular Biophysics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    J Virol 80:11881-6. 2006
    ..The original assignment of IIIa was based largely on indirect evidence, and the data presented herein support the reassignment of the IIIa density as protein IX...
  24. pmc Structure of the herpesvirus major capsid protein
    Brian R Bowman
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Graduate Program in Structural and Computational Biology, Baylor College of Medicine, Houston, TX 77030, USA
    EMBO J 22:757-65. 2003
    ..These differences may mediate the binding and release of other structural proteins during capsid maturation...
  25. ncbi request reprint Electron cryomicroscopy of biological machines at subnanometer resolution
    Wah Chiu
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
    Structure 13:363-72. 2005
    ..The consequences of these analyses can not only identify accurately some of the secondary structure elements of the molecular components in machines but also suggest structural mechanisms related to their biological functions...
  26. pmc Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus
    Xiangan Liu
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
    Nat Struct Mol Biol 17:830-6. 2010
    ..Our observations suggest a mechanism whereby, upon binding to the host cell, the tail fibers induce a cascade of structural alterations of the portal vertex complex that triggers DNA release...
  27. pmc The skeletal muscle Ca2+ release channel has an oxidoreductase-like domain
    Matthew L Baker
    Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 99:12155-60. 2002
    ..Consistent with the prediction of an oxidoreductase domain, RyR1 binds [3H]NAD+, supporting a model in which RyR1 has a oxidoreductase-like domain that could function as a type of redox sensor...
  28. pmc Rotavirus architecture at subnanometer resolution
    Zongli Li
    National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, Texas 77030, USA
    J Virol 83:1754-66. 2009
    ....
  29. pmc Common ancestry of herpesviruses and tailed DNA bacteriophages
    Matthew L Baker
    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
    J Virol 79:14967-70. 2005
    ..On the basis of this and other emerging relationships, it seems increasingly likely that the very diverse collection of extant viruses may have arisen from a relatively small number of primordial progenitors...
  30. pmc Crystal structure of the cytoplasmic N-terminal domain of subunit I, a homolog of subunit a, of V-ATPase
    Sankaranarayanan Srinivasan
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    J Mol Biol 412:14-21. 2011
    ....
  31. ncbi request reprint Deriving folds of macromolecular complexes through electron cryomicroscopy and bioinformatics approaches
    Wah Chiu
    Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
    Curr Opin Struct Biol 12:263-9. 2002
    ..Such approaches have been demonstrated with the 6.8 A structure of the rice dwarf virus to derive models for the major capsid shell proteins...
  32. ncbi request reprint Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy
    Maya Topf
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, Mission Bay Genentech Hall, 600 16th Street, Suite N472D, University of California, San Francisco, CA 94143, USA
    J Struct Biol 149:191-203. 2005
    ..Moreover, a pseudo-atomic model of a component in an assembly may be built better with comparative models of the native subunit sequences than with experimentally determined structures of their homologs...
  33. ncbi request reprint Refinement of protein structures by iterative comparative modeling and CryoEM density fitting
    Maya Topf
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, QB3, 1700 4th Street, Suite 503B, University of California at San Francisco, San Francisco, CA 94143 2552, USA
    J Mol Biol 357:1655-68. 2006
    ..The method is being implemented in our program MODELLER for protein structure modeling by satisfaction of spatial restraints and will be applicable to the rapidly increasing number of cryoEM density maps of macromolecular assemblies...
  34. doi request reprint Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy
    Wen Jiang
    Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
    Nature 451:1130-4. 2008
    ..Beyond epsilon15, this method potentially offers a new approach for modelling the backbone conformations of the protein subunits in other macromolecular assemblies at near-native solution states...