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MATTHEW L BAKER

TitleAssistant Professor
InstitutionBaylor College of Medicine
DepartmentDepartment of Biochemistry & Molecular Biology
DivisionBiochemistry & Molecular Biology
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    R21GM100229     (BAKER, MATTHEW LOWELL)Sep 10, 2013 - Aug 31, 2015
    NIH/NIGMS
    Atomic Resolution Cryo-EM using Model-Based Constraints
    Role: Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Samaha H, Pignata A, Fousek K, Ren J, Lam FW, Stossi F, Dubrulle J, Salsman VS, Krishnan S, Hong SH, Baker ML, Shree A, Gad AZ, Shum T, Fukumura D, Byrd TT, Mukherjee M, Marrelli SP, Orange JS, Joseph SK, Sorensen PH, Taylor MD, Hegde M, Mamonkin M, Jain RK, El-Naggar S, Ahmed N. Retraction Note: A homing system targets therapeutic T cells to brain cancer. Nature. 2019 03; 567(7746):132. PMID: 30787441.
      View in: PubMed
    2. Fan G, Baker MR, Wang Z, Seryshev AB, Ludtke SJ, Baker ML, Serysheva II. Cryo-EM reveals ligand induced allostery underlying InsP3R channel gating. Cell Res. 2018 Dec; 28(12):1158-1170. PMID: 30470765.
      View in: PubMed
    3. Chen M, Baker ML. Automation and assessment of de novo modeling with Pathwalking in near atomic resolution cryoEM density maps. J Struct Biol. 2018 12; 204(3):555-563. PMID: 30237066.
      View in: PubMed
    4. Samaha H, Pignata A, Fousek K, Ren J, Lam FW, Stossi F, Dubrulle J, Salsman VS, Krishnan S, Hong SH, Baker ML, Shree A, Gad AZ, Shum T, Fukumura D, Byrd TT, Mukherjee M, Marrelli SP, Orange JS, Joseph SK, Sorensen PH, Taylor MD, Hegde M, Mamonkin M, Jain RK, El-Naggar S, Ahmed N. A homing system targets therapeutic T cells to brain cancer. Nature. 2018 09; 561(7723):331-337. PMID: 30185905.
      View in: PubMed
    5. Byrd TT, Fousek K, Pignata A, Szot C, Samaha H, Seaman S, Dobrolecki L, Salsman VS, Oo HZ, Bielamowicz K, Landi D, Rainusso N, Hicks J, Powell S, Baker ML, Wels WS, Koch J, Sorensen PH, Deneen B, Ellis MJ, Lewis MT, Hegde M, Fletcher BS, St Croix B, Ahmed N. TEM8/ANTXR1-Specific CAR T Cells as a Targeted Therapy for Triple-Negative Breast Cancer. Cancer Res. 2018 01 15; 78(2):489-500. PMID: 29183891.
      View in: PubMed
    6. Dou H, Burrows DW, Baker ML, Ju T. Flexible Fitting of Atomic Models into Cryo-EM Density Maps Guided by Helix Correspondences. Biophys J. 2017 Jun 20; 112(12):2479-2493. PMID: 28636906.
      View in: PubMed
    7. Hegde M, Mukherjee M, Grada Z, Pignata A, Landi D, Navai SA, Wakefield A, Fousek K, Bielamowicz K, Chow KK, Brawley VS, Byrd TT, Krebs S, Gottschalk S, Wels WS, Baker ML, Dotti G, Mamonkin M, Brenner MK, Orange JS, Ahmed N. Tandem CAR T cells targeting HER2 and IL13Ra2 mitigate tumor antigen escape. J Clin Invest. 2016 08 01; 126(8):3036-52. PMID: 27427982.
      View in: PubMed
    8. Chen M, Baldwin PR, Ludtke SJ, Baker ML. De Novo modeling in cryo-EM density maps with Pathwalking. J Struct Biol. 2016 12; 196(3):289-298. PMID: 27436409.
      View in: PubMed
    9. Lawson CL, Patwardhan A, Baker ML, Hryc C, Garcia ES, Hudson BP, Lagerstedt I, Ludtke SJ, Pintilie G, Sala R, Westbrook JD, Berman HM, Kleywegt GJ, Chiu W. EMDataBank unified data resource for 3DEM. Nucleic Acids Res. 2016 Jan 04; 44(D1):D396-403. PMID: 26578576.
      View in: PubMed
    10. Fan G, Baker ML, Wang Z, Baker MR, Sinyagovskiy PA, Chiu W, Ludtke SJ, Serysheva II. Gating machinery of InsP3R channels revealed by electron cryomicroscopy. Nature. 2015 Nov 19; 527(7578):336-41. PMID: 26458101.
      View in: PubMed
    11. Zhang Z, He F, Constantine R, Baker ML, Baehr W, Schmid MF, Wensel TG, Agosto MA. Domain organization and conformational plasticity of the G protein effector, PDE6. J Biol Chem. 2015 Jul 10; 290(28):17131-2. PMID: 26163476.
      View in: PubMed
    12. Zhang Z, He F, Constantine R, Baker ML, Baehr W, Schmid MF, Wensel TG, Agosto MA. Domain organization and conformational plasticity of the G protein effector, PDE6. J Biol Chem. 2015 May 15; 290(20):12833-43. PMID: 25809480.
      View in: PubMed
    13. Gipson P, Baker ML, Raytcheva D, Haase-Pettingell C, Piret J, King JA, Chiu W. Corrigendum: Protruding knob-like proteins violate local symmetries in an icosahedral marine virus. Nat Commun. 2015 Jan 12; 6:6040. PMID: 25581040.
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    14. Wang Z, Hryc CF, Bammes B, Afonine PV, Jakana J, Chen DH, Liu X, Baker ML, Kao C, Ludtke SJ, Schmid MF, Adams PD, Chiu W. An atomic model of brome mosaic virus using direct electron detection and real-space optimization. Nat Commun. 2014 Sep 04; 5:4808. PMID: 25185801.
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    15. Gipson P, Baker ML, Raytcheva D, Haase-Pettingell C, Piret J, King JA, Chiu W. Protruding knob-like proteins violate local symmetries in an icosahedral marine virus. Nat Commun. 2014 Jul 02; 5:4278. PMID: 24985522.
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    16. Rizzo AA, Suhanovsky MM, Baker ML, Fraser LC, Jones LM, Rempel DL, Gross ML, Chiu W, Alexandrescu AT, Teschke CM. Multiple functional roles of the accessory I-domain of bacteriophage P22 coat protein revealed by NMR structure and CryoEM modeling. Structure. 2014 Jun 10; 22(6):830-41. PMID: 24836025.
      View in: PubMed
    17. Baker ML, Hryc CF, Zhang Q, Wu W, Jakana J, Haase-Pettingell C, Afonine PV, Adams PD, King JA, Jiang W, Chiu W. Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling. Proc Natl Acad Sci U S A. 2013 Jul 23; 110(30):12301-6. PMID: 23840063.
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    18. Grada Z, Hegde M, Byrd T, Shaffer DR, Ghazi A, Brawley VS, Corder A, Schönfeld K, Koch J, Dotti G, Heslop HE, Gottschalk S, Wels WS, Baker ML, Ahmed N. TanCAR: A Novel Bispecific Chimeric Antigen Receptor for Cancer Immunotherapy. Mol Ther Nucleic Acids. 2013 Jul 09; 2:e105. PMID: 23839099.
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    19. Baker ML, Baker MR, Hryc CF, Ju T, Chiu W. Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps. Biopolymers. 2012 Sep; 97(9):655-68. PMID: 22696403.
      View in: PubMed
    20. Kramer DB, Baker M, Ransford B, Molina-Markham A, Stewart Q, Fu K, Reynolds MR. Security and privacy qualities of medical devices: an analysis of FDA postmarket surveillance. PLoS One. 2012; 7(7):e40200. PMID: 22829874.
      View in: PubMed
    21. Baker MR, Rees I, Ludtke SJ, Chiu W, Baker ML. Constructing and validating initial Ca models from subnanometer resolution density maps with pathwalking. Structure. 2012 Mar 07; 20(3):450-63. PMID: 22405004.
      View in: PubMed
    22. Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL. Outcome of the first electron microscopy validation task force meeting. Structure. 2012 Feb 08; 20(2):205-14. PMID: 22325770.
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    23. Chang J, Liu X, Rochat RH, Baker ML, Chiu W. Reconstructing virus structures from nanometer to near-atomic resolutions with cryo-electron microscopy and tomography. Adv Exp Med Biol. 2012; 726:49-90. PMID: 22297510.
      View in: PubMed
    24. Baker ML, Baker MR, Cong, Y. Computational Methods for Interpretation of EM Maps at Subnanometer Resolution. 2012.
    25. Zhang R, Hryc CF, Cong Y, Liu X, Jakana J, Gorchakov R, Baker ML, Weaver SC, Chiu W. 4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus. EMBO J. 2011 Aug 09; 30(18):3854-63. PMID: 21829169.
      View in: PubMed
    26. Srinivasan S, Vyas NK, Baker ML, Quiocho FA. Crystal structure of the cytoplasmic N-terminal domain of subunit I, a homolog of subunit a, of V-ATPase. J Mol Biol. 2011 Sep 09; 412(1):14-21. PMID: 21787787.
      View in: PubMed
    27. Baker ML, Abeysinghe SS, Schuh S, Coleman RA, Abrams A, Marsh MP, Hryc CF, Ruths T, Chiu W, Ju T. Modeling protein structure at near atomic resolutions with Gorgon. J Struct Biol. 2011 May; 174(2):360-73. PMID: 21296162.
      View in: PubMed
    28. Chen DH, Baker ML, Hryc CF, DiMaio F, Jakana J, Wu W, Dougherty M, Haase-Pettingell C, Schmid MF, Jiang W, Baker D, King JA, Chiu W. Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. Proc Natl Acad Sci U S A. 2011 Jan 25; 108(4):1355-60. PMID: 21220301.
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    29. Lawson CL, Baker ML, Best C, Bi C, Dougherty M, Feng P, van Ginkel G, Devkota B, Lagerstedt I, Ludtke SJ, Newman RH, Oldfield TJ, Rees I, Sahni G, Sala R, Velankar S, Warren J, Westbrook JD, Henrick K, Kleywegt GJ, Berman HM, Chiu W. EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res. 2011 Jan; 39(Database issue):D456-64. PMID: 20935055.
      View in: PubMed
    30. Baker ML, Zhang J, Ludtke SJ, Chiu W. Cryo-EM of macromolecular assemblies at near-atomic resolution. Nat Protoc. 2010 Sep; 5(10):1697-708. PMID: 20885381.
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    31. Liu X, Zhang Q, Murata K, Baker ML, Sullivan MB, Fu C, Dougherty MT, Schmid MF, Osburne MS, Chisholm SW, Chiu W. Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus. Nat Struct Mol Biol. 2010 Jul; 17(7):830-6. PMID: 20543830.
      View in: PubMed
    32. Haspel N, Moll M, Baker ML, Chiu W, Kavraki LE. Tracing conformational changes in proteins. BMC Struct Biol. 2010 May 17; 10 Suppl 1:S1. PMID: 20487508.
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    33. Cong Y, Baker ML, Jakana J, Woolford D, Miller EJ, Reissmann S, Kumar RN, Redding-Johanson AM, Batth TS, Mukhopadhyay A, Ludtke SJ, Frydman J, Chiu W. 4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement. Proc Natl Acad Sci U S A. 2010 Mar 16; 107(11):4967-72. PMID: 20194787.
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    34. Zhang J, Baker ML, Schröder GF, Douglas NR, Reissmann S, Jakana J, Dougherty M, Fu CJ, Levitt M, Ludtke SJ, Frydman J, Chiu W. Mechanism of folding chamber closure in a group II chaperonin. Nature. 2010 Jan 21; 463(7279):379-83. PMID: 20090755.
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    35. Baker M, Prasad BV. Rotavirus cell entry. Curr Top Microbiol Immunol. 2010; 343:121-48. PMID: 20397068.
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    36. Baker ML, Baker MR, Hryc CF, Dimaio F. Analyses of subnanometer resolution cryo-EM density maps. Methods Enzymol. 2010; 483:1-29. PMID: 20888467.
      View in: PubMed
    37. Baker ML, Marsh MP, Chiu W. Nanotechnology. Electron Cryomicroscopy of Molecular Nanomachines and Cells. 2010; 89-111.
    38. Abeysinghe S, Baker ML, Chiu W, Ju T. Semi-isometric registration of line features for flexible fitting of protein structures. Comput Graph Forum. 2010; 29(7):2243-2252. PMID: 21124809.
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    39. DiMaio F, Tyka MD, Baker ML, Chiu W, Baker D. Refinement of protein structures into low-resolution density maps using rosetta. J Mol Biol. 2009 Sep 11; 392(1):181-90. PMID: 19596339.
      View in: PubMed
    40. Li Z, Baker ML, Jiang W, Estes MK, Prasad BV. Rotavirus architecture at subnanometer resolution. J Virol. 2009 Feb; 83(4):1754-66. PMID: 19036817.
      View in: PubMed
    41. Serysheva II, Ludtke SJ, Baker ML, Cong Y, Topf M, Eramian D, Sali A, Hamilton SL, Chiu W. Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel. Proc Natl Acad Sci U S A. 2008 Jul 15; 105(28):9610-5. PMID: 18621707.
      View in: PubMed
    42. Ludtke SJ, Baker ML, Chen DH, Song JL, Chuang DT, Chiu W. De novo backbone trace of GroEL from single particle electron cryomicroscopy. Structure. 2008 Mar; 16(3):441-8. PMID: 18334219.
      View in: PubMed
    43. Jiang W, Baker ML, Jakana J, Weigele PR, King J, Chiu W. Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy. Nature. 2008 Feb 28; 451(7182):1130-4. PMID: 18305544.
      View in: PubMed
    44. Abeysinge, S., Ju, T., Baker, M.L., Chiu, W. Shape modeling and matching in identifying 3D protein structures. Computer Aided-Design. 2008; (40):708-720.
    45. Baker ML, Zhou ZH, Chiu W. Segmented Double-stranded RNA Viruses: Structure and Molecular Biology, J. T. Patton, ed. Structure of Phytoreovirus. 2008; 89-103.
    46. Abeysinge S, Baker ML, Chiu W, Ju T. IEEE International Conference on Shape Modeling and Applications 2008. Segmentation-free skeletonization of grayscale volumes for shape understanding. 2008; 63-71.
    47. Ju T, Baker ML, Chiu W. Computing a family of skeletons of volumetric models for shape description. Comput Aided Des. 2007 May; 39(5):352-360. PMID: 18449328.
      View in: PubMed
    48. Abeysinghe S, Ju T, Baker ML, Chiu W. ACM Symposium on Solid and Physical Modeling 2007. Shape modeling and matching in identifying protein structure from low-resolution images. 2007.
    49. Baker ML, Ju T, Chiu W. Identification of secondary structure elements in intermediate-resolution density maps. Structure. 2007 Jan; 15(1):7-19. PMID: 17223528.
      View in: PubMed
    50. Baker ML, Jiang W, Wedemeyer WJ, Rixon FJ, Baker D, Chiu W. Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density. PLoS Comput Biol. 2006 Oct 27; 2(10):e146. PMID: 17069457.
      View in: PubMed
    51. Marsh MP, Campos SK, Baker ML, Chen CY, Chiu W, Barry MA. Cryoelectron microscopy of protein IX-modified adenoviruses suggests a new position for the C terminus of protein IX. J Virol. 2006 Dec; 80(23):11881-6. PMID: 16987967.
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    52. Baker ML, Yu Z, Chiu W, Bajaj C. Automated segmentation of molecular subunits in electron cryomicroscopy density maps. J Struct Biol. 2006 Dec; 156(3):432-41. PMID: 16908194.
      View in: PubMed
    53. Chiu W, Baker ML, Almo SC. Structural biology of cellular machines. Trends Cell Biol. 2006 Mar; 16(3):144-50. PMID: 16459078.
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    54. Topf M, Baker ML, Marti-Renom MA, Chiu W, Sali A. Refinement of protein structures by iterative comparative modeling and CryoEM density fitting. J Mol Biol. 2006 Apr 14; 357(5):1655-68. PMID: 16490207.
      View in: PubMed
    55. Ju T, Baker ML, Chiu W. Proceedings of Geometric Modeling and Processing 2006. Computing a family of skeletons of volumetric models for shape description. 2006; 235-247.
    56. Baker ML, Jiang W, Rixon FJ, Chiu W. Common ancestry of herpesviruses and tailed DNA bacteriophages. J Virol. 2005 Dec; 79(23):14967-70. PMID: 16282496.
      View in: PubMed
    57. Chiu W, Baker ML, Jiang W, Dougherty M, Schmid MF. Electron cryomicroscopy of biological machines at subnanometer resolution. Structure. 2005 Mar; 13(3):363-72. PMID: 15766537.
      View in: PubMed
    58. Topf M, Baker ML, John B, Chiu W, Sali A. Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. J Struct Biol. 2005 Feb; 149(2):191-203. PMID: 15681235.
      View in: PubMed
    59. Booth CR, Jiang W, Baker ML, Zhou ZH, Ludtke SJ, Chiu W. A 9 angstroms single particle reconstruction from CCD captured images on a 200 kV electron cryomicroscope. J Struct Biol. 2004 Aug; 147(2):116-27. PMID: 15193640.
      View in: PubMed
    60. Jiang W, Baker ML, Wu Q, Bajaj C, Chiu W. Applications of a bilateral denoising filter in biological electron microscopy. J Struct Biol. 2003 Oct-Nov; 144(1-2):114-22. PMID: 14643214.
      View in: PubMed
    61. Baker ML, Jiang W, Bowman BR, Zhou ZH, Quiocho FA, Rixon FJ, Chiu W. Architecture of the herpes simplex virus major capsid protein derived from structural bioinformatics. J Mol Biol. 2003 Aug 08; 331(2):447-56. PMID: 12888351.
      View in: PubMed
    62. Bowman BR, Baker ML, Rixon FJ, Chiu W, Quiocho FA. Structure of the herpesvirus major capsid protein. EMBO J. 2003 Feb 17; 22(4):757-65. PMID: 12574112.
      View in: PubMed
    63. Jiang W, Li Z, Zhang Z, Baker ML, Prevelige PE, Chiu W. Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions. Nat Struct Biol. 2003 Feb; 10(2):131-5. PMID: 12536205.
      View in: PubMed
    64. Baker ML, Serysheva II, Sencer S, Wu Y, Ludtke SJ, Jiang W, Hamilton SL, Chiu W. The skeletal muscle Ca2+ release channel has an oxidoreductase-like domain. Proc Natl Acad Sci U S A. 2002 Sep 17; 99(19):12155-60. PMID: 12218169.
      View in: PubMed
    65. Chiu W, Baker ML, Jiang W, Zhou ZH. Deriving folds of macromolecular complexes through electron cryomicroscopy and bioinformatics approaches. Curr Opin Struct Biol. 2002 Apr; 12(2):263-9. PMID: 11959506.
      View in: PubMed
    66. Jiang W, Li Z, Zhang Z, Booth CR, Baker ML, Chiu W. Semi-automated icosahedral particle reconstruction at sub-nanometer resolution. J Struct Biol. 2001 Dec; 136(3):214-25. PMID: 12051901.
      View in: PubMed
    67. Zhou ZH, Baker ML, Jiang W, Dougherty M, Jakana J, Dong G, Lu G, Chiu W. Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus. Nat Struct Biol. 2001 Oct; 8(10):868-73. PMID: 11573092.
      View in: PubMed
    68. Jiang W, Baker ML, Ludtke SJ, Chiu W. Bridging the information gap: computational tools for intermediate resolution structure interpretation. J Mol Biol. 2001 May 18; 308(5):1033-44. PMID: 11352589.
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    69. Petrosino JF, Baker M, Palzkill T. Susceptibility of beta-lactamase to core amino acid substitutions. Protein Eng. 1999 Sep; 12(9):761-9. PMID: 10506286.
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    70. Lu G, Zhou ZH, Baker ML, Jakana J, Cai D, Wei X, Chen S, Gu X, Chiu W. Structure of double-shelled rice dwarf virus. J Virol. 1998 Nov; 72(11):8541-9. PMID: 9765392.
      View in: PubMed
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