Structural Biology

Structural Biology

Resources for the determination of three dimensional protein structure.

Shared Facilities:

Stanford Magnetic Resonance Laboratory (SMRL)

• Description — Nuclear Magnetic Resonance (NMR) spectroscopy, instrumentation, and expertise. Primarily solution state spectroscopy of bio-molecules - also including, but not limited to, studies of polymers, minerals, soils, extracts. Equipment and services include: 800 MHz Varian Inova Spectrometer, 600 MHz Varian Inova Spectrometer, 500 MHz Bruker Avance Spectrometer, and staff assistance/consultation.
• Location — Fairchild Rm D026, and Organic Chemistry Bldg Rm 101
• Questions — Contact Corey Liu, PhD  , (650) 724-7445
• Website — http://smrl.stanford.edu/
• Selected References

  Ligand-specific regulation of the extracellular surface of a G-protein-coupled receptor. Bokoch MP, Zou Y, Rasmussen SG, Liu CW, Nygaard R, Rosenbaum DM, Fung JJ, Choi HJ, Thian FS, Kobilka TS, Puglisi JD, Weis WI, Pardo L, Prosser RS, Mueller L, Kobilka BK. Nature. 2010 Jan 7;463(7277):108-12. PubMedID: 20054398.

  Phosphorus forms and chemistry in the soil profile under long-term conservation tillage: a phosphorus-31 nuclear magnetic resonance study. Cade-Menun BJ, Carter MR, James DC, Liu CW. J Environ Qual. 2010 Sep-Oct;39(5):1647-56. PubMedID: 21043270.

  Small-molecule displacement of a cryptic degron causes conditional protein degradation. Bonger KM, Chen LC, Liu CW, Wandless TJ. Nat Chem Biol. 2011 Jul 3;7(8):531-7. PubMedID: 21725303.

Stanford Synchrotron Radiation Lightsource (SSRL)

• Description — SSRL is a Department of Energy Office of Science user facility that provides synchrotron radiation facilities used to study our world at the atomic and molecular level, leading to advances in drug discovery, medicine, energy production, environmental remediation, nanotechnology and new materials. The facility supports (with instrumentation and staff) researchers using macromolecular crystallography, small-angle x-ray scattering, x-ray imaging and microscopy, x-ray absorption spectroscopy, and scattering techniques, among others. Access is obtained by submitting a proposal and is provided at no charge for scientists who conduct non-proprietary research, with the understanding that significant results are to be publicly disseminated.
• Location — SLAC National Accelerator Laboratory
• Questions — Contact Cathy Knotts  , (650) 926-3191
• Website — http://www-ssrl.slac.stanford.edu
• Selected References

  High-Resolution Analysis of Zn(2+) Coordination in the Alkaline Phosphatase Superfamily by EXAFS and X-ray Crystallography. Bobyr E, Lassila JK, Wiersma-Koch HI, Fenn TD, Lee JJ, Nikolic-Hughes I, Hodgson KO, Rees DC, Hedman B, Herschlag DJ. Mol Biol. 2012 Jan 6;415(1):102-17. PubMedID: 22056344.

  Identification of NVP-BKM120 as a Potent, Selective, Orally Bioavailable Class I P13 Kinase Inhibitor for Treating Cancer. Burger MT, Pecchi S, Wagman A, Ni Z-J, Knapp M, Hendrickson T, Atallah G, Pfister K, Zhang Y, Bartulis S, Frazier K, Ng S, Smith A, Verhagen J, Haznedar J, Huh K, Iwanowicz E, Xin X, Menezes D, Merritt H, Lee I, Wiesmann M, Kaugman S, Crawford K, Chin M, Bussiere D, Shoemaker K, Zaror I, Maira S-M and Voliva CF. ACS Med. Chem. Lett. (2011)

  Improved Molecular Replacement by Density- and Energy-guided Protein Structure Optimization. DiMaio F, Terwilliger TC, Read RJ, Wlodawer A, Oberdorfer G, Wagner U, Valkov E, Alon A, Fass D, Axelrod HL, Das D, Vorobiev SM, Iwaï H, Pokkuluri PR, Baker D. Nature. 2011 May 26;473(7348):540-3. PubMedID: 21532589.