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Raquel Godoy Ruiz, PhD

Academic Title:

Research Associate

Primary Appointment:

Biochemistry and Molecular Biology

Additional Title:

Section Leader, Protein Production and Biophysics, Center for Bimolecular Therapeutics

Location:

9600 Gudelsky Dr. Rockville, MD 20850

Phone (Primary):

2403146393

Phone (Secondary):

2403146517

Education and Training

  • University of Granada (Spain), BS, Chemistry, 2000
  • University of Granada (Spain), PhD, 2006
  • University of Maryland College-Park, Postdoctoral Human Frontier Science Program (HFSP) Fellow, 2007
  • University of Maryland School of Medicine, Postdoctoral Fellow, 2011

Biosketch

Dr Godoy-Ruiz works for the Protein Production and Biophysics (PPB) Center for Biomolecular Therapeutics (CBT) of University of Maryland School of Medicine since 2011. She is PPB section's leader of the CBT at the Institute for Bioscience and Biotechnological Research (IBBR), Shady Grove campus. The PPB section of the CBT has the technical expertise, equipment (such as fast protein liquid chromatography (FPLC) and high performance liquid chromatography (HPLC) systems), bioreactors, incubators, and DNA and protein libraries. They also assist in the development and testing of therapeutic proteins as biological therapies that interfere with specific molecules involved in tumor growth and progression, and developing methods to express therapeutic proteins in E. coli, baculovirus, and mammalian cells. The majority of the proteins expressed and purified in the PPB section are studied using both NMR and X-ray crystallography to either characterize protein stability, create or improve binding affinity to other molecules relevant in the disease mechanism.

In addition, another major component of Dr Godoy-Ruiz's position is to assist the NMR core director (Dr. Kristen Varney) with day-to-day operations of the NMR spectrometers (400 MHz, 600 MHz, 800 MHz, and the recently purchased 950 MHz) in the UMB NMR Shared Service Facility. This includes a variety of tasks including cryogen fills, spectrometer maintenance, setting up NMR experiments and training new users.

 

Research/Clinical Keywords

Protein expression & purification, protein folding, structural biology

Highlighted Publications

Kerr C, Szmacinski H, Fisher ML, Nance B, Lakowicz JR, Akbar A, Keillor JW, Lok Wong T, Godoy-Ruiz R, Toth EA, Weber DJ, Eckert RL. Transamidase site-targeted agents alter the conformation of the transglutaminase cancer stem cell survival protein to reduce GTP binding activity and cancer stem cell survival. Oncogene. 2016 Dec 12. [Epub ahead of print]. PMID: 27941875.

Chen Y, Clarke OB, Kim J, Stowe S, Kim YK, Assur Z, Cavalier M, Godoy-Ruiz R, von Alpen DC, Manzini C, Blaner WS, Frank J, Quadro L, Weber DJ, Shapiro L, Hendrickson WA, Mancia F. Structure of the STRA6 receptor for retinol uptake. Science. 2016 Aug 26; 353 (6302). PMID: 27563101

 Mazalouskas MD, Godoy-Ruiz R, Weber DJ, Zimmer DB, Honkanen RE, Wadzinski BE. Small G proteins, Rac1 and Ras, regulate serine/threonine protein phosphatase 5 (PP5)-extracellular signal-regulated (ERK) complexes involved in the feedback regulation of Raf1. J Biol Chem. 2013 Dec 26. PMCID: PMC3924286

McKnight LE, Raman EP, Bezawada P, Kudrimoti S, Wilder PT, Hartman KG, Godoy-Ruiz R, Toth EA, Coop A, Mackerell AD Jr, Weber DJ. Structure-Based Discovery of a Novel Pentamidine-Related Inhibitor of the Calcium-Binding Protein S100B. ACS Med Chem Lett. 2012 Dec 13;3(12):975-979. PMCID: PMC3524579

Godoy-Ruiz R, Krejcirikova A, Gallagher DT, Tugarinov V. “Solution NMR evidence for symmetry in functionally or crystallographic asymmetric homodimers”. J Am Chem Soc. 2011 Dec 14; 133(49): 19578-81. PMID: 22074452.

Additional Publication Citations

Sun H, Godoy-Ruiz R, Tugarinov V. Estimating side-chain order in methyl-protonated, perdeuterated proteins via multiple-quantum relaxation violated coherence transfer NMR spectroscopy. J Biomol NMR. 2012 Mar;52(3):233-43.

Liao X, Godoy-Ruiz R, Guo C, Tugarinov V. “Simultaneous measurement of 1H-15N and methyl 1Hm-13Cm residual dipolar couplings in large proteins”. J Biomol NMR. 2011 Sep; 51(1-2):191-8. PMID: 21947927.

Guo C, Godoy-Ruiz R, Tugarinov V. “Isotope labeling of alanine methyl groups on a deuterated background for NMR Studies of high-molecular-weight-proteins”. Cambridge Isotope Laboratories, Inc. Application Note 24, 2011.

Godoy-Ruiz R, Guo C, Tugarinov V. J Am Chem Soc. 2010 Dec 29; 132(51):18340-50. “Alanine methyl groups as NMR probes of molecular structure and dynamics in high-molecular-weight proteins”. J Biomol NMR. 2011 Sep ;51(1-2):191-8. PMID: 21138300.

Guo C, Godoy-Ruiz R, Tugarinov V. “High resolution measurement of methyl 13C(m)-13C and 1H(m)-13C(m) residual dipolar couplings in large proteins”. J Am Chem Soc. 2010 Oct 13; 132(40):13984-7. PMID: 20860373.

Sheppard D, Li DW, Godoy-Ruiz R, Brüschweiler R, Tugarinov V. “Variation in quadrupole couplings of alpha deuterons in ubiquitin suggests the presence of Ca-Ha...O=C hydrogen bonds”. J Am Chem Soc. 2010 Jun 9; 132(22):7709-19. PMID: 20476744.

Suarez M, Tortosa P, Garcia-Mira MM, Rodríguez-Larrea D, Godoy-Ruiz R, Ibarra-Molero B, Sanchez-Ruiz JM, Jaramillo A. “Using multi-objective computational design to extend protein promiscuity”. Biophys Chem. 2009 Dec 22. PMID: 20034725.

Fung A, Li P, Godoy-Ruiz R, Sanchez-Ruiz JM, Muñoz V. “Expanding the realm of ultrafast protein folding: gpW, a midsize natural single-domain with alpha+beta topology that folds downhill”. J Am Chem Soc. 2008 Jun 11;130(23):7489-95. PMID: 18479088.

Godoy-Ruiz R, Henry E.R., Kubelka J., Hofrichter J., Muñoz V., Sanchez-Ruiz J.M. and Eaton W.A. “Estimating Free-Energy Barrier Heights for an Ultrafast Folding Protein from Calorimetric and Kinetic Data”. J Phys Chemistry B 2008 May 15; 112(19):5938-49. PMID: 18278894.

Pey AL, Rodriguez-Larrea D, Bomke S, Dammers S, Godoy-Ruiz R, Garcia-Mira MM, Sanchez-Ruiz JM. “Engineering proteins with tunable thermodynamic and kinetic stabilities”. Proteins. 2007 Apr;71(1):165-74. PMID: 17932922.

Godoy-Ruiz R, Ariza F, Rodriguez-Larrea D, Perez-Jimenez R, Ibarra-Molero B, Sanchez-Ruiz JM. “Natural Selection for Kinetic Stability is a Likely Origin of Correlations between Mutational Effects on Protein Energetics and Frequencies of Amino Acid Occurrences in Sequence Alignments”. J Mol Biol. 2006. Oct 6; 362 (5): 966-78. PMID: 16239060.

Perez-Jimenez R, Godoy-Ruiz R, Parody-Morreale A, Ibarra-Molero B, Sanchez-Ruiz JM. “A simple tool to explore the distance distribution of correlated mutations in proteins”. Biophys Chem. 2006; 119(3):240-6. PMID: 16239060.

Godoy-Ruiz R, Perez-Jimenez R, Ibarra-Molero B, Sanchez-Ruiz JM. “A stability pattern of protein hydrophobic mutations that reflects evolutionary structural optimization”. Biophys J. 2005 Nov; 89(5):3320-31. PMID: 16100262.

Godoy-Ruiz R, Perez-Jimenez R, Garcia-Mira MM, Plaza del Pino IM, Sanchez-Ruiz JM. “Empirical parametrization of pK values for carboxylic acids in proteins using a genetic algorithm”. Biophys Chem. 2005 Apr 1;115(2-3):263-6. PMID: 15752616.

Perez-Jimenez R, Godoy-Ruiz R, Ibarra-Molero B, Sanchez-Ruiz JM. “The effect of charge-introduction mutations on E. coli thioredoxin stability”. Biophys Chem. 2005;115(2-3):105-7. PMID: 15752590.

Campos LA, Garcia-Mira MM, Godoy-Ruiz R, Sanchez-Ruiz JM, Sancho J. “Do proteins always benefit from a stability increase? Relevant and residual stabilization in a three-state protein by charge optimization”. J Mol Biol. 2004;344(1):223-37. PMID: 15504413.

Lopez-Llano J, Maldonado S, Jain S, Lostao A, Godoy-Ruiz R, Sanchez-Ruiz JM, Cortijo M, Fernandez-Recio J, Sancho J. “The long and short flavodoxins: II. The role of the differentiating loop in apoflavodoxin stability and folding mechanism”. J Biol Chem. 2004; 279(45):47184-91. PMID: 

Perez-Jimenez R, Godoy-Ruiz R, Ibarra-Molero B, Sanchez-Ruiz JM. “The efficiency of different salts to screen charge interactions in proteins: a Hofmeister effect?” Biophys J. 2004;86(4):2414-29. PMID: 15041679.

Godoy-Ruiz R, Perez-Jimenez R, Ibarra-Molero B, Sanchez-Ruiz JM. “Relation between protein stability, evolution and structure, as probed by carboxylic acid mutations”. J Mol Biol. 2004 Feb 13;336(2):313-8. PMID: 14757046.

B. Ibarra-Molero, R. Perez-Jimenez, R. Godoy-Ruiz and Jose M. Sanchez-Ruiz. Book chapter: “Linkage between temperature and chemical denaturant effects on protein stability: The interpretation of calorimetrycally-determined m values”. Biocalorimetry 2: Application of calorimetry in the biological sciences. Ed. J.E. Ladbury Science B. V. and John Wiley and Sons. New York. 2004.