Recommended Reading

A running list of recently published papers of interest to the Burstyn Group. Suggestions for this list should be sent to Hannah

CBS:

1. Koutmos, M., Kabil, O., Smith, J. L., and Banerjee, R. (2010) Structural basis for substrated activation and regulation by cystathionine beta-synthase (CBS) domains in cystathionine β-synthase, Proc. Natl. Acad. Sci. U.S.A. 107, 20958-20963.

2. Majtan, T., and Kraus, J. P. (2012) Folding and activity of mutant cystathionine β-synthase depends on the position and nature of the purification tag: Characterization of the R266K CBS mutant, Protein Expression and Purification 82, 317-324.

3. Karunakaran, V., Benabbas, A., Sun, Y., Zhang, Z., Singh, S., Banerjee, R., and Champion, P. M. (2010) Investigations of Low-Frequency Vibrational Dynamics and Ligand Binding Kinetics of Cystathionine β-Synthase, The Journal of Physical Chemistry B 114, 3294-3306.

4. Yammamoto, T., Takano, N., Ishiwata, K., Suematsu, M. (2011) Carbon Monoxide Stimulates Global Protein Methylation via its Inhibitory Action on Cystathionine beta-Synthase. J. Clin. Biochem. Nutr. 96-100.

5. Gupta, S. Kruger, W.D. (2011) Cystathionine beta-Synthase Deficiency Causes Fat Loss in Mice. PLoS One. 6(11)e27598.

6. Hnizda, A., Spiwok, V., Jurga, V., Kozich, V., Kodicek, M., Kraus, J.P. (2010). Cross-talk Between the Catalytic Core and the Regulatory Domain in Cystathionine beta-Synthase: Study by Differential Covalent Labeling and Computational Modeling. Biochemistry. 49(49), 10526-34.

7. Baykov, A. A., Tuominen, H. K., Lahti, R. (2011) The CBS Domain: a Protein Module with an Emerging Prominent Role in Regulation. ACS Chem. Biol. 6(11), 1156-63.

8. Hnízda, A.; et al. (2012), Conformational Properties of Nine Purified Cystathionine β-Synthase Mutants. Biochemistry.

9. Yadav, P.K.; Xie, P.; Banerjee, R. (2012) Allosteric Communication Between the Pyridoxal 5'-Phosphate (PLP) and Heme Sites in the H2S Generator Human Cystathionine β-Synthase. J. Biol. Chem. 287(45), 37611-37620

10. Oyenarte, I.; Majtan, T.; Ereno, J.; Angeles Corral-Rodriguez, M.; Klaudiny, J.; Majtan, J.; Kraus, J.P; Martinez-Cruz, L.A. (2012) Purification, Crystallization, and Preliminary Crystallographic Analysis of the Full-Length Cystathionine β-Synthase from Apis mellifera. Acta Cryst. F68, 1323-1328.

11. Oyenartes, I; Majtan, T.; Erno, J.; Corral-Rodriguez, M.A.; Kraus, J.P.; and Martiniez-Cruz, L.A. (2012) Purification, Crystallization and Preliminary Crystallographic Analysis of Human Cystathionine beta-Synthase. Acta Cyst. F68, 1318-1322.

12. Smith, D.E.C.; Mendes, M.I.S.; Kluitjtmans, L.A.J.; Janssen, M.C.H.; Smulders, Y.M.; Blom, H.J. (2012) A Liquid Chromatography Mass Spectrometry Method for the Measurement of Cystathionine β-Synthase Activity in Cell Extracts. J. Chromatogr. B. 911, 186-191.

13. Carballal, S.; Cuevasanta, E.; Marmisolle, I.; Kabil, O.; Gerasim, C.; Ballous, D.P.; Banerjee, R.; Alvarez, B.; (2013) Kinetics of Reversible Reductive Carbonylation of Heme in Human Cystathionine beta-Synthase. Biochem. 52(26) 4553-4562.

14. Ereno-Orbea, J.; Majtan, T.; Oyenarte, I.; Kraus, J.P.; Martinez-Cruz, L.A.; (2013) Structural Basis of Regulation and Oligomerization of Human Cystathionine beta-Synthase, the Central Enzyme of Transsulfuration. PNAS, ASAP

15. Dimster-Denk, D.; Tripp, K.W.; Marini, N.J.; Marqusee, S.; Rine, J.; (2013) Mono and Dual Cofactor Dependence of Human Cystathionine beta-Synthase Enzyme Variants In Vivo and In Vitro. G3-Genes Genomes Genet. 3(10). 1619-1628.

16. Ereno-ORbea, J.; Oyenarte, I.; Martinez-Cruz, L.A.; (2013) CBS domains: Ligand binding sites and conformational variabilty. Arch. Biochem. Biophys. 540(1-2), 70-81.

17. Gherasim, C.; Yadav, P.K.; Kabil, O.; Niu, W.N.; Banerjee, R.; (2014) Nitirite Reductase Activity and Inhibition of H2S Biogenesis by Human Cystathionine beta-Synthase. PLOS One, 9(1).

18. Mendes, M. I. S.; Colaco, H. G.; Smith, D. E. C.; Ramos, R.; Pop, A.; van Dooren, S. J. M.; de Almeida, I. T.; Kluijtmans, L. A. J.; Janssen, M. C. H.; Rivera, I.; Salomons, G. S.; Leandro, P.; Blom, H. J., (2104) Reduced response of Cystathionine Beta-Synthase (CBS) to S-Adenosylmethionine (SAM): Identification and functional analysis of CBS gene mutations in Homocystinuria patients. J. Inherit. Metab. Dis. 37 (2), 245-254.

19. Vicente, J.B.; Colaco, H.G.; Mendes, M.I.S.; Sarti, P.; Leandro, P.; Giuffre, A.; (2014) NO Binds Human Cystathionine beta-Synthase Quickly and Tightly. J. Biol. Chem. 289(12), 8579-8587.

Gas-Regulated Transcription Factors:

1. Brown, J. H. (2012) Deriving How Far Structural Information is Transmitted Through Parallel Homodimeric Coiled Coils: A correlation analysis of helical staggers. Proteins. doi: 10.1002/prot.24218.

2. Ishida, T.; Aono, S.; (2013) A Model Theoretical Study on Ligand Exchange Reactions of CooA. PCCP, 15(16), 6139-6148.\

3. Levy, C.; Pike, K.; Heyes, D.J.; Joyce, M.G.; Gabor, K.; Smidt, H.; van der Oost, J.; Leys, D.; (2008) Molecular Basis of Haloresipration control by CprK, a CRP-FNR type transcriptional regulator. Mol. Microbio. 70(1) 151-167.

4. Otomo, A.; Ishikawa, H.; Mizuno, M.; Mizutani, Y.; Aono, S.; (2014) Structural Changesin the Heme and Heme Pocket upon CO Dissociation of CooA Observed by Time-Resolved Resonance Raman Spectroscopy. J. Biol. Inorg. Chem. 19, S287.

5. Matta-Camacho, E.; Banerjee, S.; Hughes, T.S.; Solt, L.A.; Wang, Y.; Burris, T.P.; Kojetin, D.J.; (2014) Structure of REV-ERBß Ligand-Binding Domian Bound to a Porphyrin Antagonist. J. Biol. Chem.   ASAP.

DGCR8:  

Other Hemoproteins:

1. Tsai, A.-L., Berka, V., Martin, E., and Olson, J. S. (2012) A "Sliding Scale Rule" for Selectivity among NO, CO, and O2 by Heme Protein Sensors, Biochemistry 51, 172-186.

2. Winter, M. B., Herzik Jr., M. A., Kuriyan, J., and Marletta, M. A. (2011) Tunnels modulate ligand flux in a heme nitric oxide/oxygen binding (H-NOX) domain, Proc. Natl. Acad. Sci. U.S.A. 108, E881-E889.

3. Muralidharan, S., and Boon, E. M. (2012) Heme Flattening Is Sufficient for Signal Transduction in the H-NOX Family, J. Am. Chem. Soc. 134, 2044-2046.

4. Shimizu, T. (2011) Binding of cysteine thiolate to the Fe(III) heme complex is critical for the function of heme sensor proteins, J. Inorg. Biochem. doi:10.1016/j.jinorgbio.2011.08.018.

5. El-Mashtoly, S. F., Kubo, M., Nakashima, S., Shimizu, T., and Kitagawa, T. (2011) Structural Dynamics of EcDOS Heme Domain Revealed by Time-Resolved Ultraviolet Resonance Raman Spectroscopy, J. Phys. Chem. Lett. 2, 2212-2217.

6. Jones, E. M.; Balakrishnan, G.; Spiro, T. G., Heme Reactivity is Uncoupled from Quaternary Structure in Gel-Encapsulated Hemoglobin: A Resonance Raman Spectroscopic Study. Journal of the American Chemical Society 2012.

7. Murakawa, Y.; Nagai, M.; Mizutani, Y., Differences between Protein Dynamics of Hemoglobin upon Dissociation of Oxygen and Carbon Monoxide. Journal of the American Chemical Society 2012, 134 (3), 1434-1437.

8. Nuernberger, P.; Lee, K. F.; Bonvalet, A.; Bouzhir-Sima, L.; Lambry, J. C.; Liebl, U.; Joffre, M.; Vos, M. H., Strong Ligand-Protein Interactions Revealed by Ultrafast Infrared Spectroscopy of CO in the Heme Pocket of the Oxygen Sensor FixL. Journal of the American Chemical Society 2011, 133 (43), 17110-17113.

10. Vos, M. H.; Bouzhir-Sima, L.; Lambry, J.-C.; Luo, H.; Eaton-Rye, J. J.; Ioanoviciu, A.; Ortiz de Montellano, P. R.; Liebl, U., (2011) Ultrafast Ligand Dynamics in the Heme-Based GAF Sensor Domains of the Histidine Kinases DosS and DosT from Mycobacterium tuberculosis. Biochemistry.

11. Owens, C.P.; Du J.; Dawson, J. H.; Goulding, C. W. (2012) Characterization of Heme Ligation Properities of Rv0203, a Secreted Heme Binding Protein Involved in Mycobacterium tuberculosis Heme Uptake. Biochemistry. 51(7), 1518-31.

12. Yin, L.; Dragnea, V.; and Bauer, C. E. (2012) PpsR, A Regulator of Heme and Bacteriochlorophyll Biosynthesis, Is a Heme-sensing Protein. J. Biol. Chem. 287 (17), 13850-13858.

13. Ghosh, A.; and Steuhr, D.J. (2012) Soluble Guanylyl Cyclase Requires Heat Shock Protein 90 for Heme Insertion During Maturation of the NO-active Enzyme. PNAS. 109 (32) 12998-13003.

14. Hannibal, L.; Collins, D.; Brassard, J.; Chakravarti, R.; et al. (2012) Heme Binding Properties of Glyceraldehyde-3-Phosphate Dehydrogenase. Biochemistry. 51(43), 8514-8529.

15. Cáceres, L.; Necakov, A.S.; Schwartz, C.; et al. (2011) Nitric Oxide Coordinates Metabolism, Growth, and Development via the Nuclear Receptor E75. Genes and Development. 25: 1476-1485.

16. Aono, S. (2013) The Dos Family of Globin-Related Sensors Using PAS Domains to Accomodate Haem Aciting as the Active Site for Sensing External Signals. Microbial Globins- Status and Oppertunities. Vol. 63, Academic Press Ltd.-Elsevier Science Ltd., London, 273-327.

17. Rios-Gonzalez, B.B.; Roman-Morales, E.M.; Pietri, R.; Lopez-Garriga, J.; (2014) Hydrogen Sulfide Activation in Hemeproteins: The Sulfheme Scenario. J. Inorg. Biochem. ASAP.

General Interest:

1. Banerjee, R. (2012) Redox outside the Box: Linking Extracellular Redox Remodeling with Intracellular Redox Metabolism, J. Biol. Chem. 287, 4397-4402.

2. Nicoletti, F. P.; Droghetti, E.; Boechi, L.; Bonamore, A.; Sciamanna, N.; Estrin, D. A.; Feis, A.; Boffi, A.; Smulevich, G., (2011) Fluoride as a Probe for H-Bonding Interactions in the Active Site of Heme Proteins: The Case of Thermobifida fusca Hemoglobin. Journal of the American Chemical Society.

3. Rebouças, J. S.; Patrick, B. O.; James, B. R., (2012)Thiol, Disulfide, and Trisulfide Complexes of Ru Porphyrins: Potential Models for Iron–Sulfur Bonds in Heme Proteins. Journal of the American Chemical Society, 134 (7), 3555-3570.

4. Thielges, M. C.; Chung, J. K.; Axup, J. Y.; Fayer, M. D., (2011) Influence of Histidine Tag Attachment on Picosecond Protein Dynamics. Biochemistry.

5. Kerby, R. L., and Roberts, G. P. (2011) Sustaining N2-Dependent Growth in the Presence of CO, J. Bacteriol. 193, 774-777.

6. Morikawa, T. et al. (2012) Hypoxic Regulation of the Cerebral Microcirculation is Mediated by a Carbon Monoxide-Sensitive Hydrogen Sulfide Pathway. Proc. Natl. Acad. Sci. USA. 109 (4), 1293-8.

7. Selwood, T.; Jaffe, E. K., (2012) Dynamic dissociating homo-oligomers and the control of protein function. Archives of Biochemistry and Biophysics , 519 (2), 131-143.

8. Toth-Petroczy, A. and Tawfik, D. (2011) Slow Protein Evolutionary Rates are Dictated By Surface-Core Association. PNAS, 108(27) 11151-11156.

9. Bar-Even, A.; Noor, E.; Savir, Y.; Liebermeister, W.; Davidi, D.; Tawfik, D.; Milo, R. (2011) The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters.  Biochemistry, 50, 4402-4410.

10. Jackson, M.R., et al. (2012) Human Sulfide: Quinone Oxidoreductase Catalyzes the First Step in Hydrogen Sulfide Metabolism and Produces a Sulfane Sulfur Metabolite. Biochemistry. ASAP

11. Spiro, T.G.; Soldatova, A.V.; (2012) Ambidentate H-bonding of NO and O-2 in Heme Proteins. J. Inorg. Biol. 115, 204-210.

12. Crawford, R.; Erben, C.M.; Periz, J.; Hall, L.M.; Brown, T.; Tuberfield, A.J.; Kapanidis, A.N. (2013) Non-Covalent Single Transcription Factor Encapsulation Inside a DNA Cage. Angew. Chem. Int. Ed. 52, 1-6 (ASAP).

13. Balakrishnan, G.; Soldatova, A.V.; Spiro, T.G. (2013) CO, NO, and O2 as Vibrational Probes of Heme Protein Interactions. Coord. Chem. Rev. 257(2, SI) 511-527.

14. Chang, C.J.; He, C.; (2013) Using Chemistry to Study and Control Metals in Biology. Curr. Opin. Chem. Biol. ASAP.

15. Girvan, H.M.; Munro, A.W.; (2013) Heme Sensor Proteins. J. Biol.Chem. ASAP.

16. Bonnet, M.; Kurz, M.; Mesa, S.; Briand, C.; Hennecke, H.; Grütter, M.G.; (2013) Structure of Bradyhizobium japonicum Transcription Factor FixK2 Unveils Sites of DNA Binding and Oxidation. J. Biol. Chem. ASAP.

17. Zhao, Y.; Bhushan, S.; Yang, C.; Otsuka, H.; Stein, J.D.; Pacheco, A.; Peng, B.; Devaire-Baez, N.O.; Aguilar, H.C.; Lefer, D.J.; Xian, M.; (2013) Controllable Hydrogen Sulfide Donors and Their Activity Against Myocardial Ischemia-Reperfusion Injury. ACS Chem. Biol. ASAP.

18. Franke, A.; van Eldik, R.; (2013) Factors that Determine the Mechanism of NO Activation by Metal Complexes of Biological and Environmental Relevance. Euro. J. Inorg. Chem. 4, 460-480.

19. Itoh, R.; Fujita, K.; Mu, A.; Kim, D.H.T.; Tai, T.T.; Sagami, I.; Taketani, S.; (2013) Imagining of Heme/Hemeproteins in Nucleus of the Living Cells Expressing Heme-Binding Nuclear Receptors. FEBS Letters. 587(14) 2131-2136.

20. Liebl, U., Lambry, J. C., and Vos, M. H. (2013) Biochimica Et Biophysica Acta-Proteins and Proteomics 1834, 1684-1692

21. Bailey, T.S.; Pluth, M.D.; (2013)Chemiluminescent Detection of Enzymatically Produced Hydrogen Sulfide: Substrate Hydrogen Bonding Influences Selectivity for H2S over Biological Thiols. J. Am. Chem. Soc. ASAP.

22. Weinert, E.E.; Phillips-Piro, C.M.; Marletta, M.A.; (2013) Porphyrin π-stacking in a Heme Protein Scaffold Tunes Gas Ligand Affinity. J. Inorg. Biochem. 127(0), 7-12.

23. Germani, F.; Moens, L.; Dewilde, S.; (2013) Haem-Based Sensors: A Still Growing Old Superfamily. Advances in Microbial Physiology: Microbial Globins- Status and Oppertunities. Vol. 63, Academic Press Ltd.-Elsevier Science Ltd., London, 1-47