NMR spectroscopy, DNA-binding proteins, membrane proteins, cancer
Recent advances in high-field NMR spectroscopy have provided exciting new opportunities to characterize both the structure and dynamics of large proteins. My research goals are to define the conformations and dynamics of soluble DNA-binding proteins and to develop strategies to study membrane protein structures using NMR spectroscopy and other biophysical techniques.
CNS Regeneration: Nogo is a membrane protein known to inhibit axonal growth within the central nervous system (CNS). Disabling Nogo following spinal cord injury or stroke may allow regrowth of damaged axons. One domain of Nogo, termed Nogo-66, is present extracellularly on the oligodentrocyte cells of the CNS. Nogo-66 achieves axonal growth inhibition by binding to the Nogo Receptor (NgR) on neuronal cells. We are interested in characterizing the structure of Nogo-66 and how it interacts with the Nogo Receptor. A detailed understanding of the interaction between Nogo-66 and NgR will prove useful for designing drugs that will interfere with the ligand-receptor interaction and provide recovery from CNS injury.
Natural Antibiotics: Defensins are family of antimicrobial peptides having activity against a range of microorganisms: gram-positive and gram-negative bacteria, fungi and some viruses. In addition to their antimicrobial activity, emerging evidence suggests that they can also assume fundamental roles in both innate and adaptive immunity. More than 300 defensins have been identified to date and they are represented in a range of organisms including mammals, birds, invertebrates, plants and recently in the ebony-cup fungus. Our lab focuses on structural characterization of some of these defensins and their interactions with membranes to understand their mode of action.
DNA Binding Proteins
Tumor Suppressor: Mutations in the protein p53 are strongly correlated with the transformation of a healthy cell into a cancerous cell. Many cancers can be traced to a set of several individual point mutations in this protein that result in destabilization of the structure and thus inactivation of the protein. Several rescue mutations have been identified that when combined with the cancerous mutation restore stability and function in model systems. Our goal is to establish the mechanism through which these rescue mutations stabilize the structure through NMR dynamics measurements. Ultimately, we hope to use this knowledge for intelligent drug design of small molecules that can mimic the rescue mechanism. NMR also provides the avenue for testing promising compounds for their affect on protein dynamics to give support to drug design choices.
DNA Repair: Lesion bypass polymerases play an essential cellular role as they allow replication to proceed through damaged DNA. Mutation of a member of this class of polymerases, Pol eta, results in the condition xeroderma pigmentosum that can lead to cancer; thus Pol eta is a proven tumor supressor. Recently the structures of the bypass polymerases S. solfataricus DinB homologue (Dbh) and polymerase IV (Dpo4), and S. cerevisiae Pol eta were found to resemble the classic polymerase fold. The fidelity of the replicative polymerase is believed to rely on a protein conformational change from an open to closed state. The closed state has been proposed to be a crucial determinant of fidelity by restricting nucleotide incorporation to the base that fits correctly (induced fit mechanism). An unusual feature was noticed in the bypass polymerase structures: both Dbh and Pol eta are in a closed conformation even in the absence of substrate. This raises a question as to whether the bypass polymerase mechanism involves a protein conformational change similar to that of the replicative enzymes. Using NMR spectroscopy, we will probe the conformation of the protein in solution to determine if the closed state is the most populated or merely one of the existing conformations trapped by the crystallization process. To date, the polymerase mechanism has largely been studied from the substrate DNA perspective. These NMR studies will provide insight from the protein point of view; this will be the first characterization of polymerase motions with atomic level detail.
Gene Regulation: CytR is a bacterial transcription factor that represses production of the genes of the cytidine regulation pathway. While containing high sequence and functional homology to LacR, the lactose repressor, CytR has unique DNA sequence recognition ability in its dimeric form. While many DNA binding proteins form dimers to bind to palindromic sequences with a defined spacing, only CytR has been shown to have the ability to bind to half sites separated by a varying number of bases. Our NMR studies allow us to elucidate the structure and dynamics of the protein as it binds DNA. In collaboration with the Senear lab, we are working toward a greater understanding of the mechanism of gene recognition and expression regulation in general.
38. Feinstein, HE, Tifrea, DF, Popot, J-L, de la Maza, LM, Cocco, MJ*. (2014) Long-term stability of a vaccine formulated with the amphipol-trapped major outer membrane protein from Chlamydia trachomatis. J. Membrane Biology, in press
37. Alhoshani, A,Vithayathil R, Bandong J, Chrunyk, KM, Moreno, GO, Weiss, GA and Cocco, MJ*. (2014) Glutamate is a Key Structural Contact Between Nogo-66 and Phosphocholine. BBA – Biomembranes, 1838: 2350-6
36. Tifrea, DF, Pal, S, Cocco, MJ, Popot, J-L and de la Maza, LM. Increased immuno accessibility of MOMP epitopes in a vaccine formulated with amphipols may account for the very robust protection elicited against a vaginal challenge with C. muridarum. (2014) J. Immunology 192: 5201-13
35. Vithayathil R, Hooy RM, Cocco MJ, Weiss GA. (2011) The Scope of phage display for membrane proteins. J. Mol. Biol. 414:499-510
34. Popot JL, Althoff T, Bagnard D, Banères JL, Bazzacco P, Billon-Denis E, Catoire LJ, Champeil P, Charvolin D, Cocco MJ, Crémel G, Dahmane T, de la Maza LM, Ebel C, Gabel F, Giusti F, Gohon Y, Goormaghtigh E, Guittet E, Kleinschmidt JH, Kühlbrandt W, Le Bon C, Martinez KL, Picard M, Pucci B, Sachs JN, Tribet C, van Heijenoort C, Wien F, Zito F, Zoonens M. (2011) Amphipols from A to Z. Annu Rev Biophys. 2011 40:379-408
33. Moody, CL, Tretyachenko-Ladokhina, V, Laue, T., Senear, DF and Cocco, MJ* (2011) Multiple Conformations of the Cytidine Repressor DNA-Binding Domain Coalesce to One Upon Recognition of a Specific DNA Surface. Biochemistry, 50:6622-32
32. Tifrea, DF, Sun, G, Pal, S, Zardeneta1, G, Cocco, MJ, Popot, J-L, de la Maza, LM (2011) Amphipols stabilize the Chlamydia major outer membrane protein and enhance vaccine protection based on a membrane-protein formulation. Vaccine 29:4623-31
31. Corbin-Lickfett, KA, Souki, SK, Li, L, Cocco, MJ and Sandri-Goldin, RM. (2010) Three arginine residues within the RGG-box are crucial for ICP27 binding to herpes simplex virus 1 GC-rich sequences and for efficient viral RNA export. Journal of Virology, 84:6367-76
30. Vasudevan, SV, Schulz, J, Zhou, C and Cocco, MJ*. (2010) Protein Folding at the Membrane Interface, the Structure of Nogo-66. Proceedings of the National Academy of Sciences, 107:6847-51
29. Corbin-Lickfett, KA, Rojas, S, Li, L, Cocco, MJ and Sandri-Goldin, RM. (2010) ICP27 Phosphorylation Site Mutants Display Altered Functional Interactions with Cellular Export Factors Aly/REF and TAP/NXF1 but Are Able to Bind Herpes Simplex Virus 1 RNA. Journal of Virology, 84:2212-22.
28. Corbin-Lickfett, KA, Chen, I-HB, Cocco, MJ* and Sandri-Goldin, RM* (2009) The HSV-1 ICP27 RGG box specifically binds flexible, GC-rich sequences but not G-quartet structures. Nucleic Acids Research, 37:7290-301.
27. Llenado, RA, Weeks, CS, Cocco, MJ and Ouellette, AJ (2009) Electropositive charge in a-Defensin Bactericidal Activity: Functional Effects of Arg?Lys Substitutions Vary with Peptide Primary Structure. Infection and Immunity, 77:5035-43
26. Sasaki, H, Arai, H, Cocco, MJ and White, SH (2008) pH-Dependence of Sphingosine Aggregation, Biophysical Journal, 96:2727-33
25. Vasudevan, S, Yuan, J, Ösapay, G, Tran, P, Tai, K, Liang, W, Kumar, V, Selsted, ME*, and Cocco, MJ* (2008) Synthesis, Structure and Activities of an Oral Mucosal Alpha-Defensin from Rhesus Macaque, Journal of Biological Chemistry, 283:35869-77
24. Gehman, JD, Cocco, MJ and Grindley, ND (2008) Chemical Shift Mapping of ?d resolvase Dimer and Activated Tetramer: Mechanistic Implications for DNA Strand Exchange. BBA - Proteins and Proteomics 1784:2086-92
23. Liu D, Ren D, Huang, H, Dankberg, J, Rosenfeld, R, Cocco, MJ, Li, L, Brems, DN, and Remmele, RL (2008) Structure and Stability Changes of Human IgG1 Fc as a Consequence of Methionine Oxidation. Biochemistry 47: 5088-5100
22. Liu D, Cocco, MJ, Matsumura M, Ren D, Becker, B, Remmele, RL and Brems, DN (2007) Assignment of backbone (1)H, (13)C and (15)N resonances of human IgG1 Fc (51.4 kDa). Biomolecular NMR Assignments 1: 233-235
21. Liu D, Cocco, MJ, Matsumura M, Ren D, Becker, B, Remmele, RL and Brems, DN (2007) Assignment of backbone resonances of the reduced human IgG1 CH3 domain. Biomolecular NMR Assignments 1: 93-94
20. Sun, G, Pal, S, Sarcon, AK, Kim, S, Sugawara, E, Nikaido, H, Cocco, MJ, Ellena M. Peterson, EM, de la Maza, LM (2007) Structural and functional analyses of the major outer membrane protein of Chlamydia trachomatis. Journal of Biological Chemistry, 189: 6222-35
19. Levin, A., Coroneus, J., Cocco, MJ., and Weiss, G. (2006) “Exploring the Interaction between the Protein Kinase A Catalytic Subunit and Caveolin-1 Scaffolding with Shotgun Scanning, Oligomer Complementation, NMR, and Docking” Protein Science, 15: 478-86
18. Weeks, C, Tanabe, H, Cuymmings, JE, Crampton, SP, Sheynis, T, Jelinek, R, Vanderlick, TK, Cocco, MJ, Ouellette, AJ. (2006) Matrix metalloproteinase-7 activation of mouse paneth cell Pro-alpha-defensins: Ser43*?Ile44 proteolysis enables membrane disruptive activity. Journal of Biological Chemistry, 281: 28932-42
17. Tretyachenko-Ladokhina, V, Cocco, MJ, Senear, DF, (2006) Flexibility and Adaptability in Binding of E. coli Cytidine Repressor to Different Operators Suggests a Role in Differential Gene Regulation. Journal of Molecular Biology, 362: 271-86
16. Kamtekar, S, Ho, RS, Cocco, MJ, Li, W, Wenwieser, SVCT, Boocock, MR, Grindley, NDF, Steitz, TA, (2006) Implications of Structure of Synaptic Tetramers of ?d Resolvase for the Mechanism of Recombination. Proceedings of the National Academy of Sciences, 103: 10642-7
15. Tanabe, H, Ouellette, AJ, Cocco, MJ and Robinson, WE. (2004) Differential Effects on Human Immunodificiency Virus Type 1 Replication by a-Defensins of Comparable Bactericidal Activities. Journal of Virology, 78: 11622-31
14. Cortajarena, AL, Kajander, T, Pan, W, Cocco, MJ, and Regan, L. (2004) Protein Design to Understand Peptide Ligand Recognition by Tetratricopeptide Repeat Proteins. Protein Design Engineering and Selection, 17: 399-409
13. Cocco, MJ*, Hanakahi, L, Huber, MD, and Maizels, N. (2003) Distamysin Binds G4 DNA and Maps the Interaction Surface of Nucleolin RGG Domain Recognition. Nucleic Acids Research. 31: 2944-2951; *corresponding author
12. Main, E, Xoing, Y, Cocco, MJ, D’Andrea, L and Regan, L. (2003) Design of Stable a-Helical Arrays from an Idealized TPR Motif. Structure 11: 497-508.
11. Cocco, MJ1, Ramirez-Alvarado, M1 and Regan, L. (2003) Mutations in the B1 Domain of Protein G that Delay the Onset of Amyloid Fibril Formation in Vitro. Protein Science 12: 567-576; 1co-first authors
10. Li H, Cocco MJ, Steitz TA, and Engelman DM. (2001) Conversion of Phospholamban Into a Soluble Pentameric Helical Bundle. Biochemistry 40: 6636-6645.
9. Zhou, FX, Cocco, MJ, Russ, WP, Brunger, AT, and DM Engelman, DM. (2000) Interhelical Hydrogen Bonding Drives Strong Interactions in Membrane Proteins. Nature Struct. Biol. 7: 154-160.
8. Basu, S, Szewczak, AA, Cocco, MJ, Strobel, SA. (2000) Direct Detection of Monovalent Metal Ion Binding to a DNA G-quartet by 205Tl NMR. J. Am. Chem. Soc. 122: 3240-3241.
7. Lecomte, JTJ, Kao, YH, and Cocco, MJ. (1996) The Native State of Apomyoglobin Described by Proton NMR Spectroscopy: The A-B-G-H Interface of Wild-Type Sperm Whale Apomyoglobin. Proteins: Structure, Function and Genetics 25: 267-285.
6. Wynn, R, Cocco, MJ, and Richards, FM. (1995) Mixed Disulfide Intermediates During the Reduction of Disulfides by Eschericia coli Thioredoxin. Biochemistry 34: 11807-11813.
5. Cocco, MJ and Lecomte, JTJ. (1994) The Native State of Apomyoglobin Described by Proton NMR Spectroscopy: Interaction with the Paramagnetic Probe HyTEMPO and the Fluorescent Dye ANS. Protein Science 3: 267-281.
4. Cocco, MJ, Barrick, D, Taylor, SV, and Lecomte, JTJ. (1992) Histidine 82 Influences Heme Orientational Isomerization in Sperm Whale Myoglobin. Long-Range Effect due to Mutation of a Conserved Residue. J. Am. Chem. Soc. 114: 11000-11001.
3. Cocco, MJ, Kao, YH, Phillips, AT and Lecomte, JTJ. (1992) Structural Comparison of Apomyoglobin and Metaquomyoglobin: pH Titration of Histidines by NMR Spectroscopy. Biochemistry 31: 6481-6491.
2. Cocco, MJ and Lecomte, JTJ. (1990) Characterization of Hydrophobic Cores in Apomyoglobin: A Proton NMR Spectroscopy Study. Biochemistry 29: 11067-11072.
1. Lecomte, JTJ and Cocco, MJ. (1990) Structural Features of the Protoporphyrin-Apomyoglobin Complex: A Proton NMR Spectroscopy Study. Biochemistry 29: 11057-11067.
American Chemical Society,
Cellular and Molecular Biosciences
Medicinal Chemistry and Pharmacology
Multiple Sclerosis Research Center