Amide proton exchange of a dynamic loop in cell extracts

Protein Science

Volumn 22, Issue 10, 2013, Pages 1313-1319

  Smith, Austin E ^a   Sarkar, Mohona ^a   Young, Gregory B ^b   Pielak, Gary J ^a,b,c  

^a University of North Carolina at Chapel Hill   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

Amide 1H exchange; Macromolecular crowding; NMR; SOLEXSY; Solvent exchange

Indexed keywords

AMIDE; CELL EXTRACT; CHYMOTRYPSIN INHIBITOR; GLOBULAR PROTEIN; HYDROGEN; SOLVENT;

ARTICLE; BACTERIAL CELL; CARBON NUCLEAR MAGNETIC RESONANCE; CELL LYSATE; CYTOPLASM; DRY WEIGHT; ESCHERICHIA COLI; HYDROGEN BOND; MACROMOLECULAR CROWDING; MACROMOLECULE; NITROGEN NUCLEAR MAGNETIC RESONANCE; NONHUMAN; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTON NUCLEAR MAGNETIC RESONANCE; PROTON TRANSPORT;

AMIDE 1H EXCHANGE; MACROMOLECULAR CROWDING; NMR; SOLEXSY; SOLVENT EXCHANGE;

AMIDES; BUFFERS; DEUTERIUM EXCHANGE MEASUREMENT; ESCHERICHIA COLI; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PEPTIDES; PLANT PROTEINS; PROTEIN STABILITY; PROTEIN STRUCTURE, TERTIARY; PROTONS;

EID: 84888327393     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.2318     Document Type: Article

References (42)

1. McGuffee SR, Elcock AH (2010) Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Comput Biol 6:e1000694.
2. Zimmerman SB, Trach SO (1991) Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli. J Mol Biol 222:599-620.
3. Zhou HX, Rivas G, Minton AP (2008) Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences. Annu Rev Biophys 37:375-397.
4. Elcock AH (2010) Models of macromolecular crowding effects and the need for quantitative comparisons with experiment. Curr Opin Struct Biol 20:196-206.
5. Hvidt A, Linderstr-M-Lang K (1954) Exchange of hydrogen atoms in insulin with deuterium atoms in aqueous solutions. Biochim Biophys Acta 14:574-575.
6. Berger A, Linderstr-M-Lang K (1957) Deuterium exchange of poly-DL-Alanine in aqueous solution. Arch Biochem Biophys 69:106-118.
7. Englander SW, Mayne L, Bai Y, Sosnick TR (1997) Hydrogen exchange: The modern legacy of Linderstr-M-Lang. Protein Sci 6:1101-1109.
8. Englander SW, Kallenbach NR (1983) Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q Rev Biophys 16:521-655.
9. Hern-Andez G, Anderson JS, LeMaster DM (2009) Polarization and polarizability assessed by protein amide acidity. Biochemistry 48:6482-6494.
10. Miklos AC, Li C, Pielak GJ (2009) Using NMRdetected backbone amide 1H exchange to assess macromolecular crowding effects on globular-Protein stability. Methods Enzymol 466:1-18.
11. Hvidt A, Nielsen SO (1966) Hydrogen exchange in proteins. Adv Protein Chem 21:287-386.
12. Bai Y, Milne JS, Mayne L, Englander SW (1994) Protein stability parameters measured by hydrogen exchange. Proteins 20:4-14.
13. Neira JL, Itzhaki LS, Otzen DE, Davis B, Fersht AR (1997) Hydrogen exchange in chymotrypsin inhibitor 2 probed by mutagenesis. J Mol Biol 270:99-110.
14. Bai Y, Milne JS, Mayne L, Englander SW (1993) Primary structure effects on peptide group hydrogen exchange. Proteins 17:75-86.
15. Connelly GP, Bai Y, Jeng MF, Englander SW (1993) Isotope effects in peptide group hydrogen exchange. Proteins 17:87-92.
16. Molday RS, Englander SW, Kallen RG (1972) Primary structure effects on peptide group hydrogen exchange. Biochemistry 11:150-158.
17. Zhang Y-Z (1995) Protein and peptide structure and interactions studied by hydrogen exchange and NMR. Ph.D. Dissertation, University of Pennsylvania, Philadelphia.
18. Benton LA, Smith AE, Young GB, Pielak GJ (2012) Unexpected effects of macromolecular crowding on protein stability. Biochemistry 51:9773-9775.
19. Charlton LM, Barnes CO, Li C, Orans J, Young GB, Pielak GJ (2008) Residue-Level interrogation of macromolecular crowding effects on protein stability. J Am Chem Soc 130:6826-6830.
20. Miklos AC, Sarkar M, Wang Y, Pielak GJ (2011) Protein crowding tunes protein stability. J Am Chem Soc 133:7116-7120.
21. Wang Y, Sarkar M, Smith AE, Krois AS, Pielak GJ (2012) Macromolecular crowding and protein stability. J Am Chem Soc 134:16614-16618.
22. Wang A, Robertson AD, Bolen DW (1995) Effects of a naturally occurring compatible osmolyte on the internal dynamics of ribonuclease A. Biochemistry 34: 15096-15104.
23. The PyMOL Molecular Graphics System, Version 1.3. Schrodinger, LLC. Available at: Www.pymol.org.Last accessed: 2010.
24. Cavallo L, Kleinjung J, Fraternali F (2003) POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level. Nucleic Acids Res 31:3364-3366.
25. McPhalen CA, James MN (1987) Crystal and molecular structure of the serine proteinase inhibitor CI-2 from barley seeds. Biochemistry 26:261-269.
26. De Prat Gay G, Ruiz-Sanz J, Neira JL, Itzhaki LS, Fersht AR (1995) Folding of a nascent polypeptide chain in vitro: Cooperative formation of structure in a protein module. Proc Natl Acad Sci U S A 92:3683-3686.
27. Itzhaki LS, Neira JL, Fersht AR (1997) Hydrogen exchange in chymotrypsin inhibitor 2 probed by denaturants and temperature. J Mol Biol 270:89-98.
28. Shaw GL, Davis B, Keeler J, Fersht AR (1995) Backbone dynamics of chymotrypsin inhibitor 2: Effect of breaking the active site bond and its implications for the mechanism of inhibition of serine proteases. Biochemistry 34:2225-2233.
29. Hwang TL, van Zijl PC, Mori S (1998) Accurate quantitation of water-Amide proton exchange rates using the phase-Modulated CLEAN chemical exchange (CLEANEX- PM) approach with a fast-HSQC (FHSQC) detection scheme. J Biomol NMR 11:221-226.
30. Li C, Charlton LM, Lakkavaram A, Seagle C, Wang G, Young GB, Macdonald JM, Pielak GJ (2008) Differential dynamical effects of macromolecular crowding on an intrinsically disordered protein and a globular protein: Implications for in-Cell NMR spectroscopy. J Am Chem Soc 130:6310-6311.
31. Li C, Wang G-F, Wang Y, Creager-Allen R, Lutz EA, Scronce H, Slade KM, Ruf RAS, Mehl RA, Pielak GJ (2009) Protein 19F NMR in Escherichia coli. J Am Chem Soc 132:321-327.
32. Barnes CO, Monteith WB, Pielak GJ (2011) Internal and global protein motion assessed with a fusion construct and in-Cell NMR spectroscopy. ChemBioChem 12:390-391.
33. Barnes CO, Pielak GJ (2011) In-Cell protein NMR and protein leakage. Proteins 79:347-351.
34. Chevelkov V, Xue Y, Rao DK, Forman-Kay JD, Skrynnikov NR (2010) 15N H/D-SOLEXSY experiment for accurate measurement of amide solvent exchange rates: Application to denatured drkN SH3. J Biomol NMR 46:227-244.
35. Li C, Pielak GJ (2009) Using NMR to distinguish viscosity effects from nonspecific protein binding under crowded conditions J Am Chem Soc 131:1368-1369.
36. Li C, Wang Y, Pielak GJ (2009) Translational and rotational diffusion of a small globular protein under crowded conditions. J Phys Chem B 113:13390-13392.
37. Wang Y, Li C, Pielak GJ (2010) Effects of proteins on protein diffusion. J Am Chem Soc 132:9392-9397.
38. Covington AK, Robinson RA, Bates RG (1966) The ionization constant of deuterium oxide from 5 to 50-. J Phys Chem 70:3820-3824.
39. Mori S, van Zijl PCM, Shortle D (1997) Measurement of water-Amide proton exchange rates in the denatured state of staphylococcal nuclease by a magnetization transfer technique. Proteins 28:325-332.
40. Miklos AC, Li C, Sharaf NG, Pielak GJ (2010) Volume exclusion and soft interaction effects on protein stability under crowded conditions. Biochemistry 49:6984-6991.
41. Roesler KR, Rao AG (1999) Conformation and stability of barley chymotrypsin inhibitor-2 (CI-2) mutants containing multiple lysine substitutions. Protein Eng 12: 967-973.
42. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: A multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277-293.