Associated Faculty, CHEMISTRY
Frick Lab, 360
Biophysical chemistry: Molecular origins of macromolecular affinity and specificity
The research in our laboratory is focused on understanding the molecular basis of interactions involving biological macromolecules. Molecular recognition is at the root of essentially all biological processes, and hence much of medicine. All cellular functions depend on protein-protein, protein-small molecule, protein-nucleic acid, or other intermolecular interactions. How do the correct partners identify each other against the background of numerous similar molecules present in the biological milieu? How are appropriate levels of affinity set? Our interest is centered on obtaining a detailed understanding of the underlying chemical and physical processes at work in these interactions. In doing so, we apply both structural and thermodynamic analysis in order to achieve an integrated picture.
All molecular interactions have characteristic values of affinity and specificity. Biology demands that each molecular interaction has a unique combination of affinity and specificity in order to serve its physiological purpose in the organism. It is commonly thought that affinity and specificity arise from favorable bonding interactions between partners that can be observed in structural analysis of complexes. However, many examples of biological interactions have an enthalpy change for complex formation that is near zero or even positive. This kind of result indicates that the net contribution from bonding interactions is not the principal driving force for complex formation. In some cases of this kind it has been shown that entropy changes arising from such cryptic sources as surface solvation can dominate the overall free energy change for complex formation. Thus, differences in solvation or other properties of two related molecules can lead to large differences in their affinities even when differences in their bonding interactions are minor. These and other cryptic contributions are, by definition, undetected by structural methods. Thus, there is no simple relationship between bonding (structure) and the strength or specificity of interaction, which may have unforeseen (and unseen) molecular origins.
We are currently working on several systems that exemplify different molecular mechanisms for achieving the values of affinity and specificity required to serve their biological purpose. In each system under study, our experimental approaches range from basic molecular biology such as cloning, through biochemistry including purification and characterization and quantitative analysis of binding equilibria, to biophysical methods including calorimetry and electronic and NMR spectroscopies. By comparing and contrasting the structural and thermodynamic features in several cases, we hope to distill out the generalities that are essential for understanding the basis of recognition. The general conclusions also have impact in related areas, including drug development.
Note: A complete list of publications can be found at www.princeton.edu/chemistry/carey.
Strawn R, Melichercik M, Green M, Stockner T, Carey J, Ettrich R. (2010) Symmetric allosteric mechanism of hexameric Escherichia coli arginine repressor exploits competition between L-arginine ligands and resident arginine residues. PLoS Comput Biol. 6: e1000801. PubMed
Carey J, Lindman S, Bauer M, Linse S. (2007) Protein reconstitution and three-dimensional domain swapping: benefits and constraints of covalency. Protein Sci 16: 2317-2333 PubMed
Carey J, Brynda J, Wolfová J, Grandori R, Gustavsson T, Ettrich R, Smatanová IK. (2007) WrbA bridges bacterial flavodoxins and eukaryotic NAD(P)H:quinone oxidoreductases. Protein Sci 16: 2301-2305. PubMed
Natalello A, Doglia SM, Carey J, Grandori R. (2006) Role of flavin mononucleotide in the thermostability and oligomerization of Escherichia coli stress-defense orotein WrbA. Biochemistry 46: 543-553. PubMed
Ji H, Shen L, Carey J, Grandori R, Zhang H. (2006) Weaker binding of FMN by WrbA than by flavodoxin: a molecular modeling study. J Molec Struct Theo Chem 764: 155-160.
Nöll G, Kozma E, Grandori R, Carey J, Schödl T, Hauska G, Daub J. (2006) Spectroelectrochemical investigation of a flavoprotein with a flavin-modified gold electrode. Langmuir 22: 2378-2383. PubMed
Wolfova J, Grandori R, Kozma E, Chatterjee N, Carey J, Smatanova I. (2005) Crystallization of the flavoprotein WrbA optimized by using additives and gels. J Cryst Growth 284: 502-505.
Samalikova M, Carey J, Grandori R. (2005) Assembly of the hexameric Escherichia coli arginine repressor investigated by nano-ESI-TOF mass spectrometry. Rapid Comm Mass Spec 19: 2549-2552. PubMed
Patel KA, Bartoli K, Ngatchou AN, Wocj G, Carey J, Tanaka JC. (2005) Impaired function and trafficking of cyclic nucleotide-gated channel mutants from human cone CNGA3 causing achromatopsia 2. Invest Ophthamol Visual Sci 46: 2282-2290.
Jin L, Xue W-F, Fukayama JW, Yetter J, Pickering M, Carey J. (2005) Asymmetric allosteric activation of the symmetric ArgR hexamer. J Mol Biol 346: 43-56. PubMed
Xue W-F, Carey J, Linse S. (2004) Multi-method global analysis of thermodynamics and kinetics in reconstitution of monellin. Proteins: Structure, Function, and Bioinformatics. 57: 586-595. PubMed
Pursglove SE, Fladvad M, Bellanda M, Moshref A, Henriksson M, Carey J, Sunnerhagen M. (2004) Biophysical properties of regions flanking the bHLH-Zip motif in the p22 Max protein. Biochem Biophys Res Commun 323: 750-759. PubMed
Carey J (2004). Quantifying molecular recognition for drug discovery, in NMR in Drug Screening, Oxford University Press, in press.
Lawson CL, Benhoff B, Berger T, Berman HM, Carey J (2004). E. coli trp repressor forms a domain-swapped array in aqueous alcohol. Structure 12: 1099-1107. PubMed
Szwajkajzer D, Carey J (2003). RaPID plots: Affinity and mechanism at a glance. Biacore J 3: 19.
McWhirter A and Carey J (2003). T-cell receptor recognition of peptide antigen/MHC complexes. Biacore J 3: 18.
Tyler R, Pelczer I, Carey J, Copie V (2002). Three-dimensional solution NMR structure of apo-L75F-TrpR, a temperature-sensitive mutant of the tryptophan repressor protein. Biochemistry 41: 11954-11962. PubMed
Szwajkajzer D, Dai L, Fukayama JW, Abramczyk B, Fairman R, Carey J (2001). Quantitative analysis of DNA binding by E. coli arginine repressor. J Mol Biol 312: 949-962. PubMed
Scott S-P, Weber IT, Harrison RW, Carey J, Tanaka JC (2001). A functioning chimera of the cyclic nucleotide-binding domain from the bovine retinal rod ion channel and the DNA-binding domain from catabolite gene-activating protein. Biochemistry 40: 7464-7473. PubMed
Carey J (2000). Globularity and protein function. J Biomol Str Dyn 11: 87-88.
Carey J (2000). A systematic and general proteolytic method for defining structural and functional domains of proteins. Methods Enzymol 328: 499-514. PubMed
Jin L, Fukayama JW, Pelczer I and Carey J (1999). Long-range effects on dynamics in a temperature-sensitive mutant of trp repressor. J Mol Biol 285: 361-378. PubMed
Grandori R, Khalifah P, Boice JA, Fairman R, Giovanielli K, Carey J (1998). Biochemical characterization of WrbA, founding member of a new family of multimeric flavodoxin-like proteins. J Biol Chem 273: 20960-20966. PubMed
Szwajkajzer D and Carey J (1997). Molecular and biological constraints on ligand-binding affinity and specificity. Biopolymers 44: 181-198. PubMed
Sunnerhagen M, Nilges M, Otting G and Carey J (1997). Solution structure of the DNA-binding domain and model for the complex of multifunctional hexameric arginine repressor with DNA. Nat Struct Biol 4: 819-826. PubMed
Grandori R, Lavoie TA, Pflumm M, Tian G, Niersbach H, Maas WK, Fairman R, Carey J (1995). The DNA-binding domain of the hexameric arginine repressor. J Mol Biol 254: 150-162. PubMed
Wu LC, Grandori R and Carey J (1994). Autonomous subdomains in protein folding. Protein Sci 3: 369-371. PubMed
Grandori R and Carey J (1994). Six new candidate members of the alpha/beta twisted open-sheet family detected by sequence similarity to flavodoxin. Protein Sci 3: 2185-2193. PubMed
Wu LC, Laub PB, Elove GA, Carey J and Roder H (1993). A noncovalent peptide complex as a model for an early folding intermediate of cytochrome c. Biochemistry 32: 10271-10276. PubMed
Lawson CL and Carey J (1993). Tandem binding in crystals of a trp repressor/operator half-site complex. Nature 366: 178-182. PubMed
Jin L, Yang J and Carey J (1993). Thermodynamics of ligand binding to trp repressor. Biochemistry 32: 7302-7309. PubMed
Tasayco ML and Carey J (1992). Ordered self-assembly of polypeptide fragments to form nativelike dimeric trp repressor. Science 255: 594-597. PubMed