Cloning techniques have made many previously scarce proteins and nucleic acids available for study. Moreover, the sequence of these molecules is generally available, but information about their three-dimensional structure is frequently lacking. Site-directed mutagenesis can be applied to readily generate a wide variety of modified proteins, and it is important to characterize these proteins structurally. Our experimental studies are frequently coupled with theoretical calculations using energy minimization, molecular dynamics, and molecular orbital theory. Examples of systems which we have studied include myoglobin, hemoglobin, cytochrome oxidase, MHC proteins, bovine pancreatic trypsin inhibitor, tropomyosin, trypsin inhibitor, acyl carrier protein, RNA polymerase, pectate lyase C, and cytochrome b5.

E. A. Bienkiewicz, A-Y. M. Woody and R.W. Woody, Conformation of the RNA polymerase II C-terminal domain: Circular dichroism of long and short fragments, J. Mol. Biol. 297, 119-133 (2000).

N. Berova, K. Nakanishi, and R.W. Woody, eds., Circular dichroism: Interpretation and applications, 2nd ed., John Wiley & Sons, Inc., New York (2000).

N. Sreerama, S. Venyaminov, and R. W. Woody, Estimation of protein secondary structure from CD spectra: Inclusion of denatured proteins with native proteins in the analysis, Anal. Biochem. 287, 243-251 (2000).

N. Sreerama and R. W. Woody, Estimation of protein secondary structure from CD spectra: Comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set, Anal. Biochem. 287, 252-260 (2000).

D. Kamen, Y. Griko, and R. W. Woody, The stability, structural organization, and denaturation of pectate lyase C, a parallel beta-helix protein, Biochemistry 40, 15932-15943 (2000).

Y. Griko, N. Sreerama, P. Osumi-Davis, R. W. Woody, and A.-Y. M. Woody, Thermal and urea-induced unfolding in T7 RNA polymerase: Calorimetry, circular dichroism and fluorescence study, Protein Sci. 10, 845-853 (2001).

D. E. Kamen and R. W. Woody, A partially unfolded intermediate conformation is induced in pectate lyase C by the addition of 8-anilino-1-naphthalenesulfonate, Protein Sci. 10, 2123-2130 (2001).

R. M. Watson, R. W. Woody, R. V. Lewis, D. S. Bohle, A. H. Andreotti, and K. W. Miller, Conformational changes in pediocin AcH upon vesicle binding, and the approximation of the membrane-bound structure in detergent vesicles, Biochemistry 40, 14037-14046 (2001).

N. Sreerama, S. Yu. Venyaminov, and R. W. Woody, Analysis of protein CD spectra based on the tertiary structure classification, Anal. Biochem. 299, 271-274 (2001).

T. C. Mou, N. Sreerama, T. C. Terwilliger, R. W. Woody, and D. M. Gray, Independent tyrosyl contributions to the CD of Ff gene 5 protein and the distinctive effects of Y41H and Y41F mutants on protein-protein cooperative interactions, Protein Sci. 11, 601-613 (2002).

C. Kiefl, N. Sreerama, R. Haddad, L. Sun, W. Jentzen, Y. Lu, Y. Qiu, J. A. Shelnutt, and R. W. Woody, Heme distortions in sperm-whale carbonmonoxy myoglobin: Correlations between rotational strengths and heme distortions in MD-generated structures, J. Am. Chem. Soc. 124, 3385-3394 (2002).

D. E. Kamen and R. W. Woody, The folding kinetics of the protein pectate lyase C reveal fast-forming intermediates and slow proline isomerization, Biochemistry 41, 4713-4723 (2002).

D. E. Kamen and R. W. Woody, Identification of proline residues responsible for the slow folding kinetics in pectate lyase C by mutagenesis, Biochemistry 41, 4724-4732 (2002).

R. W. Woody, C. Kiefl, N. Sreerama, Y. Liu, Y. Qiu, and J. A. Shelnutt, Molecular dynamics simulations of carbonmonoxy myoglobin and calculations of heme circular dichroism, in Insulin and Related Proteins - from Structure to Function and Pharmacology, M. Federwisch, M. L. Dieken, and P. De Meyts, eds., Kluwer Academic Publishers, Dordrecht, The Netherlands, pp. 233-248 (2002).

Z. Shi, R. W. Woody, and N. R. Kallenbach, Is polyproline II a major backbone conformation in unfolded proteins?, Adv. Protein Chem. 62, 163-240 (2002).

D.-H. Chin, R. W. Woody, C. A. Rohl, and R. L. Baldwin, Helix propagation behavior and circular dichroism spectra of short prenucleated alanine helices, Proc. Natl. Acad. Sci. USA 99, 15416-15421 (2002).

R. W. Woody and A. Koslowski, Recent developments in the electronic spectroscopy of amides and alpha-helical polypeptides, Biophys. Chem. 101-102, 535-551 (2002).

R. W. Woody, Circular dichroism, in Synthesis of Peptides and Peptidomimetics, M. Goodman, A. Felix, L. Moroder, and C. Toniolo, eds., vol. E22a, Houben-Weyl Methods of Organic Chemistry, Georg Thieme Verlag, Stuttgart, pp. 739-765 (2002).

N. Sreerama and R. W. Woody, Structural composition of beta I and beta II proteins, Protein Sci. 12, 384-388 (2003).

G. Pescitelli, S. Gabriel, Y. Wang, J. Fleischhauer, R. W. Woody, and N. Berova, Theoretical analysis of the porphyrin-porphyrin exciton interaction in CD spectra of dimeric tetraarylporphyins, J. Am. Chem. Soc. 125, 7613-7628 (2003).

A-Y. M. Woody and R. W. Woody, Individual tyrosine side-chain contributions to the circular dichroism of ribonuclease A, Biopolymers (BioSpectroscopy) 72, 500-512 (2003).

N. Sreerama and R. W. Woody, On the analysis of membrane protein circular dichroism spectra, Protein Sci. 13, 100-112 (2004).

R. W. Woody, The circular dichroism of protein folding intermediates, Meth. Enzymol. 380, 242-285 (2004).

N. Sreerama and R. W. Woody, Computation and analysis of protein circular dichroism spectra, Meth. Enzymol. 383, 318-351 (2004).

Z. Liu, K. Chen, A. Ng, Z. Shi, R. W. Woody, and N. R. Kallenbach, Solvent dependence of PII conformation in model alanine peptides, J. Am. Chem. Soc. 126, 15141-15150 (2004).

R. W. Woody, The exciton model and the circular dichroism of polypeptides, Monatsh. Chem. 136, 347-366 (2005).

I. Gokce, R. W. Woody, G. Anderluh, and J. H. Lakey, Single peptide bonds exhibit poly(Pro)II (random coil) circular dichroism spectra, J. Am. Chem. Soc. 127, 9700-9701 (2005).

R. W. Woody, Heme-heme interactions in tetramers and dimers of hemoglobin subunits -- DeVoe theory calculations, Chirality 17, 450-455 (2005).

J. C. Hansen, X. Lu, E. D. Ross, and R. W. Woody, Intrinsic protein disorder, amino acid composition, and the histone terminal domains, J. Biol. Chem. 281, 1853-1857 (2006).

S. Jang, N. Sreerama, V. H.-C. Liao, S.-F. Lu, F.-Y. Li, S. Shin, R. W. Woody, and S.-H. Lin, Theoretical investigation of the photo-initiated folding of HP-36, Protein Sci. 15, 2290-2299 (2006).

L. Settimo, S. Donnini, A. H. Juffer, R. W. Woody, and O. Mariano, Conformational changes upon calcium binding and phosphorylation in a synthetic fragment of calmodulin, Pept. Sci. 88, 373-385 (2007).

M. A. Khan, C. Neale, C. Michaux, R. Pomés, G. G. Privé, R. W. Woody, and R. E. Bishop, Gauging a hydrocarbon ruler by an intrinsic exciton probe, Biochemistry 46, 4565-4579 (2007).