Biochemical and Clinical Aspects of Hemoglobin Abnormalities, 1978
Circular dichroism (CD) is a spectroscopic technique which is highly sensitive to stereochemical ... more Circular dichroism (CD) is a spectroscopic technique which is highly sensitive to stereochemical details of protein structure. CD has been used to probe three different levels of structure in normal and abnormal hemoglobins: (a) the folding of the polypeptide chain, which is reflected in the CD below 250 nm; (b) the environment of aromatic side-chains, as seen in the 280 nm region; (c) the environment of the heme, which affects the CD bands in the near infrared, visible and near ultraviolet. Of these, the latter two have proven most useful in probing conformational changes in hemoglobin. For example, Perutz and co-workers have used a band near 285 nm as an indicator of R vs. T conformation. Correlations have also been suggested between quaternary structure and the CD of the Soret band. These correlations are critically discussed in the light of experimental and theoretical CD studies. CD studies of abnormal hemoglobins are reviewed and the potential for further work indicated.
Bovine microtubule protein preparations have been examined by proton nuclear magnetic resonance (... more Bovine microtubule protein preparations have been examined by proton nuclear magnetic resonance (1H NMR) spectroscopy at 270 MHz. Sharp resonances have been identified as deriving from microtubule-associated proteins. These resonances persist after self-assembly of microtubule protein. Brief tryptic treatment of assembled microtubules, specifically cleaving the microtubule-associated protein HMW2 (Mr = 270 000), releases the pendant portion of HMW2 (Mr = 240 000), three-quarters of which is in a flexible conformation. Isolated tau protein and HMW2 protein both show substantial flexibility; on recombination with tubulin dimer, tau shows considerable decrease in flexibility whereas HMW2 is unaffected. The observations may have important implications for the interactions between microtubules and other cytoskeletal structures.
Core and linker histones are the most abundant protein components of chromatin. Even though they ... more Core and linker histones are the most abundant protein components of chromatin. Even though they lack intrinsic structure, the N-terminal "tail" domains (NTDs) of the core histones and the C-terminal tail domain (CTD) of linker histones bind to many different macromolecular partners while functioning in chromatin. Here we discuss the underlying physicochemical basis for how the histone terminal domains can be disordered and yet specifically recognize and interact with different macromolecules. The relationship between intrinsic disorder and amino acid composition is emphasized. We also discuss the potential structural consequences of acetylation and methylation of lysine residues embedded in intrinsically disordered histone tail domains.
Proceedings of the National Academy of Sciences, 1989
We have examined the secondary structures of human class I and class II histocompatibility antige... more We have examined the secondary structures of human class I and class II histocompatibility antigens in solution by Fourier transform infrared spectroscopy and circular dichroism in order to compare the relative amounts of alpha-helix, beta-sheet, and other structures, which are crucial elements in the comparison of the protein structures. Quantitation of infrared spectra of papain-solubilized HLA-A2, HLA-B7, and DR1 in phosphate buffer gave alpha-helix contents of 17%, 8%, and 10% and beta-sheet contents of 41%, 48%, and 53%, respectively. By circular dichroism, papain-solubilized HLA-A2, HLA-B7, and DR1 were also found to have comparable alpha-helix contents (e.g., 8%, 20%, and 17%, respectively). Circular dichroism analysis for beta-sheet gave 29% for papain-solubilized HLA-B7 and 42% for papain-solubilized DR1. The value for papain-solubilized HLA-A2 (74%) was anomalous. It is proposed that Trp-107 of HLA-A2, missing in both HLA-B7 and DR1, may be responsible for much of the anom...
In the solid state, the conformation of N-actetylprolinamide is stabilized by two intermolecular ... more In the solid state, the conformation of N-actetylprolinamide is stabilized by two intermolecular O···H bridges and one intramolecular N···H hydrogen bond. According to quantum chemical ab initio calculations with the 6-31+G* basis set at the one-determinant level, the intramolecular N ···H bond is not strong enough to maintain the solid-state molecular conformation the gas phase. The conformational changes predominantly consist in a rotation of the amide group about its C-C bond to the proline ring, resulting in a c/s-like conformation which is stabilized by a presumably stronger intramolecular O···H bond between one hydrogen atom of the NH These confirmational changes cause a reduction of the molecular dipole moment by about 50%, indicating that the conformation in solution might be strongly solvent dependent. While both the MINDO/3 and the MNDO method in their standard parametrizations fail to reproduce the ab initio results, the lattice effect is reproduced at least qualitatively...
8766-8770. Scott, TW, Friedman, J. M., Ikeda-Saito, M., & Yonetani, ... Shaanan, B. (1983) J. Mol... more 8766-8770. Scott, TW, Friedman, J. M., Ikeda-Saito, M., & Yonetani, ... Shaanan, B. (1983) J. Mol. Biol. 171, 31-59. Shibayama, N., Morimoto, H., & Kitagawa, T. (1986) J. Mol. Biol. 192, 331-336. Shibayama, N., Inubushi, T., Morimoto, H., & Yonetani, T. (1987) Biochemistry ...
Natural and synthetic peptides that contain detectable intramolecular α-helical structure in aque... more Natural and synthetic peptides that contain detectable intramolecular α-helical structure in aqueous solution have been used to evaluate the helical propensities for the common amino acids. Experimental spectroscopic data must be fit to a model of the helixcoil transition in order to determine ...
Biochemical and Clinical Aspects of Hemoglobin Abnormalities, 1978
Circular dichroism (CD) is a spectroscopic technique which is highly sensitive to stereochemical ... more Circular dichroism (CD) is a spectroscopic technique which is highly sensitive to stereochemical details of protein structure. CD has been used to probe three different levels of structure in normal and abnormal hemoglobins: (a) the folding of the polypeptide chain, which is reflected in the CD below 250 nm; (b) the environment of aromatic side-chains, as seen in the 280 nm region; (c) the environment of the heme, which affects the CD bands in the near infrared, visible and near ultraviolet. Of these, the latter two have proven most useful in probing conformational changes in hemoglobin. For example, Perutz and co-workers have used a band near 285 nm as an indicator of R vs. T conformation. Correlations have also been suggested between quaternary structure and the CD of the Soret band. These correlations are critically discussed in the light of experimental and theoretical CD studies. CD studies of abnormal hemoglobins are reviewed and the potential for further work indicated.
Bovine microtubule protein preparations have been examined by proton nuclear magnetic resonance (... more Bovine microtubule protein preparations have been examined by proton nuclear magnetic resonance (1H NMR) spectroscopy at 270 MHz. Sharp resonances have been identified as deriving from microtubule-associated proteins. These resonances persist after self-assembly of microtubule protein. Brief tryptic treatment of assembled microtubules, specifically cleaving the microtubule-associated protein HMW2 (Mr = 270 000), releases the pendant portion of HMW2 (Mr = 240 000), three-quarters of which is in a flexible conformation. Isolated tau protein and HMW2 protein both show substantial flexibility; on recombination with tubulin dimer, tau shows considerable decrease in flexibility whereas HMW2 is unaffected. The observations may have important implications for the interactions between microtubules and other cytoskeletal structures.
Core and linker histones are the most abundant protein components of chromatin. Even though they ... more Core and linker histones are the most abundant protein components of chromatin. Even though they lack intrinsic structure, the N-terminal "tail" domains (NTDs) of the core histones and the C-terminal tail domain (CTD) of linker histones bind to many different macromolecular partners while functioning in chromatin. Here we discuss the underlying physicochemical basis for how the histone terminal domains can be disordered and yet specifically recognize and interact with different macromolecules. The relationship between intrinsic disorder and amino acid composition is emphasized. We also discuss the potential structural consequences of acetylation and methylation of lysine residues embedded in intrinsically disordered histone tail domains.
Proceedings of the National Academy of Sciences, 1989
We have examined the secondary structures of human class I and class II histocompatibility antige... more We have examined the secondary structures of human class I and class II histocompatibility antigens in solution by Fourier transform infrared spectroscopy and circular dichroism in order to compare the relative amounts of alpha-helix, beta-sheet, and other structures, which are crucial elements in the comparison of the protein structures. Quantitation of infrared spectra of papain-solubilized HLA-A2, HLA-B7, and DR1 in phosphate buffer gave alpha-helix contents of 17%, 8%, and 10% and beta-sheet contents of 41%, 48%, and 53%, respectively. By circular dichroism, papain-solubilized HLA-A2, HLA-B7, and DR1 were also found to have comparable alpha-helix contents (e.g., 8%, 20%, and 17%, respectively). Circular dichroism analysis for beta-sheet gave 29% for papain-solubilized HLA-B7 and 42% for papain-solubilized DR1. The value for papain-solubilized HLA-A2 (74%) was anomalous. It is proposed that Trp-107 of HLA-A2, missing in both HLA-B7 and DR1, may be responsible for much of the anom...
In the solid state, the conformation of N-actetylprolinamide is stabilized by two intermolecular ... more In the solid state, the conformation of N-actetylprolinamide is stabilized by two intermolecular O···H bridges and one intramolecular N···H hydrogen bond. According to quantum chemical ab initio calculations with the 6-31+G* basis set at the one-determinant level, the intramolecular N ···H bond is not strong enough to maintain the solid-state molecular conformation the gas phase. The conformational changes predominantly consist in a rotation of the amide group about its C-C bond to the proline ring, resulting in a c/s-like conformation which is stabilized by a presumably stronger intramolecular O···H bond between one hydrogen atom of the NH These confirmational changes cause a reduction of the molecular dipole moment by about 50%, indicating that the conformation in solution might be strongly solvent dependent. While both the MINDO/3 and the MNDO method in their standard parametrizations fail to reproduce the ab initio results, the lattice effect is reproduced at least qualitatively...
8766-8770. Scott, TW, Friedman, J. M., Ikeda-Saito, M., & Yonetani, ... Shaanan, B. (1983) J. Mol... more 8766-8770. Scott, TW, Friedman, J. M., Ikeda-Saito, M., & Yonetani, ... Shaanan, B. (1983) J. Mol. Biol. 171, 31-59. Shibayama, N., Morimoto, H., & Kitagawa, T. (1986) J. Mol. Biol. 192, 331-336. Shibayama, N., Inubushi, T., Morimoto, H., & Yonetani, T. (1987) Biochemistry ...
Natural and synthetic peptides that contain detectable intramolecular α-helical structure in aque... more Natural and synthetic peptides that contain detectable intramolecular α-helical structure in aqueous solution have been used to evaluate the helical propensities for the common amino acids. Experimental spectroscopic data must be fit to a model of the helixcoil transition in order to determine ...
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Papers by Robert Woody