Rina Dukor - Academia.edu (original) (raw)
Papers by Rina Dukor
Science Access, 2004
A new scattered circular polarization (SCP) Raman optical activity (ROA) fast Raman spectrometer ... more A new scattered circular polarization (SCP) Raman optical activity (ROA) fast Raman spectrometer has been designed and constructed with the coordinated efforts of many of those who have designed and built ROA spectrometers in recent years. Examples of spectra collected with this nstrument, ranging from small molecules to proteins and viruses will be presented and discussed. i A new scattered circular polarization (SCP) Raman optical activity (ROA) has been designed and constructed with the coordinated efforts of many of those who have designed and built ROA spectrometers in recent years. The SCP-ROA spectra are measured by introducing completely unpolarized laser radiation at the sample and measuring the difference in intensity of right circularly polarized (RCP) versus left circularly polarized (LCP) Raman scattering.[1] The design is based closely on papers published in recent years for the novel instrumental layout [2] and elimination of interfering offset intensities.[3] A key f...
Journal of Biological Chemistry, 1990
for their ability to teach research methods and statistics in a way that was relatable and applic... more for their ability to teach research methods and statistics in a way that was relatable and applicable to our own projects. Many thanks to Ms. Teri Simpson and Ms. Ruth Tilden for giving me the opportunity to round out my doctoral training with classroom experience by teaching field seminars. Plus, your kindness and encouragement helped me realize why I was working toward a Ph.D. in the first place! I would especially like to thank those who have been part of my committee, particularly to mention the immense appreciation and gratefulness I have for Dr. Lisa Rapp-McCall, without whom I would not be at this point now. Your leadership and expertise in the juvenile justice field gave me opportunities that have yet to even be realized. Your patient, thoughtful critique and feedback of my work helped me regain my confidence and to keep pressing forward. I really appreciate your commitment to teaching and research and I hope to keep learning from you. Thank you so much! Dr. Anne Strozier, I will always remember and be forever appreciative to you for the opportunity as a new social work researcher to see how "real" research is conducted. You have also been enormously patient as I moved through this long process, but throughout it all, your unflagging encouragement and support has meant so much. Thank you for believing in me from the beginning! Dr. Mario Hernandez, I am so thankful to you for agreeing to be part of my committee! You have many, many other responsibilities and obligations, but yet you took the time to talk to me, offer guidance and provide resources. I really appreciate your kindness and generosity. Lastly, Dr. David Kondrat… words can't adequately express my gratitude for you! You guided me through the most nerve-wracking part of this process in the midst of major changes within your own life with extreme calm, patience and encouragement. Your statistical prowess helped win the day and you showed me an exciting future of research and teaching that I could not imagine before. Thank you for everything! Along the way, I have also benefitted from the mentorship and friendship of Dr. Pam Alvarez. You already know how much you mean to me and my personal life and professional career would not be where it is today without you. Thank you for giving me opportunities to grow and tackle challenges that allow me to be a credible social work leader and scholar. But more importantly, thank you for the chance to work at Bay Area Youth Services, Inc. This gave me insight to an interesting research topic and access to a group of dynamic Juvenile Justice Service Professionals whose willingness to participate made this study possible.
Chirality, 2017
Supramolecular chirality of amyloid fibrils, protein aggregates related to many neurodegenerative... more Supramolecular chirality of amyloid fibrils, protein aggregates related to many neurodegenerative diseases, is a remarkable property associated with fibril structure and polymorphism. Since its discovery almost 10 years ago there is still little understanding of this phenomenon, including the cause of the highly enhanced vibrational circular dichroism (VCD) intensity arising from fibril supramolecular chirality. In this study, VCD spectra, enhanced by filament supramolecular chirality, are presented for lysozyme and insulin fibrils above and below pH 2 and after deuterium exchange, above and below pD 2. Supramolecular chirality (observed by VCD) and fibril morphology (documented by atomic force microscopy) are not affected by protein deuteriation. In D 2 O the fibril VCD sign pattern changes to fewer bands, with implications for the amide I/II origin of enhanced VCD intensity. Separation of amide I and II signals will facilitate calculations of enhanced VCD spectra of amyloid fibrils and enable a better understanding of the origin of the VCD sign pattern.
Bba Protein Struct Mol Enzym, 2000
Chirality, Jan 4, 2016
Searching the 3D structural fragments of organic molecules is challenging because of structural d... more Searching the 3D structural fragments of organic molecules is challenging because of structural differences between X-ray and theoretically calculated geometries and the conformational flexibility of substituents. The codification program called Conformational Code for Organic Molecules (CCOM) can be used to unambiguously convert 3D conformational data for various molecules to 1D data. Two deviations from Rule E-5.6 of the International Union of Pure and Applied Chemistry (IUPAC) Rules for Nomenclature of Organic Chemistry were introduced to the CCOM program for 3D fragment searching. First, the search for the highest priority atom was limited to a distance of two bonds from the center bond for dihedral angle determination. Second, for indistinguishable atoms in experimentally observed solution structures, the smallest number of atom index in the molecular model was chosen as the priority atom for dihedral angle determination. A search of the 3D conformational fragment mb_3a6c4c of ...
Angewandte Chemie (International ed. in English), Jan 22, 2015
Inorganic nanomaterials endowed with hierarchical chirality could open new horizons in physical t... more Inorganic nanomaterials endowed with hierarchical chirality could open new horizons in physical theory and applications because of their fascinating properties. Here, we report chiral ZnO films coated on quartz substrates with a hierarchical nanostructure ranging from atomic to micrometer scale. Three levels of hierarchical chirality exist in the ZnO films: helical ZnO crystalline structures that form primary helically coiled nanoplates, secondary helical stacking of these nanoplates, and tertiary nanoscale circinate aggregates formed by several stacked nanoplates. These films exhibited optical activity (OA) at 380 nm and in the range of 200-800 nm and created circularly polarized luminescence centered at 510 nm and Raman OA at 50-1400 cm(-1) , which was attributed to electronic transitions, scattering, photoluminescent emission, and Raman scattering in a dissymmetric electric field. The unprecedented strong OA could be attributed to multiple light scattering and absorption-enhanced...
The sensitivity of vibrational optical activity (VOA) to long-range chirality in molecular struct... more The sensitivity of vibrational optical activity (VOA) to long-range chirality in molecular structures is of considerable interest both for the properties of the systems investigated and for an understanding of the origin and theoretical basis of VOA intensities that are over an order of magnitude larger than typical VOA intensities. After reviewing the various classes of enhanced VOA, two areas of novel interest will be described in more detail. The first is intense VCD associated with the formation and growth of protein fibrils which is of importance due to the association of protein fibrils in the development of neurodegenerative diseases. Enhanced VCD of similar, signs, intensities and frequencies have been observed for fibrils of lysozyme and insulin prepared by heating pH 2 solutions [1]. The growth of fibrils can be followed by VCD yielding spectra related to the development of supramolecular structural chirality, or braiding, in protein fibril assemblies. Sign reversal of thi...
Determination of the absolute configuration (AC) of chiral molecules is of great importance. Enan... more Determination of the absolute configuration (AC) of chiral molecules is of great importance. Enantiomers of chiral drugs, for instance, can have significantly different biological and pharmacological properties. Chirality can be determined using the vibrational optical activity (VOA) of molecules in solution. VOA is the differential absorbance intensity to left vs. right circularly polarized radiation during vibrational transition. Vibrational circular dichroism (VCD) measures the difference in IR absorption, while Raman optical activity (ROA) is a corresponding difference in intensity of Raman scattered light. Both methods are used for many types of analysis related to the structure and conformations of molecules of biological interest. Unlike other techniques for AC assignments, VCD and ROA require no crystallization, no foreign additive or chemical modification of the sample, nor any physical separation of the enantiomers. We will demonstrate examples of the use of VCD for solvin...
Biomolecular Spectroscopy, 1989
... Authors: Keiderling, Timothy A.; Yasui, Sritana C.; Pancoska, Petr; Dukor, RK; Yang, L. Affil... more ... Authors: Keiderling, Timothy A.; Yasui, Sritana C.; Pancoska, Petr; Dukor, RK; Yang, L. Affiliation: AA(Univ. of Illinois/Chicago). Publication: Proc. SPIE Vol. 1057, p. 7, Biomolecular Spectroscopy, Robert R. Birge; Henry H. Mantsch; Eds. Publication Date: 05/1989. Origin: SPIE. ...
7th Intl Conf on Fourier Transform Spectroscopy, 1989
ABSTRACT
ABSTRACT The structure of a plasma proteinase inhibitor alpha2-Macroglobulin (alpha2m) is determi... more ABSTRACT The structure of a plasma proteinase inhibitor alpha2-Macroglobulin (alpha2m) is determined by FTIR spectroscopy and a number of sequence-structure prediction algorithms. In addition, alpha2M dimers and complexes with methylamine and trypsin are examined. Our FTIR results estimate a helix content of 5-15% and a beta-sheet content of 28-36%. None of the sequence prediction algorithms used in this study predicted values close to experimental data. Considerable differences in the FTIR spectra of alpha2M dimer are observed and somewhat smaller changes are seen upon reaction of alpha2M with methylamine and dithiodipyridine (DTP).
Science Access, 2004
A new scattered circular polarization (SCP) Raman optical activity (ROA) fast Raman spectrometer ... more A new scattered circular polarization (SCP) Raman optical activity (ROA) fast Raman spectrometer has been designed and constructed with the coordinated efforts of many of those who have designed and built ROA spectrometers in recent years. Examples of spectra collected with this nstrument, ranging from small molecules to proteins and viruses will be presented and discussed. i A new scattered circular polarization (SCP) Raman optical activity (ROA) has been designed and constructed with the coordinated efforts of many of those who have designed and built ROA spectrometers in recent years. The SCP-ROA spectra are measured by introducing completely unpolarized laser radiation at the sample and measuring the difference in intensity of right circularly polarized (RCP) versus left circularly polarized (LCP) Raman scattering.[1] The design is based closely on papers published in recent years for the novel instrumental layout [2] and elimination of interfering offset intensities.[3] A key f...
Journal of Biological Chemistry, 1990
for their ability to teach research methods and statistics in a way that was relatable and applic... more for their ability to teach research methods and statistics in a way that was relatable and applicable to our own projects. Many thanks to Ms. Teri Simpson and Ms. Ruth Tilden for giving me the opportunity to round out my doctoral training with classroom experience by teaching field seminars. Plus, your kindness and encouragement helped me realize why I was working toward a Ph.D. in the first place! I would especially like to thank those who have been part of my committee, particularly to mention the immense appreciation and gratefulness I have for Dr. Lisa Rapp-McCall, without whom I would not be at this point now. Your leadership and expertise in the juvenile justice field gave me opportunities that have yet to even be realized. Your patient, thoughtful critique and feedback of my work helped me regain my confidence and to keep pressing forward. I really appreciate your commitment to teaching and research and I hope to keep learning from you. Thank you so much! Dr. Anne Strozier, I will always remember and be forever appreciative to you for the opportunity as a new social work researcher to see how "real" research is conducted. You have also been enormously patient as I moved through this long process, but throughout it all, your unflagging encouragement and support has meant so much. Thank you for believing in me from the beginning! Dr. Mario Hernandez, I am so thankful to you for agreeing to be part of my committee! You have many, many other responsibilities and obligations, but yet you took the time to talk to me, offer guidance and provide resources. I really appreciate your kindness and generosity. Lastly, Dr. David Kondrat… words can't adequately express my gratitude for you! You guided me through the most nerve-wracking part of this process in the midst of major changes within your own life with extreme calm, patience and encouragement. Your statistical prowess helped win the day and you showed me an exciting future of research and teaching that I could not imagine before. Thank you for everything! Along the way, I have also benefitted from the mentorship and friendship of Dr. Pam Alvarez. You already know how much you mean to me and my personal life and professional career would not be where it is today without you. Thank you for giving me opportunities to grow and tackle challenges that allow me to be a credible social work leader and scholar. But more importantly, thank you for the chance to work at Bay Area Youth Services, Inc. This gave me insight to an interesting research topic and access to a group of dynamic Juvenile Justice Service Professionals whose willingness to participate made this study possible.
Chirality, 2017
Supramolecular chirality of amyloid fibrils, protein aggregates related to many neurodegenerative... more Supramolecular chirality of amyloid fibrils, protein aggregates related to many neurodegenerative diseases, is a remarkable property associated with fibril structure and polymorphism. Since its discovery almost 10 years ago there is still little understanding of this phenomenon, including the cause of the highly enhanced vibrational circular dichroism (VCD) intensity arising from fibril supramolecular chirality. In this study, VCD spectra, enhanced by filament supramolecular chirality, are presented for lysozyme and insulin fibrils above and below pH 2 and after deuterium exchange, above and below pD 2. Supramolecular chirality (observed by VCD) and fibril morphology (documented by atomic force microscopy) are not affected by protein deuteriation. In D 2 O the fibril VCD sign pattern changes to fewer bands, with implications for the amide I/II origin of enhanced VCD intensity. Separation of amide I and II signals will facilitate calculations of enhanced VCD spectra of amyloid fibrils and enable a better understanding of the origin of the VCD sign pattern.
Bba Protein Struct Mol Enzym, 2000
Chirality, Jan 4, 2016
Searching the 3D structural fragments of organic molecules is challenging because of structural d... more Searching the 3D structural fragments of organic molecules is challenging because of structural differences between X-ray and theoretically calculated geometries and the conformational flexibility of substituents. The codification program called Conformational Code for Organic Molecules (CCOM) can be used to unambiguously convert 3D conformational data for various molecules to 1D data. Two deviations from Rule E-5.6 of the International Union of Pure and Applied Chemistry (IUPAC) Rules for Nomenclature of Organic Chemistry were introduced to the CCOM program for 3D fragment searching. First, the search for the highest priority atom was limited to a distance of two bonds from the center bond for dihedral angle determination. Second, for indistinguishable atoms in experimentally observed solution structures, the smallest number of atom index in the molecular model was chosen as the priority atom for dihedral angle determination. A search of the 3D conformational fragment mb_3a6c4c of ...
Angewandte Chemie (International ed. in English), Jan 22, 2015
Inorganic nanomaterials endowed with hierarchical chirality could open new horizons in physical t... more Inorganic nanomaterials endowed with hierarchical chirality could open new horizons in physical theory and applications because of their fascinating properties. Here, we report chiral ZnO films coated on quartz substrates with a hierarchical nanostructure ranging from atomic to micrometer scale. Three levels of hierarchical chirality exist in the ZnO films: helical ZnO crystalline structures that form primary helically coiled nanoplates, secondary helical stacking of these nanoplates, and tertiary nanoscale circinate aggregates formed by several stacked nanoplates. These films exhibited optical activity (OA) at 380 nm and in the range of 200-800 nm and created circularly polarized luminescence centered at 510 nm and Raman OA at 50-1400 cm(-1) , which was attributed to electronic transitions, scattering, photoluminescent emission, and Raman scattering in a dissymmetric electric field. The unprecedented strong OA could be attributed to multiple light scattering and absorption-enhanced...
The sensitivity of vibrational optical activity (VOA) to long-range chirality in molecular struct... more The sensitivity of vibrational optical activity (VOA) to long-range chirality in molecular structures is of considerable interest both for the properties of the systems investigated and for an understanding of the origin and theoretical basis of VOA intensities that are over an order of magnitude larger than typical VOA intensities. After reviewing the various classes of enhanced VOA, two areas of novel interest will be described in more detail. The first is intense VCD associated with the formation and growth of protein fibrils which is of importance due to the association of protein fibrils in the development of neurodegenerative diseases. Enhanced VCD of similar, signs, intensities and frequencies have been observed for fibrils of lysozyme and insulin prepared by heating pH 2 solutions [1]. The growth of fibrils can be followed by VCD yielding spectra related to the development of supramolecular structural chirality, or braiding, in protein fibril assemblies. Sign reversal of thi...
Determination of the absolute configuration (AC) of chiral molecules is of great importance. Enan... more Determination of the absolute configuration (AC) of chiral molecules is of great importance. Enantiomers of chiral drugs, for instance, can have significantly different biological and pharmacological properties. Chirality can be determined using the vibrational optical activity (VOA) of molecules in solution. VOA is the differential absorbance intensity to left vs. right circularly polarized radiation during vibrational transition. Vibrational circular dichroism (VCD) measures the difference in IR absorption, while Raman optical activity (ROA) is a corresponding difference in intensity of Raman scattered light. Both methods are used for many types of analysis related to the structure and conformations of molecules of biological interest. Unlike other techniques for AC assignments, VCD and ROA require no crystallization, no foreign additive or chemical modification of the sample, nor any physical separation of the enantiomers. We will demonstrate examples of the use of VCD for solvin...
Biomolecular Spectroscopy, 1989
... Authors: Keiderling, Timothy A.; Yasui, Sritana C.; Pancoska, Petr; Dukor, RK; Yang, L. Affil... more ... Authors: Keiderling, Timothy A.; Yasui, Sritana C.; Pancoska, Petr; Dukor, RK; Yang, L. Affiliation: AA(Univ. of Illinois/Chicago). Publication: Proc. SPIE Vol. 1057, p. 7, Biomolecular Spectroscopy, Robert R. Birge; Henry H. Mantsch; Eds. Publication Date: 05/1989. Origin: SPIE. ...
7th Intl Conf on Fourier Transform Spectroscopy, 1989
ABSTRACT
ABSTRACT The structure of a plasma proteinase inhibitor alpha2-Macroglobulin (alpha2m) is determi... more ABSTRACT The structure of a plasma proteinase inhibitor alpha2-Macroglobulin (alpha2m) is determined by FTIR spectroscopy and a number of sequence-structure prediction algorithms. In addition, alpha2M dimers and complexes with methylamine and trypsin are examined. Our FTIR results estimate a helix content of 5-15% and a beta-sheet content of 28-36%. None of the sequence prediction algorithms used in this study predicted values close to experimental data. Considerable differences in the FTIR spectra of alpha2M dimer are observed and somewhat smaller changes are seen upon reaction of alpha2M with methylamine and dithiodipyridine (DTP).