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Characterizing Dynamics of DNA Binding Proteins; p53 and DinB Homolog Polymerase (Dbh)- [electronic resource]
Characterizing Dynamics of DNA Binding Proteins; p53 and DinB Homolog Polymerase (Dbh)- [electronic resource]
상세정보
- 자료유형
- 학위논문파일 국외
- 최종처리일시
- 20240214101910
- ISBN
- 9798380858519
- DDC
- 574.191
- 저자명
- Soto, Jenaro.
- 서명/저자
- Characterizing Dynamics of DNA Binding Proteins; p53 and DinB Homolog Polymerase (Dbh) - [electronic resource]
- 발행사항
- [S.l.]: : University of California, Irvine., 2023
- 발행사항
- Ann Arbor : : ProQuest Dissertations & Theses,, 2023
- 형태사항
- 1 online resource(125 p.)
- 주기사항
- Source: Dissertations Abstracts International, Volume: 85-05, Section: B.
- 주기사항
- Advisor: Cocco, Melanie.
- 학위논문주기
- Thesis (Ph.D.)--University of California, Irvine, 2023.
- 사용제한주기
- This item must not be sold to any third party vendors.
- 초록/해제
- 요약Solution state NMR was used to study two DNA-binding proteins. Chapter one covers the different NMR techniques used, including hydrogen exchange, relaxation, chemical shift analysis, and temperature coefficients. In addition, I also implement circular dichroism and protein sequence analysis to supplement the NMR studies. Chapter two covers the p53 project, in which we compare protein dynamics between WT and rescue mutants to understand the mechanism of stabilization. We measured and compared dynamics from NMR hydrogen exchange rates of backbone amides and find that both rescue mutants impose a global stabilizing effect that dampens their motions in the beta-sandwich compared to WT DBD. We also compared NMR relaxation results to obtain flexibility information in the ps to ns timescale regime. Chapter three covers the dynamics of the DinB homolog polymerase (Dbh). This polymerase belongs to the Y-family of translesion DNA polymerases that can synthesize using a damaged DNA template. Since Dbh comes from the thermophilic archaeon Sulfolobus acidocaldarius, it is capable of functioning in a wide range of temperatures. Here we use NMR and circular dichroism to understand how the structure and dynamics of Dbh are affected by temperature (2-65°C) magnesium and manganese. HX reveals that both the thumb and finger domains are very dynamic relative to the palm and LF domains. These trends remain true at high temperatures with dynamics increasing as temperatures increase from 35 °C to 50 °C. Notably, NMR and CD spectra show that Dbh tertiary structure cold denatures beginning at 25 °C and increasing in denaturation as the temperature is lowered to 5 °C with little change observed by CD. Chemical shift perturbation analysis in the presence and absence of magnesium and manganese reveals three ion binding sites, even in the absence of DNA.
- 일반주제명
- Biophysics.
- 일반주제명
- Biology.
- 일반주제명
- Pharmaceutical sciences.
- 키워드
- NMR
- 키워드
- Protein dynamics
- 기타저자
- University of California, Irvine Pharmacological Sciences
- 기본자료저록
- Dissertations Abstracts International. 85-05B.
- 기본자료저록
- Dissertation Abstract International
- 전자적 위치 및 접속
- 로그인 후 원문을 볼 수 있습니다.
MARC
008240612s2023 us |||||||||||||||c||eng d■001000016935252
■00520240214101910
■006m o d
■007cr#unu||||||||
■020 ▼a9798380858519
■035 ▼a(MiAaPQ)AAI30686682
■040 ▼aMiAaPQ▼cMiAaPQ
■0820 ▼a574.191
■1001 ▼aSoto, Jenaro.
■24510▼aCharacterizing Dynamics of DNA Binding Proteins; p53 and DinB Homolog Polymerase (Dbh)▼h[electronic resource]
■260 ▼a[S.l.]:▼bUniversity of California, Irvine. ▼c2023
■260 1▼aAnn Arbor :▼bProQuest Dissertations & Theses, ▼c2023
■300 ▼a1 online resource(125 p.)
■500 ▼aSource: Dissertations Abstracts International, Volume: 85-05, Section: B.
■500 ▼aAdvisor: Cocco, Melanie.
■5021 ▼aThesis (Ph.D.)--University of California, Irvine, 2023.
■506 ▼aThis item must not be sold to any third party vendors.
■520 ▼aSolution state NMR was used to study two DNA-binding proteins. Chapter one covers the different NMR techniques used, including hydrogen exchange, relaxation, chemical shift analysis, and temperature coefficients. In addition, I also implement circular dichroism and protein sequence analysis to supplement the NMR studies. Chapter two covers the p53 project, in which we compare protein dynamics between WT and rescue mutants to understand the mechanism of stabilization. We measured and compared dynamics from NMR hydrogen exchange rates of backbone amides and find that both rescue mutants impose a global stabilizing effect that dampens their motions in the beta-sandwich compared to WT DBD. We also compared NMR relaxation results to obtain flexibility information in the ps to ns timescale regime. Chapter three covers the dynamics of the DinB homolog polymerase (Dbh). This polymerase belongs to the Y-family of translesion DNA polymerases that can synthesize using a damaged DNA template. Since Dbh comes from the thermophilic archaeon Sulfolobus acidocaldarius, it is capable of functioning in a wide range of temperatures. Here we use NMR and circular dichroism to understand how the structure and dynamics of Dbh are affected by temperature (2-65°C) magnesium and manganese. HX reveals that both the thumb and finger domains are very dynamic relative to the palm and LF domains. These trends remain true at high temperatures with dynamics increasing as temperatures increase from 35 °C to 50 °C. Notably, NMR and CD spectra show that Dbh tertiary structure cold denatures beginning at 25 °C and increasing in denaturation as the temperature is lowered to 5 °C with little change observed by CD. Chemical shift perturbation analysis in the presence and absence of magnesium and manganese reveals three ion binding sites, even in the absence of DNA.
■590 ▼aSchool code: 0030.
■650 4▼aBiophysics.
■650 4▼aBiology.
■650 4▼aPharmaceutical sciences.
■653 ▼aDinB homolog polymerase
■653 ▼aHydrogen exchange
■653 ▼aNMR
■653 ▼aDNA binding domain
■653 ▼aProtein dynamics
■653 ▼aTemperature coefficients
■690 ▼a0786
■690 ▼a0306
■690 ▼a0572
■71020▼aUniversity of California, Irvine▼bPharmacological Sciences.
■7730 ▼tDissertations Abstracts International▼g85-05B.
■773 ▼tDissertation Abstract International
■790 ▼a0030
■791 ▼aPh.D.
■792 ▼a2023
■793 ▼aEnglish
■85640▼uhttp://www.riss.kr/pdu/ddodLink.do?id=T16935252▼nKERIS▼z이 자료의 원문은 한국교육학술정보원에서 제공합니다.
■980 ▼a202402▼f2024
