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Modeling Dynamics and Conformational Ensembles of Biological Macromolecules With Time-Resolved X-Ray Scattering and Molecular Simulations
Modeling Dynamics and Conformational Ensembles of Biological Macromolecules With Time-Resolved X-Ray Scattering and Molecular Simulations
상세정보
- 자료유형
- 학위논문 서양
- 최종처리일시
- 20260202103045
- ISBN
- 9798315799191
- DDC
- 540
- 서명/저자
- Modeling Dynamics and Conformational Ensembles of Biological Macromolecules With Time-Resolved X-Ray Scattering and Molecular Simulations
- 발행사항
- [Sl] : Northwestern University, 2025
- 발행사항
- Ann Arbor : ProQuest Dissertations & Theses, 2025
- 형태사항
- 310 p
- 주기사항
- Source: Dissertations Abstracts International, Volume: 86-12, Section: B.
- 주기사항
- Advisor: Chen, Lin X.;Kohlstedt, Kevin L.
- 학위논문주기
- Thesis (Ph.D.)--Northwestern University, 2025.
- 초록/해제
- 요약The functionality of biomacromolecules (BMMs), such as proteins and nucleic acids, is intrinsically tied to their three-dimensional structures, which are dictated by a one- dimensional sequence of amino acids or nucleotides. Although the intrinsic forces driving this folding process have been well studied, our understanding of how environmental factors, such as pH and temperature, influence structure formation and dynamics remains incomplete.This work employs time-resolved X-ray solution scattering (TRXSS) and molecular simulations to provide insight into the structural dynamics and conformational ensembles following changes in temperature or pH. Chapter 1 provides an introduction to the importance of studying the structural dynamics of BMMs and the challenges present in extracting atomic-level information from ensemble-averaged measurements. Chapter 2 details the experimental and computational methodologies used in this work. Chapter 3 illustrates how the computational and experimental techniques discussed in Chapter 2 can be combined to study the response of BMMs to various environmental perturbations. Chapter 4 highlights how TRXSS results can bias molecular simulations to sample physically relevant structures. Chapter 5 showcases how enhanced sampling simulations can be coupled with a genetic algorithm to determine a heterogeneous set of conformations along unfolding pathways. Chapter 6 compares the dynamics and ensembles of Markov state models with TRXSS results. Chapter 7 introduces a merocyanine photoacid for TRXSS experiments that was used to induce the dissociation of double-stranded DNA into noncanonical structures. Finally, Chapter 8 provides a methodology for Multicanonical Monte Carlo Ensemble Growth that efficiently computes equilibrium thermodynamic properties for proteins. This work demonstrates how TRXSS and molecular simulations can be combined, underscoring the ideal applications for each use.
- 일반주제명
- Chemistry
- 일반주제명
- Physical chemistry
- 일반주제명
- Computational chemistry
- 일반주제명
- Biochemistry
- 일반주제명
- Genetics
- 키워드
- TRXSS
- 키워드
- Nucleotides
- 기타저자
- Northwestern University Chemistry
- 기본자료저록
- Dissertations Abstracts International. 86-12B.
- 전자적 위치 및 접속
- 로그인 후 원문을 볼 수 있습니다.
MARC
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■007cr#unu||||||||
■020 ▼a9798315799191
■035 ▼a(MiAaPQ)AAI31930790
■040 ▼aMiAaPQ▼cMiAaPQ
■0820 ▼a540
■1001 ▼aNijhawan, Adam Kumar.▼0(orcid)0000-0001-5527-1850
■24510▼aModeling Dynamics and Conformational Ensembles of Biological Macromolecules With Time-Resolved X-Ray Scattering and Molecular Simulations
■260 ▼a[Sl]▼bNorthwestern University▼c2025
■260 1▼aAnn Arbor▼bProQuest Dissertations & Theses▼c2025
■300 ▼a310 p
■500 ▼aSource: Dissertations Abstracts International, Volume: 86-12, Section: B.
■500 ▼aAdvisor: Chen, Lin X.;Kohlstedt, Kevin L.
■5021 ▼aThesis (Ph.D.)--Northwestern University, 2025.
■520 ▼aThe functionality of biomacromolecules (BMMs), such as proteins and nucleic acids, is intrinsically tied to their three-dimensional structures, which are dictated by a one- dimensional sequence of amino acids or nucleotides. Although the intrinsic forces driving this folding process have been well studied, our understanding of how environmental factors, such as pH and temperature, influence structure formation and dynamics remains incomplete.This work employs time-resolved X-ray solution scattering (TRXSS) and molecular simulations to provide insight into the structural dynamics and conformational ensembles following changes in temperature or pH. Chapter 1 provides an introduction to the importance of studying the structural dynamics of BMMs and the challenges present in extracting atomic-level information from ensemble-averaged measurements. Chapter 2 details the experimental and computational methodologies used in this work. Chapter 3 illustrates how the computational and experimental techniques discussed in Chapter 2 can be combined to study the response of BMMs to various environmental perturbations. Chapter 4 highlights how TRXSS results can bias molecular simulations to sample physically relevant structures. Chapter 5 showcases how enhanced sampling simulations can be coupled with a genetic algorithm to determine a heterogeneous set of conformations along unfolding pathways. Chapter 6 compares the dynamics and ensembles of Markov state models with TRXSS results. Chapter 7 introduces a merocyanine photoacid for TRXSS experiments that was used to induce the dissociation of double-stranded DNA into noncanonical structures. Finally, Chapter 8 provides a methodology for Multicanonical Monte Carlo Ensemble Growth that efficiently computes equilibrium thermodynamic properties for proteins. This work demonstrates how TRXSS and molecular simulations can be combined, underscoring the ideal applications for each use.
■590 ▼aSchool code: 0163.
■650 4▼aChemistry
■650 4▼aPhysical chemistry
■650 4▼aComputational chemistry
■650 4▼aBiochemistry
■650 4▼aGenetics
■653 ▼aConformational ensembles
■653 ▼aMolecular dynamics
■653 ▼aStructural dynamics
■653 ▼aTRXSS
■653 ▼aNucleotides
■690 ▼a0485
■690 ▼a0494
■690 ▼a0219
■690 ▼a0487
■690 ▼a0369
■71020▼aNorthwestern University▼bChemistry.
■7730 ▼tDissertations Abstracts International▼g86-12B.
■790 ▼a0163
■791 ▼aPh.D.
■792 ▼a2025
■793 ▼aEnglish
■85640▼uhttp://www.riss.kr/pdu/ddodLink.do?id=T17356836▼nKERIS▼z이 자료의 원문은 한국교육학술정보원에서 제공합니다.
