03991nam 22007335 450 991089019020332120250807152831.03-031-70602-110.1007/978-3-031-70602-8(MiAaPQ)EBC31692136(Au-PeEL)EBL31692136(CKB)36213807800041(DE-He213)978-3-031-70602-8(EXLCZ)993621380780004120240927d2024 u| 0engurcnu||||||||txtrdacontentcrdamediacrrdacarrierBiomolecules' Conformational Changes Studied by Simulations and Enhanced Sampling /by Yui Tik (Andrew) Pang1st ed. 2024.Cham :Springer Nature Switzerland :Imprint: Springer,2024.1 online resource (104 pages)Springer Theses, Recognizing Outstanding Ph.D. Research,2190-50613-031-70601-3 Chapter 1: Introduction and Background -- Chapter 2: Parameterization of a drug molecule with a halogen-hole particle using ffTK: Implementation, testing, and comparison -- Chapter 3: Uncovering the folding mechanism of pertactin: A comparative study of isolated and vectorial folding -- Chapter 4: SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact -- Chapter 5: Conclusions and Future Work.This thesis illuminates the critical roles biomolecules, from small molecules to proteins, play in cellular functionality, particularly highlighting their conformational changes in response to environmental cues or binding events—a cornerstone concept in drug design as well as the manifestations of disease. It explores the conformational flexibility of small molecules and proteins, essential for predicting drug interactions and understanding biological processes. Through advanced molecular dynamics simulations and enhanced sampling techniques, this research offers unprecedented insights into the structural dynamics of three distinct biomolecular systems: the capsid assembly modulator AT130, the passenger domain of pertactin, and the SARS-CoV-2 spike protein. Each system represents a unique facet of biological complexity, underscoring the thesis's contribution to our understanding of biomolecular behavior across various scales. Furthermore, the thesis advances the field by updating the Force Field Toolkit for improved simulation accuracy. This work not only showcases the adaptability and importance of simulation techniques in modern biological research but also paves the way for novel therapeutic strategies by deepening our understanding of biomolecular dynamics.Springer Theses, Recognizing Outstanding Ph.D. Research,2190-5061BiophysicsBiomoleculesMathematical physicsComputer simulationVirologyProteinsBiomaterialsMolecular biologyMolecular BiophysicsComputational Physics and SimulationsVirologyBiomaterials-ProteinsMolecular BiologyBiophysics.Biomolecules.Mathematical physics.Computer simulation.Virology.Proteins.Biomaterials.Molecular biology.Molecular Biophysics.Computational Physics and Simulations.Virology.Biomaterials-Proteins.Molecular Biology.571.4Pang Yui Tik (Andrew)1772184MiAaPQMiAaPQMiAaPQBOOK9910890190203321Biomolecules' Conformational Changes Studied by Simulations and Enhanced Sampling4272672UNINA