Article
Biochemistry & Molecular Biology
Vivian Lorena Leguizamon Herrera, Alexander K. Buell, Dieter Willbold, Bogdan Barz
Summary: The study elucidates the structural interaction and thermodynamics of binding between three D-peptides and A beta 42 monomers, revealing that the binding is mainly driven by electrostatic and hydrophobic interactions and leads to more compact conformations.
ACS CHEMICAL NEUROSCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Iga Biskupek, Cezary Czaplewski, Justyna Sawicka, Emilia Ilowska, Maria Dzierzynska, Sylwia Rodziewicz-Motowidlo, Adam Liwo
Summary: The UNited RESidue (UNRES) model was used to study the aggregation behavior of 20 peptides with different lengths. The majority of peptides showed inter-strand beta-sheet formation, except for glutamine- and asparagine-rich peptides, which require modification of the UNRES model.
Article
Chemistry, Medicinal
Ke Wang, Xueguang Shao, Wensheng Cai
Summary: In this study, the binding mechanism of the full-length A beta 42 monomer with POPC/POPS/CHOL bilayers was investigated using all-atom and coarse-grained simulations. The results revealed that the binding model with the central hydrophobic core buried inside the membrane was the dominant one. The study provides new insights into the peptide-bilayer binding mechanism of the A beta peptide.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemistry & Molecular Biology
Asis K. Jana, Ozgur Guven, Fatih Yasar
Summary: This study investigates the molecular-level interactions between β-amyloid 40 (Aβ40) and β-amyloid 42 (Aβ42) in Alzheimer's disease (AD). The researchers used molecular dynamics simulation and found that the interlaced mixed fibril composed of Aβ40 and Aβ42 is energetically more favorable than the homogeneous Aβ40 fibril. They also identified key interfaces contributing to the increased stability of the mixed fibril. These findings provide valuable insights into the pathogenesis of AD and may have implications for therapeutic strategies.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Krzysztof Kuczera, Robert Szoszkiewicz, Christopher Shaffer, Gouri Jas
Summary: In this study, we used molecular dynamics and replica-exchange simulations to investigate the folding of the GB1 hairpin peptide in aqueous solution. The results supported a cooperative zipper folding model and provided insights into the formation of hydrogen bonds and hydrophobic contacts during the folding process. Additionally, kinetic models constructed using the Optimal Dimensionality Reduction approach revealed the folding and unfolding times, as well as the formation of transition states and off-path intermediates.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Alessandro Nucara, Francesca Ripanti, Simona Sennato, Giacomo Nisini, Emiliano De Santis, Mahta Sefat, Marina Carbonaro, Dalila Mango, Velia Minicozzi, Marilena Carbone
Summary: This paper presents a detailed analysis of in vitro A beta 42 fibril formation in the presence of cortisol and investigates its influence on the process. The research demonstrates that the concentration ratio of cortisol to A beta 42 plays a crucial role in promoting or inhibiting fibril formation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Prabir Khatua, Asis K. Jana, Ulrich H. E. Hansmann
Summary: The study shows that the presence of fatty acids, such as lauric acid, stabilizes both ring-like and barrel-shaped oligomer models, with a stronger effect on barrel-shaped models.
Article
Engineering, Biomedical
Huan He, Juan Xu, Chen-Qiao Li, Tian Gao, Peng Jiang, Feng-Lei Jiang, Yi Liu
Summary: By combining in vitro experiments and simulations, it was found that the thermodynamics and kinetics of fibril elongation on different oxidative degrees of graphene oxide (GO) surfaces vary. Low oxidative GO-10 promotes fibril elongation, while both high oxidative GO-20 and GO-40 inhibit it. The computational results indicate that GOs regulate filament growth by balancing the promoting and retarding effects of monomer templating and capturing during docking and locking phases.
ADVANCED HEALTHCARE MATERIALS
(2021)
Article
Chemistry, Medicinal
Defa Huang, Cong Guo
Summary: Aggregation of α-synuclein is critical in Parkinson's disease, and the E46K mutation accelerates this process. Through molecular dynamics simulations, we found that E46K mutation affects the structure of monomeric α-synuclein, promoting β-sheet formation in the fibrillization region while suppressing it in the N-terminus. The mutation also led to changes in intramolecular interactions and network topology, making the E46K mutant more similar to fibrils than the wild type. These findings shed light on the mechanism behind the faster aggregation of the E46K mutant and suggest potential therapeutic strategies.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Elias Khayat, Christopher Lockhart, Bryan M. Delfing, Amy K. Smith, Dmitri K. Klimov
Summary: Using molecular dynamics simulations, this study investigated the aggregation of oxidized A beta 25-35 peptides mediated by a lipid bilayer and found that oxidation reduces helical propensity and increases backbone fluctuations, leading to destabilization of the dimer interface and decreased aggregation propensity. On the other hand, phosphorylation has an opposite effect, preserving the wild-type aggregation interface and enhancing aggregation propensity.
ACS CHEMICAL NEUROSCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Unmesh D. Chowdhury, B. L. Bhargava
Summary: The study examines the conformational and dynamical changes of Aβ monomers in coordination with Zn2+ ions using all-atom molecular dynamics simulations. The presence of Zn2+ ions leads to differential intra-peptide interactions and shifts in hydrogen bonding, resulting in structural and dynamical variations in Aβ monomers. The transition from an alpha-helix dominated structure to an unfolded coil structure highlights the impact of Zn2+ ions on Aβ monomers under fibrillation-like conditions.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Engineering, Environmental
Samal Kaumbekova, Mehdi Amouei Torkmahalleh, Naoya Sakaguchi, Masakazu Umezawa, Dhawal Shah
Summary: Recent studies have found a correlation between environmental pollutants like PAHs and the progression of neurodegenerative disorders. This study revealed that organic pollutants may affect the structure of protein molecules and contribute to the progression of Alzheimer's disease.
FRONTIERS OF ENVIRONMENTAL SCIENCE & ENGINEERING
(2023)
Article
Chemistry, Physical
Fangying Li, Chendi Zhan, Xuewei Dong, Guanghong Wei
Summary: Resveratrol (RSV) and epigallocatechin-3-gallate (EGCG) have been found to inhibit the aggregation of amyloid-beta protein (A beta) and may be promising strategies for treating Alzheimer's disease (AD). However, the specific mechanisms of how RSV inhibits A beta(42) aggregation and disrupts A beta(42) protofibril, as well as the differences between RSV and EGCG in their inhibitory/disruptive effects, still need further investigation.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Ali A. Alizadehmojarad, Sergei M. Bachilo, R. Bruce Weisman
Summary: Aqueous suspensions of single-wall carbon nanotubes coated by ssDNA were analyzed to determine the absolute average concentrations of both components and the absorptivity values of the nanotubes. The results provide a method to measure the absolute concentrations of similar SWCNT samples in aqueous SDS using simple spectrophotometry. The study also quantifies the mass ratio of ssDNA to SWCNT and compares experimental results with molecular dynamics simulations.
Article
Chemistry, Medicinal
Karnesh Jain, Othman Ghribi, Jerome Delhommelle
Summary: The misfolding and aggregation of alpha-synuclein play a crucial role in neurodegenerative disorders, with the formation of fibrils involving various intermediates. Simulation results show that conformational rearrangements of alpha-synuclein at physiological temperature mainly exhibit alpha-helix structures. These findings provide valuable insights for understanding the formation of oligomers in neurodegenerative diseases.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Engineering, Electrical & Electronic
Ang Li, Zhenguo Jing, Yueying Liu, Qiang Liu, Zhiyuan Huang, Yang Cheung, Yang Zhang, Ming Han, Wei Peng
Summary: A self-stabilizing Q-point system based on VT-DBR laser is proposed in this paper, which utilizes a large tuning range and fast wavelength switching capability to develop a stable EFPI sensor system. Experimental results show that this method effectively achieves Q-point stability within the temperature change range.
IEEE SENSORS JOURNAL
(2021)
Article
Instruments & Instrumentation
Nezam Uddin, Qiwen Sheng, Abu Farzan Mitul, Seungsup Lee, Matthew L. Reinke, David Donovan, Morgan Shafer, Ming Han
Summary: This study presents a new design of FOB that significantly improves detection sensitivity by engineering the absorber of the FOB. By attaching a large gold disk to the silicon FPI as the absorber, the FOB achieved a responsivity and noise-equivalent-power-density about nine times larger and six times smaller, respectively, compared to the previous design. This improved NEPD and absorption over a broad frequency range will make the FOB more attractive for applications in magnetic-confinement fusion devices.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2021)
Article
Chemistry, Physical
Asis K. Jana, Chance W. Lander, Andrew D. Chesney, Ulrich H. E. Hansmann
Summary: This study investigates the role of amyloidogenic regions in SARS-COV-2 proteins in the aggregation of alpha-synuclein. Using molecular dynamics simulations, the authors find that a viral protein fragment, SK9, may promote alpha-synuclein amyloid formation by shifting its conformational ensemble. However, SK9 has little effect on the stability of pre-existing or newly formed fibrils. The study provides insights into potential virus-induced amyloid formation.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Optics
Qiwen Sheng, Nezam Uddin, Bohan Zhou, Xiaoli Wang, Ming Han
Summary: This study demonstrates the fabrication of fiber-optic Fabry-Perot interferometer (FPI) temperature sensors by bonding a silicon diaphragm to an optical fiber using low melting point glass powders. Precise temperature control and localized heating are achieved through the delivery of a heating laser and monitoring using a white-light system. The results show that this fabrication method has potential for high-precision fabrication of fiber-optic sensors.
Article
Chemistry, Multidisciplinary
Fatih Yasar, Miranda S. Sheridan, Ulrich H. E. Hansmann
Summary: Overexpression of SAA can lead to amyloidosis. Using Replica Exchange with Tunneling, the conversion of SAA(1-76) chain was studied, finding the crucial role of salt bridge 26E-34K in fibril formation.
Article
Chemistry, Physical
Emilia A. Lubecka, Ulrich H. E. Hansmann
Summary: This study utilizes molecular dynamic simulations to investigate the time evolution of PrPC in the presence of D178N mutation and polyadenosine RNA. The findings suggest that both factors reduce the helical structure of the protein and promote the formation of strand-like motifs, potentially initiating the conversion of PrPC to the PrPSC scrapie conformation.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Engineering, Electrical & Electronic
Farzia Karim, Abu Farzan Mitul, Bohan Zhou, Ming Han
Summary: In this study, a self-injection locked distributed feedback diode laser and a fiber-coil Fabry-Perot interferometer sensor were used for high-sensitivity detection of acoustic emission. Improved demodulation method and identification of mode-hopping events were employed to enhance the signal-to-noise ratio and reduce spurious signals.
IEEE PHOTONICS JOURNAL
(2022)
Article
Optics
Abu Farzan Mitul, Ming Han
Summary: We present a method to suppress wavelength drift in a semiconductor laser using filtered optical feedback from a long fiber-optic loop. By actively controlling the phase delay of the feedback light, the laser wavelength is stabilized to the filter peak. Experimental results show a significant reduction in wavelength drift compared to cases without phase delay control.
Article
Physics, Fluids & Plasmas
Seungsup Lee, David Donovan, Ming Han, Matthew Reinke, Morgan Shafer, Qiwen Sheng, Nezam Uddin
Summary: This study demonstrates the neutral pressure sensitivity of an interferometric fiber optic temperature sensor (FOTS) in various vacuum environments, with negligible susceptibility to electromagnetic interference. The compact design of the sensor makes it suitable for implementation in a tokamak environment. By measuring the thermal responsivity and response time changes caused by vacuum pressure, the FOTS enables accurate vacuum pressure measurements.
IEEE TRANSACTIONS ON PLASMA SCIENCE
(2022)
Article
Instruments & Instrumentation
S. Lee, M. Shafer, M. Reinke, N. Uddin, Q. Sheng, M. Han, D. Donovan, R. O'Neill
Summary: This study demonstrates the first observation of a fusion plasma using a fiber optic bolometer. The fiber optic bolometer shows high sensitivity to temperature changes and negligible susceptibility to electromagnetic interference, making it suitable for tokamak environments. The comparison with resistive bolometers confirms the comparable performance of the fiber optic bolometer.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2022)
Article
Optics
Farzia Karim, Ming Han
Summary: Homodyne demodulation using a phase-generated carrier (PGC) is used to counteract signal fading and distortion in fiber-optic interferometric sensors caused by operating point drift. This method assumes that the sensor output is a sinusoidal function of the phase delay, achievable with a two-beam interferometer. This study investigates the impact of three-beam interference on the PGC scheme and proposes strategies to eliminate undesirable terms for valid implementation.
Article
Chemistry, Analytical
Hasanur R. R. Chowdhury, Ming Han
Summary: We present a high-resolution fiber optic temperature sensor system using an air-filled Fabry-Perot cavity, where the spectral fringes shift with precise pressure variation. The absolute temperature is derived from the spectral shift and pressure variation. The sensor is fabricated by splicing a fused-silica tube with a single-mode fiber and a side-hole fiber to form the Fabry-Perot cavity. By passing air through the side-hole fiber, the pressure in the cavity can be changed, resulting in spectral shift. The sensor achieves a high wavelength resolution (<0.2 pm) and minimal pressure fluctuation (approximately 0.015 kPa), allowing for high-resolution temperature measurement (+/- 0.32 degrees C) with good stability up to 800 degrees C.
Article
Chemistry, Multidisciplinary
Andrew D. Chesney, Buddhadev Maiti, Ulrich H. E. Hansmann
Summary: COVID-19 may induce type-II diabetes by affecting the equilibrium between amylin monomers and fibrils. Molecular dynamics simulations were used to investigate the interaction between SARS-COV-2 protein fragments and amylin structures. The results were compared with previous studies on different proteins.
Article
Engineering, Electrical & Electronic
Hasanur R. Chowdhury, Ming Han
Summary: A method for high temperature measurement using fiber-optic Fabry-Pérot cavities filled with gas is presented. The temperature of the measuring cavity can be deduced by analyzing the spectral fringe shift vs. pressure of a reference cavity placed in a known temperature environment. This approach eliminates the need for pressure measurement or knowledge of the gas's optical properties. The fabricated sensor shows good linearity and stability at temperatures up to 800 degrees C.
IEEE PHOTONICS TECHNOLOGY LETTERS
(2023)
Article
Physics, Fluids & Plasmas
Fatih Yasar, Alan J. Ray, Ulrich H. E. Hansmann
Summary: Simulations of protein folding and protein association typically take much longer timescales than can be covered in all-atom molecular dynamics simulations. To address this challenge, researchers have introduced a replica-exchange-based multiscale sampling technique that combines the faster sampling in coarse-grained simulations with the potentially higher accuracy of all-atom simulations. By testing the efficiency of this technique in simulations of the Trp-cage protein and comparing the landscapes of wild-type and A2T mutant A beta(1-42) peptides, the researchers found a mechanism by which a small hydrophobic alanine (A) mutation to a bulky polar threonine (T) may interfere with the self-assembly of A beta fibrils.