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kinesin-microtubule interaction reveals the mechanism of kinesin-1 for discriminating the binding site on microtubule

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Chinese Physics B 2023年第10期32卷 738-748页

作者：耿轶钊鲁丽爱贾宁张冰冰纪青 School of Science Hebei University of TechnologyTianjin 300401China Institute of Biophysics Hebei University of TechnologyTianjin 300401China

Microtubule catalyzes the mechanochemical cycle of kinesin,a kind of molecular motor,through its crucial roles in kinesin's gating,ATPase and force-generation process.These functions of microtubule are realized through the kinesin-microtubule interaction.The binding site of kinesin on the microtubule surface is fixed.For most of the kinesin-family members,the binding site on microtubule is in the groove betweenα-tubulin andβ-tubulin in a protofilament.The mechanism of kinesin searching for the appropriate binding site on microtubule is still unclear.Using the molecular dynamics simulation method,we investigate the interactions between kinesin-1 and the different binding positions on microtubule.The key non-bonded interactions between the motor domain and tubulins in kinesin's different nucleotide-binding states are listed.The differences of the amino-acid sequences betweenα-andβ-tubulins make kinesin-1 binding to theα–βgroove much more favorable than to theβ–αgroove.From these results,a two-step mechanism of kinesin-1 to discriminate the correct binding site on microtubule is proposed.Most of the kinesin-family members have the conserved motor domain and bind to the same site on microtubule,the mechanism may also be shared by other family members of kinesin.

关键词： kinesin tubulin microtubule molecular dynamics simulation

Single Molecule Analysis of the Arabidopsis FRA1 kinesin Shows that It Is a Functional Motor Protein with Unusually High Processivity

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Molecular Plant 2011年第5期4卷 879-885页

作者： Chuanmei Zhu Ram Dixit Biology Department Washington University St Louis MO 63130 USA

The Arabidopsis FRA1 kinesin contributes to the organization of cellulose microfibrils through an unknown mechanism. The cortical localization of this kinesin during interphase raises the possibility that it transports cell wallrelated cargoes along cortical microtubules that either directly or indirectly influence cellulose microfibril patterning. To determine whether FRA1 is an authentic motor protein, we combined bulk biochemical assays and single molecule fluorescence imaging to analyze the motor properties of recombinant, GFP-tagged FRA1 containing the motor and coiled-coil domains （designated as FRAI（707）-GFP）. We found that FRAI（707）-GFP binds to microtubules in an ATP-dependent manner and that its ATPase activity is dramatically stimulated by the presence of microtubules. Using single molecule studies, we found that FRAI（707）-GFP moves processively along microtubule tracks at a velocity of about 0.4 μm s-1. In addition, we found that FRAI（707）-GFP is a microtubule plus-end-directed motor and that it moves along microtubules as a dimer. Interestingly, our single molecule analysis shows that the processivity of FRAI（707）-GFP is at least twice the processivity of conventional kinesin, making FRA1 the most processive kinesin to date. Together, our data show that FRA1 is a bona fide motor protein that has the potential to drive Iong-distance transport of cargo along cortical microtubules.

关键词： kinesin FRA1 cortical microtubule single molecule cellulose Arabidopsis.

GhKLCR1, a kinesin light chain-related gene, induces drought-stress sensitivity in Arabidopsis

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Science China(Life Sciences) 2019年第1期62卷 63-75页

作者： Jie Li Daoqian Yu Ghulam Qanmber Lili Lu Lingling Wang Lei Zheng Zhao Liu Huanhuan Wu Xiaodong Liu Quanjia Chen Fuguang Li Zuoren Yang Xinjiang Research Base State Key Laboratory of Cotton Biology Xinjiang Agricultural University State Key Laboratory of Cotton Biology Key Laboratory of Biological and Genetic Breeding of Cotton Institute of Cotton ResearchChinese Academy of Agricultural Sciences

Drought stress results in significant losses in agricultural production, and especially that of cotton. The molecular mechanisms that coordinate drought tolerance remain elusive in cotton. Here, we isolated a drought-response gene GhKLCR1, which is a close homolog of AtKLCR1, which encodes a kinesin light chain-related protein enriched with a tetratrico peptide-repeat region.A subcellular localization assay showed that GhKLCR1 is associated with the cell membrane. A tissue-specific expression profile analysis demonstrated that GhKLCR1 is a cotton root-specific gene. Further abiotic and hormonal stress treatments showed that GhKLCR1 was upregulated during abiotic stresses, especially after polyethylene glycol treatments. In addition, the glucuronidase(GUS) staining activity increased as the increment of mannitol concentration in transgenic Arabidopsis plants harboring the fusion construct PGhKLCR1::GUS. The root lengths of 35 S::GhKLCR1 lines were significantly reduced compared with that of wild type. Additionally, seed germination was strongly inhibited in 35 S::GhKLCR1 lines after 300-mmol L^(-1) mannitol treatments as compared with Columbia-0, indicating the sensitivity of GhKLCR1 to drought. These findings provide a better understanding of the structural, physiological and functional mechanisms of kinesin light chain-related proteins.

关键词： GhKLCR1 kinesin Arabidopsis mannitol seed germination drought sensitivity GUS cis-elements

Amyloid-beta-dependent phosphorylation of collapsin response mediator protein-2 dissociates kinesin in Alzheimer＇s disease

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Neural Regeneration Research 2018年第6期13卷 1066-1080页

作者： Sara H.Mokhtar Min Joung Kim Kylie A.Magee Pei Mun Aui Speros Thomas Maha M.Bakhuraysah Amani A.Alrehaili Jae Young Lee David L.Steer Rachel Kenny Catriona Mc Lean Michael F.Azari Antonis Birpanagos Ewlina Lipiec Philip Heraud Bayden Wood Steven Petratos Department of Neuroscience Central Clinical School Monash University Prahran Victoria Australia Department of Biochemistry and Molecular Biology Monash Universityl Clayton Victoria Australia Department of Anatomy & Developmental Biology Monash University Clayton Victoria Australia Department of Anatomical Pathology Alfred Hospital Prahran Victoria Australia School of Health and Biomedical Sciences RMIT University Bundoora Victoria Australia Division of Animal and Human Physiology Department of Biology National and Kapodistrian University of Athens Ilisia Athens Greece The Henryk Niewodniczanski Institute of Nuclear Physics Polish Academy of Sciences Department of Applied Spectroscopy RadzikowskiegoKrakow Poland Centre for Biospectroscopy and Department of Microbiology Monash University Clayton Victoria Australia

Alzheimer’s disease（AD）is a neurodegenerative disorder characterized by accumulation of amyloid plaques and neurofibrillary tangles.Prior to the development of these characteristic pathological hallmarks of AD,anterograde axonal transport is impaired.However,the key proteins that initiate these intracellular impairments remain elusive.The collapsin response mediator protein-2（CRMP-2）plays an integral role in kinesin-1-dependent axonal transport and there is evidence that phosphorylation of CRMP-2releases kinesin-1.Here,we tested the hypothesis that amyloid-beta（Aβ）-dependent phosphorylation of CRMP-2 disrupts its association with the kinesin-1（an anterograde axonal motor transport protein）in AD.We found that brain sections and lysates from AD patients demonstrated elevated phosphorylation of CRMP-2 at the T555 site.Additionally,in the transgenic Tg2576 mouse model of familial AD（FAD）that exhibits Aβaccumulation in the brain with age,we found substantial co-localization of p T555CRMP-2and dystrophic neurites.In SH-SY5Y differentiated neuronal cultures,Aβ-dependent phosphorylation of CRMP-2 at the T555 site was also elevated and this reduced the CRMP-2 association with kinesin-1.The overexpression of an unphosphorylatable form of CRMP-2 in neurons promoted the re-establishment of CRMP-2-kinesin association and axon elongation.These data suggest that Aβ-dependent phosphorylation of CRMP-2 at the T555 site may directly impair anterograde axonal transport protein function,leading to neuronal defects.

关键词： amyloid-beta protein kinases collapsin response mediator protein microtubules kinesin tubulin

Investigation of the structural and dynamic basis of kinesin dissociation from microtubule by atomistic molecular dynamics simulations

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Chinese Physics B 2022年第5期31卷 756-765页

作者：王建港史晓璇刘玉如王鹏业陈洪谢平 School of Material Science and Engineering Central South University of Forestry and TechnologyChangsha 410004China Key Laboratory of Soft Matter Physics Institute of PhysicsChinese Academy of SciencesBeijing 100190China

kinesin is a molecular motor that can step processively on microtubules via the hydrolysis of ATP molecules.An important factor characterizing the processivity of the kinesin motor is its dissociation from the microtubule.Here,using all-atom molecular dynamics simulations,we studied the dissociation process of the kinesin head in weak-microtubulebinding or ADP state from tubulin on the basis of the available high-resolution structural data for the head and tubulin.By analyzing the simulated snapshots of the structure of the head-tubulin complex we provided detailed structural and dynamic information for the dissociation process.We found that the dissociation of the head along different directions relative to the tubulin exhibits very different dynamic behaviors.Moreover,the potential forms or energy landscapes of the interaction between the head and tubulin along different directions were determined.The studies have important implications for the detailed molecular mechanism of the dissociation of the kinesin motor and thus are critical to the mechanism of its processivity.

关键词： kinesin dissociation energy landscape molecular dynamics simulation

Monte Carlo simulation on backward steps of single kinesin molecule

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Chinese Physics B 2008年第4期17卷 1513-1517页

作者：王宏张勇窦硕星王鹏业 Laboratory of Soft Matter Physics Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of Science

kinesin is a stepping molecular motor travelling along the microtubule. It moves primarily in the plus end direction of the microtubule and occasionally in the minus-end, backward, direction. Recently, the backward steps of kinesin under different loads and temperatures start to attract interests, and the relations among them are revealed. This paper aims to theoretically understand these relations observed in experiments. After introducing a backward pathway into the previous model of the ATPase cycle of kinesin movement, the dependence of the backward movement on the load and the temperature is explored through Monte Carlo simulation. Our results agree well with previous experiments.

关键词： kinesin backward steps Monte Carlo ATPase cycle

Initial conformation of kinesin's neck linker

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Chinese Physics B 2014年第10期23卷 597-603页

作者：耿轶钊纪青刘书霞晏世伟 College of Nuclear Science and Technology Beijing Normal University Institute of Biophysics Hebei University of Technology Beijing Radiation Center

How ATP binding initiates the docking process of kinesin＇s neck linker is a key question in understanding kinesin mechanisms. By exploiting a molecular dynamics method, we investigate the initial conformation of kinesin＇s neck linker in its docking process. We find that, in the initial conformation, the neck linker has interactions with /30 and forms a ＇cover-neck bundle＇ structure with/30. From this initial structure, the formation of extra turns and the docking of the cover- neck bundle structure can be achieved. The motor head provides a forward force on the initial cover-neck bundle structure through ATP-induced rotation. This force, together with the hydrophobic interaction of ILE327 with the hydrophobic pocket on the motor head, drives the formation of the extra turn and initiates the neck linker docking process. Based on these findings, a pathway from ATP binding-induced motor head rotation to neck linker docking is proposed.

关键词： kinesin neck linker molecular dynamics simulation

Protection-against-water-attack determined difference between strengths of backbone hydrogen bonds in kinesin＇s neck zipper region

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Chinese Physics B 2018年第2期27卷 80-87页

作者：覃静宇耿轶钊吕刚纪青方海平 Division of Interracial Water and Key Laboratory of Interfhcial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China University of Chinese Academy of Sciences Beijing 100049 China Institute of Biophysics hebei Universily of Technology Tianjin 300401 China School of Science Hebei University of Technology Tianjin 300401 China Mathematical and Physical Science School North China Electric Power University Baoding 071003 China State Key Laboratory of Theoretical Physics Institute of Theoretical Physics Chinese Academy of Sciences Beijing 1O0190 China

Docking of the kinesin＇s neck linker （NL） to the motor domain is the key force-generation process of the kinesin. In this process, NL＇sβ10 portion forms four backbone hydrogen bonds （HBs） with the motor domain. These backbone hydrogen bonds show big differences in their effective strength. The origins of these strength differences are still unclear. Using molecular dynamics method, we investigate the stability of the backbone HBs in explicit water environment. We find that the strength differences of these backbone HBs mainly arise from their relationships with water molecules which are controlled by arranging the surrounding residue sidechains. The arrangement of the residues in the C-terminal part of /310 results in the existence of the water-attack channels around the backbone HBs in this region. Along these channels the water molecules can directly attack the backbone HBs and make these HBs relatively weak. In contrast, the backbone HB at the N-terminus ofβ 10 is protected by the surrounding hydrophobic and hydrophilic residues which cooperate positively with the central backbone HB and make this HB highly strong. The intimate relationship between the effective strength of protein backbone HB and water revealed here should be considered when performing mechanical analysis for protein conformational changes.

关键词： kinesin neck linker water

Insight into the chemomechanical coupling mechanism of kinesin molecular motors

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Communications in Theoretical Physics 2021年第5期73卷 157-171页

作者： Ping Xie Key Laboratory of Soft Matter Physics Institute of PhysicsChinese Academy of SciencesBeijing 100190China

kinesin is a two-headed biological molecular motor that can walk processively on microtubule via consumption of ATP molecules.The central issue for the molecular motor is how the chemical energy released from ATP hydrolysis is converted to the kinetic energy of the mechanical motion,namely the mechanism of chemomechanical coupling.To address the issue,diverse experimental methods have been employed and a lot of models have been proposed.This review focuses on the proposed models as well as the qualitative and quantitative comparisons between the results derived from the models and those from the structural,biochemical and single-molecule experimental studies.

关键词： molecular motor kinesin dynamics mechanochemistry mechanism catch bond