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Tanaka Y, Uchihashi T, Nakamura A. Product inhibition slow down the moving velocity of processive chitinase and sliding-intermediate state blocks re-binding of product. Arch Biochem Biophys 2024; 752:109854. [PMID: 38081338 DOI: 10.1016/j.abb.2023.109854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/23/2023] [Accepted: 12/06/2023] [Indexed: 12/18/2023]
Abstract
Processive movement is the key reaction for crystalline polymer degradation by enzyme. Product release is an important phenomenon in resetting the moving cycle, but how it affects chitinase kinetics was unknown. Therefore, we investigated the effect of diacetyl chitobiose (C2) on the biochemical activity and movement of chitinase A from Serratia marcescens (SmChiA). The apparent inhibition constant of C2 on crystalline chitin degradation of SmChiA was 159 μM. The binding position of C2 obtained by X-ray crystallography was at subsite +1, +2 and Trp275 interact with C2 at subsite +1. This binding state is consistent with the competitive inhibition obtained by biochemical analysis. The apparent inhibition constant of C2 on the moving velocity of high-speed (HS) AFM observations was 330 μM, which is close to the biochemical results, indicating that the main factor in crystalline chitin degradation is also the decrease in degradation activity due to inhibition of processive movement. The Trp275 is a key residue for making a sliding intermediate complex. SmChiA W275A showed weaker activity and affinity than WT against crystalline chitin because it is less processive than WT. In addition, biochemical apparent inhibition constant for C2 of SmChiA W275A was 45.6 μM. W275A mutant showed stronger C2 inhibition than WT even though the C2 binding affinity is weaker than WT. This result indicated that Trp275 is important for the interaction at subsite +1, but also important for making sliding intermediate complex and physically block the rebinding of C2 on the catalytic site for crystalline chitin degradation.
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Affiliation(s)
- Yoshiko Tanaka
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya,Suruga-ku, Shizuoka, 422-8529, Japan
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Aichi, 464-8602, Japan; Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Higashiyama 5-1, Myodaiji, Okazaki, 444-0864, Japan
| | - Akihiko Nakamura
- Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Shizuoka Institute for the Study of Marine Biology and Chemistry, Shizuoka, Shizuoka, 422-8529, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama Myodaijicho, Okazaki, Aichi, 444-8787, Japan.
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Terada TP, Nie QM, Sasai M. Landscape-Based View on the Stepping Movement of Myosin VI. J Phys Chem B 2022; 126:7262-7270. [PMID: 36107864 PMCID: PMC9527754 DOI: 10.1021/acs.jpcb.2c03694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Myosin VI dimer walks toward the minus end of the actin
filament
with a large and variable step size of 25–36 nm. Two competing
models have been put forward to explain this large step size. The
Spudich model assumes that the myosin VI dimer associates at a distal
tail near the cargo-binding domain, which makes two full-length single
α-helix (SAH) domains serve as long legs. In contrast, the Houdusse–Sweeney
model assumes that the association occurs in the middle (between residues
913 and 940) of the SAH domain and that the three-helix bundles unfold
to ensure the large step size. Their consistency with the observation
of stepping motion with a large and variable step size has not been
examined in detail. To compare the two proposed models of myosin VI,
we computationally characterized the free energy landscape experienced
by the leading head during the stepping movement along the actin filament
using the elastic network model of two heads and an implicit model
of the SAH domains. Our results showed that the Spudich model is more
consistent with the 25–36 nm step size than the Houdusse–Sweeney
model. The unfolding of the three-helix bundles gives rise to the
free energy bias toward a shorter distance between two heads. Besides,
the stiffness of the SAH domain is a key factor for giving strong
energetic bias toward the longer distance of stepping. Free energy
analysis of the stepping motion complements the visual inspection
of static structures and enables a deeper understanding of underlying
mechanisms of molecular motors.
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Affiliation(s)
- Tomoki P. Terada
- Department of Applied Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Qing-Miao Nie
- Department of Applied Physics, Zhejiang University of Technology, 38 Zheda Road, Hangzhou 310023, P.R. China
| | - Masaki Sasai
- Department of Applied Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Department of Complex Systems Science, Nagoya University, Nagoya 464-8601, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano-Nishibiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan
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Ando J, Kawagoe H, Nakamura A, Iino R, Fujita K. Label-free monitoring of crystalline chitin hydrolysis by chitinase based on Raman spectroscopy. Analyst 2021; 146:4087-4094. [PMID: 34060547 DOI: 10.1039/d1an00581b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate a method for label-free monitoring of hydrolytic activity of crystalline-chitin-degrading enzyme, chitinase, by means of Raman spectroscopy. We found that crystalline chitin exhibited a characteristic Raman peak at 2995 cm-1, which did not appear in the reaction product, N,N'-diacetylchitobiose. We used this Raman peak as a marker of crystalline chitin degradation to monitor the hydrolytic activity of chitinase. When the crystalline chitin suspension and chitinase were mixed together, the peak intensity of crystalline chitin at 2995 cm-1 was linearly decreased depending on incubation time. The decrease in peak intensity was inversely correlated with the increase in the amount of released N,N'-diacetylchitobiose, which was measured by conventional colorimetric assay with alkaline ferricyanide. Our result, presented here, provides a new method for simple, in situ, and label-free monitoring of enzymatic activity of chitinase.
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Affiliation(s)
- Jun Ando
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan. and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan and Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa 240-0193, Japan
| | - Hiroyuki Kawagoe
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Akihiko Nakamura
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan and Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa 240-0193, Japan and Department of Applied Life Sciences, Shizuoka University, Shizuoka, Shizuoka 422-8529, Japan
| | - Ryota Iino
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan and Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa 240-0193, Japan
| | - Katsumasa Fujita
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan. and Advanced Photonics and Biosensing Open Innovation Laboratory, AIST-Osaka University, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan and Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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