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Biophysics and Physicobiology

Volume 16, Issue / 2019
English Article   Japanese Article
  • Please note that metadata of J-type articlesare generated by machine-translation and the original texts are written in Japanese.

English Article Millimeter-sized belt-like pattern formation of actin filaments in solution by interacting with surface myosin in vitro
Kentaro Ozawa1, Hirotaka Taomori1, Masayuki Hoshida1, Ituki Kunita2, Sigeru Sakurazawa3, Hajime Honda1
Biophysics and Physicobiology 16: 1-8, 2019.

English Article Dynamic and static analyses of glass-like properties of three-dimensional tissues
Hironobu Nogucci
Biophysics and Physicobiology 16: 9-17, 2019.

English Article Uncovering dehydration in cytochrome c refolding from urea- and guanidine hydrochloride-denatured unfolded state by high pressure spectroscopy
Shohei Konno1, Kentaro Doi1, Koichiro Ishimori1,2
Biophysics and Physicobiology 16: 18-27, 2019.

English Article Functional significance of HCM mutants of tropomyosin, V95A and D175N, studied with in vitro motility assays
Shuya Ishii1, Madoka Suzuki2,3, Shin'ichi Ishiwata1, Masataka Kawai4
Biophysics and Physicobiology 16: 28-40, 2019.

English Article Synchrotron-radiation vacuum-ultraviolet circular dichroism spectroscopy in structural biology : an overview
Kunihiko Gekko
Biophysics and Physicobiology 16: 41-58, 2019.

English Article Single-particle analysis of full-length human poly (ADP-ribose) polymerase 1
Kenichi Kouyama1, Kouta Mayanagi2, Setsu Nakae1, Yoshisuke Nishi1, Masanao Miwa1, Tsuyoshi Shirai1
Biophysics and Physicobiology 16: 59-67, 2019.

English Article Relationship between conformation shift and disease related variation sites in ATP-binding cassette transporter proteins
Mika Sakamoto1, Hirofumi Suzuki2, Kei Yura1,2,3
Biophysics and Physicobiology 16: 68-79, 2019.

English Article Structural and functional properties of Grb2 SH2 dimer in CD28 binding
Yuhi Hosoe1, Nobutaka Numoto2, Satomi Inaba1,3, Shuhei Ogawa4, Hisayuki Morii5, Ryo Abe4,6, Nobutoshi Ito2, Masayuki Oda1
Biophysics and Physicobiology 16: 80-88, 2019.

English Article Biophysics in oviduct : Planar cell polarity, cilia, epithelial fold and tube morphogenesis, egg dynamics
Hiroshi Koyama1,2, Dongbo Shi1,3,4, Toshihiko Fujimori1,2,5
Biophysics and Physicobiology 16: 89-107, 2019.

English Article Dynamic analysis of ribosome by a movie made from many three-dimensional electron-microscopy density maps
Atsushi Matsumoto
Biophysics and Physicobiology 16: 108-113, 2019.

English Article Targeted delivery using membrane vesicles in prokaryotes
Yosuke Tashiro1,2, Kotaro Takaki1, Hiroyuki Futamata1,2,3
Biophysics and Physicobiology 16: 114-120, 2019.

English Article Gating modulation of the KCNQ1 channel by KCNE proteins studied by voltage-clamp fluorometry
Koichi Nakajo
Biophysics and Physicobiology 16: 121-126, 2019.

English Article Ab-initio study of pyrrole ring deformation in the indole group of 5-HT interacting with water molecules
Kei Odai1, Tohru Sugimoto2,4, Etsuro Ito3
Biophysics and Physicobiology 16: 127-131, 2019.

English Article A novel role of oxytocin : Oxytocin-induced well-being in humans
Etsuro Ito1,2, Rei Shima1, Tohru Yoshioka2
Biophysics and Physicobiology 16: 132-139, 2019.

English Article Cryo-EM studies of the rotary H+-ATPase/synthase from Thermus thermophilus
Atsuko Nakanishi1, Jun-ichi Kishikawa1, Kaoru Mitsuoka2, Ken Yokoyama1
Biophysics and Physicobiology 16: 140-146, 2019.

English Article Second harmonic generation polarization microscopy as a tool for protein structure analysis
Junichi Kaneshiro1, Yasushi Okada2,3, Tomohiro Shima2,7, Mika Tsujii4, Katsumi Imada4, Taro Ichimura1,5,6, Tomonobu M.Watanabe1
Biophysics and Physicobiology 16: 147-157, 2019.

English Article ATP effects on response of human erythrocyte membrane to high pressure
Takeo Yamaguchi, Shunji Fukuzaki
Biophysics and Physicobiology 16: 158-166, 2019.

English Article Food deprivation changes chemotaxis behavior in Caenorhabditis elegans
Kei Shimizu1, Keita Ashida1, Kohji Hotta1, Kotaro Oka1,2,3
Biophysics and Physicobiology 16: 167-172, 2019.

English Article Forewords to the special issue "Progress of theoretical and computational biophysics - in honor of Professor Nobuhiro Go's outstanding contribution on the occasion of his 80th birthday"
Mikio Kataoka1, Akio Kitao2, Hidetoshi Kono3
Biophysics and Physicobiology 16: 173-175, 2019.

English Article Confirmation of the formation of salt bridges in the denatured state of CutA1 protein using molecular dynamics simulations
Katsuhide Yutani1, Yoshinori Matsuura1, Yasumasa Joti1,2
Biophysics and Physicobiology 16: 176-184, 2019.

English Article Energetics of cosolvent effect on peptide aggregation
Nobuyuki Matubayasi, Keiichi Masutani
Biophysics and Physicobiology 16: 185-195, 2019.

English Article Replica exchange molecular dynamics simulation study on the mechanism of desiccation-induced structuralization of an intrinsically disordered peptide as a model of LEA proteins
Tatsushi Nishimoto, Yuta Takahashi, Shohei Miyama, Tadaomi Furuta, Minoru Sakurai
Biophysics and Physicobiology 16: 196-204, 2019.

English Article Normal mode analysis calculation for a full-atom model with a smaller number of degrees of freedom for huge protein molecules
Shigeru Endo1, Hiroshi Wako2
Biophysics and Physicobiology 16: 205-212, 2019.

English Article How can we derive hydration water dynamics with incoherent neutron scattering and molecular dynamics simulation?
Hiroshi Nakagawa1, Mikio Kataoka2,3
Biophysics and Physicobiology 16: 213-219, 2019.

English Article Dynamic properties of oligomers that characterize low-frequency normal modes
Hiroshi Wako1, Shigeru Endo2
Biophysics and Physicobiology 16: 220-231, 2019.

English Article Allosteric response to ligand binding : Molecular dynamics study of the N-terminal domains in IP3 receptor
Kei Moritsugu, Tsubasa Ito, Akinori Kidera
Biophysics and Physicobiology 16: 232-239, 2019.

English Article Cancellation between auto- and mutual correlation contributions of protein/water dynamics in terahertz time-domain spectra
Yasumasa Joti1,2, Akio Kitao3
Biophysics and Physicobiology 16: 240-247, 2019.

English Article Go model revisited
Shoji Takada
Biophysics and Physicobiology 16: 248-255, 2019.

English Article Snake cube puzzle and protein folding
Nobuhiro Go
Biophysics and Physicobiology 16: 256-263, 2019.

English Article A collective motion description of tubulin βT7 loop dynamics
Sarbani Chattopadhyaya, Debamitra Chakravorty, Gautam Basu
Biophysics and Physicobiology 16: 264-273, 2019.

English Article Mechanism of the light-driven proton pump of bacteriorhodopsin based on the consistency principle
Mikio Kataoka1,2, Hironari Kamikubo1,2
Biophysics and Physicobiology 16: 274-279, 2019.

English Article All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins
Ryotaro Koike, Motonori Ota
Biophysics and Physicobiology 16: 280-286, 2019.

English Article Prediction of the secondary structure of short DNA aptamers
Arina Afanasyeva1, Chioko Nagao2, Kenji Mizuguchi1,2
Biophysics and Physicobiology 16: 287-294, 2019.

English Article More efficient screening of protein-protein complex model structures for reducing the number of candidates
Kazuhiro Takemura, Akio Kitao
Biophysics and Physicobiology 16: 295-303, 2019.

English Article Consistency principle for protein design
Rie Koga1, Nobuyasu Koga1,2,3
Biophysics and Physicobiology 16: 304-309, 2019.

English Article Building a macro-mixing dual-basin Go model using the Multistate Bennett Acceptance Ratio
Ai Shinobu1, Chigusa Kobayashi1, Yasuhiro Matsunaga2, Yuji Sugita1,3,4
Biophysics and Physicobiology 16: 310-321, 2019.

English Article Normal mode analysis and beyond
Takahisa Yamato1, Olivier Laprevote1,2
Biophysics and Physicobiology 16: 322-327, 2019.

English Article Methodological improvements for the analysis of domain movements in large biomolecular complexes
Ruth Veevers, Steven Hayward
Biophysics and Physicobiology 16: 328-336, 2019.

English Article Free energy profile for unwrapping outer superhelical turn of CENP-A nucleosome
Hidetoshi Kono, Shun Sakuraba, Hisashi Ishida
Biophysics and Physicobiology 16: 337-343, 2019.

English Article Protein structure predictions by enhanced conformational sampling methods
Yuko Okamoto1,2,3,4,5
Biophysics and Physicobiology 16: 344-366, 2019.

English Article Parameter optimization for 3D-reconstruction from XFEL diffraction patterns based on Fourier slice matching
Miki Nakano1, Osamu Miyashita1, Florence Tama1,2,3
Biophysics and Physicobiology 16: 367-376, 2019.

English Article Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments
Toru Ekimoto1, Yuichi Kokabu2, Tomotaka Oroguchi1,3, Mitsunori Ikeguchi1,4
Biophysics and Physicobiology 16: 377-390, 2019.

English Article Detection of cave pockets in large molecules : Spaces into which internal probes can enter, but external probes from outside cannot
Takeshi Kawabata
Biophysics and Physicobiology 16: 391-406, 2019.

English Article Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics : Relaxation mode analysis and three-dimensional reference interaction site model theory
Yutaka Maruyama1, Hiroshi Takano2, Ayori Mitsutake3
Biophysics and Physicobiology 16: 407-429, 2019.

English Article Characterization of X-ray diffraction intensity function from a biological molecule for single particle imaging
Atsushi Tokuhisa1,2,3
Biophysics and Physicobiology 16: 430-443, 2019.

English Article On the use of algebraic topology concepts to check the consistency of genome assembly
Jean-Francois Gibrat
Biophysics and Physicobiology 16: 444-451, 2019.

English Article Mutational effects of Cys113 on structural dynamics of Pin1
Teikichi Ikura1, Yasushige Yonezawa2, Nobutoshi Ito1
Biophysics and Physicobiology 16: 452-465, 2019.

English Article Polymer brush in articular cartilage lubrication : Nanoscale modelling and simulation
Nobuhiko Kajinami, Mitsuhiro Matsumoto
Biophysics and Physicobiology 16: 466-472, 2019.

English Article Molecular dynamics simulations and linear response theories jointly describe biphasic responses of myoglobin relaxation and reveal evolutionarily conserved frequent communicators
Bang-Chieh Huang1, Lee-Wei Yang1,2,3,4
Biophysics and Physicobiology 16: 473-484, 2019.

English Article A tool written in Scala for preparation and analysis in MD simulation and 3D-RISM calculation of biomolecules
Itaru Onishi, Hiroto Tsuji, Masayuki Irisa
Biophysics and Physicobiology 16: 485-489, 2019.

English Article Bohr equation and the lost allosteric Bohr effects in symmetry
Lihsin Lee
Biophysics and Physicobiology 16: 490-503, 2019.