著者
Masami Ikeda Minoru Sugihara Makiko Suwa
出版者
The Biophysical Society of Japan
雑誌
Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日
vol.15, pp.104-110, 2018 (Released:2018-04-27)
参考文献数
28
被引用文献数
3

We report the development of the SEVENS database, which contains information on G-protein coupled receptor (GPCR) genes that are identified with high confidence levels (A, B, C, and D) from various eukaryotic genomes, by using a pipeline comprising bioinformatics softwares, including a gene finder, a sequence alignment tool, a motif and domain assignment tool, and a transmembrane helix predictor.SEVENS compiles detailed information on GPCR genes, such as chromosomal mapping position, phylogenetic tree, sequence similarity to known genes, and protein function described by motif/domain and transmembrane helices. They are presented in a user-friendly interface. Because of the comprehensive gene findings from genomes, SEVENS contains a larger data set than that of previous databases and enables the performance of a genome-scale overview of all the GPCR genes. We surveyed the complete genomes of 68 eukaryotes, and found that there were between 6 and 3,470 GPCR genes for each genome (Level A data). Within these genes, the number of receptors for various molecules, including biological amines, peptides, and lipids, were conserved in mammals, birds, and fishes, whereas the numbers of odorant receptors and pheromone receptors were highly diverse in mammals. SEVENS is freely available at http://sevens.cbrc.jp or http://sevens.chem.aoyama.ac.jp.
著者
Nobuhiro Go
出版者
The Biophysical Society of Japan
雑誌
Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日
vol.16, pp.256-263, 2019 (Released:2019-11-29)
参考文献数
11

The snake cube puzzle made of a linear array of 27 cubes and its modified and extended versions are used as theoretical models to study the mechanism of folding of proteins into their sequence-specific native three-dimensional structures. Each of the three versions is characterized by the respective set of characteristics attributed to each of its constituent cubes and an array is characterized by its specific sequence of the cube characteristics. The aim of the puzzles is to fold the cube array into a compact 3×3×3 cubic structure. In all three versions, out of all possible sequences, only a limited fraction of sequences are found foldable into the compact cube. Even among foldable sequences, the structures folded into the compact 3×3×3 cube are found often not uniquely determined from the sequence. By comparing the results obtained for the three versions of models, we conclude that the power of the hydrophobic interactions to make the folded structure unique to the sequence is much weaker than the geometrical varieties of constituent cubes as modelled in the original snake cube puzzle. However, when this weak cube attribute is compounded to that of the original snake cube puzzle, the power is enhanced very effectively. This is a strong manifestation of the consistency principle: The sequence-specific native structure of protein is realized as a result of consistency of various types of interactions working in protein.
著者
Fumio Oosawa
出版者
The Biophysical Society of Japan
雑誌
Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日
vol.15, pp.151-158, 2018 (Released:2018-07-18)
参考文献数
42
被引用文献数
1

An enormous amount of research has been performed to characterize actin dynamics. Structural biology investigations have determined the localization of main chains and their changes coupled with G (Globular)-F (Filamentous) transformation of actin, whereas local thermal fluctuations that may be caused by free rotations of the tips of side chains are not yet fully investigated. This paper argues if the entropy change of actin accompanied by the G-F transformation is simply attributable to the changes in hydration. It took almost 10 years to understand that the actin filament is semi-flexible. This flexibility was visually confirmed as the development of optical microscope techniques, and the direct observation of actin severing events in the presence of actin binding proteins became possible. Finally, I expect the deep understanding of actin dynamics will lead to the elucidation of self-assembly mechanisms of the living creature.
著者
Shumpei Matsuno Masahito Ohue Yutaka Akiyama
出版者
The Biophysical Society of Japan
雑誌
Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日
vol.17, pp.2-13, 2020 (Released:2020-02-07)
参考文献数
30

Protein functions can be predicted based on their three-dimensional structures. However, many multidomain proteins have unstable structures, making it difficult to determine the whole structure in biological experiments. Additionally, multidomain proteins are often decomposed and identified based on their domains, with the structure of each domain often found in public databases. Recent studies have advanced structure prediction methods of multidomain proteins through computational analysis. In existing methods, proteins that serve as templates are used for three-dimensional structure prediction. However, when no protein template is available, the accuracy of the prediction is decreased. This study was conducted to predict the structures of multidomain proteins without the need for whole structure templates.We improved structure prediction methods by performing rigid-body docking from the structure of each domain and reranking a structure closer to the correct structure to have a higher value. In the proposed method, the score for the domain-domain interaction obtained without a structural template of the multidomain protein and score for the three-dimensional structure obtained during docking calculation were newly incorporated into the score function. We successfully predicted the structures of 50 of 55 multidomain proteins examined in the test dataset.Interaction residue pair information of the protein-protein complex interface contributes to domain reorganizations even when a structural template for a multidomain protein cannot be obtained. This approach may be useful for predicting the structures of multidomain proteins with important biochemical functions.
著者
Jean-François Gibrat
出版者
The Biophysical Society of Japan
雑誌
Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日
vol.16, pp.444-451, 2019 (Released:2019-11-29)
参考文献数
13

This paper presents a preliminary work consisting of two contributions. The first one is the design of a very efficient algorithm based on an “Overlap-Layout-Consensus” (OLC) graph to assemble the long reads provided by 3rd generation technologies. The second concerns the analysis of this graph using algebraic topology concepts to determine, in advance, whether the assembly of the genome will be straightforward, i.e., whether it will lead to a pseudo-Hamiltonian path or cycle, or whether the results will need to be scrutinized. In the latter case, it will be necessary to look for “loops” in the OLC assembly graph caused by unresolved repeated genomic regions, and then try to untie the “knots” created by these regions.
著者
Keiichi Kojima Hiroshi C. Watanabe Satoko Doi Natsuki Miyoshi Misaki Kato Hiroshi Ishikita Yuki Sudo
出版者
The Biophysical Society of Japan
雑誌
Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日
vol.15, pp.179-188, 2018 (Released:2018-09-07)
参考文献数
42
被引用文献数
2

Anion channelrhodopsin-2 (ACR2), a light-gated channel recently identified from the cryptophyte alga Guillardia theta, exhibits anion channel activity with exclusive selectivity. In addition to its novel function, ACR2 has become a focus of interest as a powerful tool for optogenetics. Here we combined experimental and computational approaches to investigate the roles of conserved carboxylates on the anion transport activity of ACR2 in Escherichia coli membrane. First, we replaced six conserved carboxylates with a neutral residue (i.e. E9Q, E56Q, E64Q, E159Q, E219Q and D230N), and measured anion transport activity using E. coli expression system. E159Q and D230N exhibited significantly lower anion transport activity compared with wild-type ACR2 (1/12~1/3.4), which suggests that E159 and D230 play important roles in the anion transport. Second, to explain its molecular aspects, we constructed a homology model of ACR2 based on the crystal structure of a cation channelrhodopsin (ChR). The model structure showed a cavity formed by four transmembrane helices (TM1, TM2, TM3 and TM7) similar to ChRs, as a putative anion conducting pathway. Although E159 is not located in the putative pathway, the model structure showed hydrogen bonds between E159 and R129 with a water molecule. D230 is located in the pathway near the protonated Schiff base (PSB) of the chromophore retinal, which suggests that there is an interaction between D230 and the PSB. Thus, we demonstrated the functional importance and the hypothetical roles of two conserved carboxylates, E159 and D230, in the anion transport activity of ACR2 in E. coli membrane.
著者
Yasumasa Joti Akio Kitao
出版者
The Biophysical Society of Japan
雑誌
Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日
vol.16, pp.240-247, 2019 (Released:2019-11-29)
参考文献数
28

Terahertz time-domain spectra (THz-TDS) were investigated using the results of molecular dynamics (MD) simulations of Staphylococcal nuclease at two hydration states in the temperature range between 100 and 300 K. The temperature dependence of THz-TDS was found to differ significantly from that of the incoherent neutron scattering spectra (INSS) calculated from the same MD simulation results. We further examined contributions of the mutual and auto-correlations of the atomic fluctuations to THz-TDS and found that the negative value of the former contribution nearly canceled out the positive value of the latter, resulting in a monotonic increase of the reduced absorption cross section. Because of this cancellation, no distinct broad peak was observed in the absorption lineshape function of THz-TDS, whereas the protein boson peak was observed in INSS. The contribution of water molecules to THz-TDS was extremely large for the hydrated protein at temperatures above 200 K, in which large-amplitude motions of water were excited. The combination of THz-TDS, INSS and MD simulations has the potential to extract function-relevant protein dynamics occurring on the picosecond to nanosecond timescale.
著者
Kazuhiro Takemura Akio Kitao
出版者
The Biophysical Society of Japan
雑誌
Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日
vol.16, pp.295-303, 2019 (Released:2019-11-29)
参考文献数
36

Rigid-body protein-protein docking is very efficient in generating tens of thousands of docked complex models (decoys) in a very short time without considering structure change upon binding, but typical docking scoring functions are not necessarily sufficiently accurate to narrow these decoys down to a small number of plausible candidates. Flexible refinements and sophisticated evaluation of the decoys are thus required to achieve more accurate prediction. Since this process is time-consuming, an efficient screening method to reduce the number of decoys is necessary immediately following rigid-body dockings. We attempted to develop an efficient screening method by clustering decoys generated by the rigid-body docking ZDOCK. We introduced the three metrics ligand-root-mean-square deviation (L-RMSD), interface-ligand-RMSD (iL-RMSD), and the fraction of common contacts (FCC), and examined various ranges of cut-offs for clusters to determine the best set of clustering parameters. Although the employed clustering algorithm is simple, it successfully reduced the number of decoys. Using iL-RMSD with a cut-off radius of 8 Å, the number of decoys that contain at least one near-native model with 90% probability decreased from 4,808 to 320, a 93% reduction in the original number of decoys. Using FCC for the clustering step, the top 1,000 success rates, defined as the probability that the top 1,000 models contain at least one near-native structure, reached 97%. We conclude that the proposed method is very efficient in selecting a small number of decoys that include near-native decoys.
著者
Hiroyuki Terashima Akihiro Kawamoto Yusuke V. Morimoto Katsumi Imada Tohru Minamino
出版者
The Biophysical Society of Japan
雑誌
Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日
vol.14, pp.191-198, 2017 (Released:2017-12-19)
参考文献数
57
被引用文献数
1 17

The bacterial flagellum is a supramolecular motility machine consisting of the basal body as a rotary motor, the hook as a universal joint, and the filament as a helical propeller. Intact structures of the bacterial flagella have been observed for different bacterial species by electron cryotomography and subtomogram averaging. The core structures of the basal body consisting of the C ring, the MS ring, the rod and the protein export apparatus, and their organization are well conserved, but novel and divergent structures have also been visualized to surround the conserved structure of the basal body. This suggests that the flagellar motors have adapted to function in various environments where bacteria live and survive. In this review, we will summarize our current findings on the divergent structures of the bacterial flagellar motor.
著者
Kazuho Yoshida Takahiro Yamashita Kengo Sasaki Keiichi Inoue Yoshinori Shichida Hideki Kandori
出版者
The Biophysical Society of Japan
雑誌
Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日
vol.14, pp.183-190, 2017 (Released:2017-12-19)
参考文献数
44
被引用文献数
2

We previously showed that the chimeric proteins of microbial rhodopsins, such as light-driven proton pump bacteriorhodopsin (BR) and Gloeobacter rhodopsin (GR) that contain cytoplasmic loops of bovine rhodopsin, are able to activate Gt protein upon light absorption. These facts suggest similar protein structural changes in both the light-driven proton pump and animal rhodopsin. Here we report two trials to engineer chimeric rhodopsins, one for the inserted loop, and another for the microbial rhodopsin template. For the former, we successfully activated Gs protein by light through the incorporation of the cytoplasmic loop of β2-adrenergic receptor (β2AR). For the latter, we did not observe any G-protein activation for the light-driven sodium pump from Indibacter alkaliphilus (IndiR2) or a light-driven chloride pump halorhodopsin from Natronomonas pharaonis (NpHR), whereas the light-driven proton pump GR showed light-dependent G-protein activation. This fact suggests that a helix opening motion is common to G protein coupled receptor (GPCR) and GR, but not to IndiR2 and NpHR. Light-induced difference FTIR spectroscopy revealed similar structural changes between WT and the third loop chimera for each light-driven pump. A helical structural perturbation, which was largest for GR, was further enhanced in the chimera. We conclude that similar structural dynamics that occur on the cytoplasmic side of GPCR are needed to design chimeric microbial rhodopsins.
著者
Yutaka Maruyama Hiroshi Takano Ayori Mitsutake
出版者
The Biophysical Society of Japan
雑誌
Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日
vol.16, pp.407-429, 2019 (Released:2019-11-29)
参考文献数
182

Molecular dynamics simulation is a fruitful tool for investigating the structural stability, dynamics, and functions of biopolymers at an atomic level. In recent years, simulations can be performed on time scales of the order of milliseconds using specialpurpose systems. Since the most stable structure, as well as meta-stable structures and intermediate structures, is included in trajectories in long simulations, it is necessary to develop analysis methods for extracting them from trajectories of simulations. For these structures, methods for evaluating the stabilities, including the solvent effect, are also needed. We have developed relaxation mode analysis to investigate dynamics and kinetics of simulations based on statistical mechanics. We have also applied the three-dimensional reference interaction site model theory to investigate stabilities with solvent effects. In this paper, we review the results for designing amino-acid substitution of the 10-residue peptide, chignolin, to stabilize the misfolded structure using these developed analysis methods.
著者
Ji-Chen Ho Chih-Hung Lee
出版者
The Biophysical Society of Japan
雑誌
BIOPHYSICS (ISSN:13492942)
巻号頁・発行日
vol.11, pp.17-24, 2015 (Released:2015-02-13)
参考文献数
70
被引用文献数
12 12

TRP channels are expressed in various cells in skin. As an organ system to border the host and environment, many nonneuronal cells, including epidermal keratinocytes and melanocytes, express several TRP channels functionally distinct from sensory processing. TRPV1 and TRPV3 in keratinocytes of the epidermis and hair apparatus inhibit proliferation, induce terminal differentiation, induce apoptosis, and promote inflammation. Activation of TRPV4, 6, and TRPA1 promotes regeneration of the severed skin barriers. TRPA1 also enhances responses in contact hypersensitivity. TRPCs in keratinocytes regulate epidermal differentiation. In human diseases with pertubered epidermal differentiation, the expression of TRPCs are altered. TRPMs, which contribute to melanin production in melanocytes, serve as significant prognosis markers in patients with metastatic melanoma. In summary, not only act in sensory processing, TRP channels also contribute to epidermal differentiation, proliferation, barrier integration, skin regeneration, and immune responses. In diseases with aberrant TRP channels, TRP channels might be good therapeutic targets.
著者
Sumita Das Tomoki P. Terada Masaki Sasai
出版者
The Biophysical Society of Japan
雑誌
Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日
vol.15, pp.136-150, 2018 (Released:2018-05-26)
参考文献数
47
被引用文献数
1

When three cyanobacterial proteins, KaiA, KaiB, and KaiC, are incubated with ATP in vitro, the phosphorylation level of KaiC hexamers shows stable oscillation with approximately 24 h period. In order to understand this KaiABC clockwork, we need to analyze both the macroscopic synchronization of a large number of KaiC hexamers and the microscopic reactions and structural changes in individual KaiC molecules. In the present paper, we explain two coarse-grained theoretical models, the many-molecule (MM) model and the single-molecule (SM) model, to bridge the gap between macroscopic and microscopic understandings. In the simulation results with these models, ATP hydrolysis in the CI domain of KaiC hexamers drives oscillation of individual KaiC hexamers and the ATP hydrolysis is necessary for synchronizing oscillations of a large number of KaiC hexamers. Sensitive temperature dependence of the lifetime of the ADP bound state in the CI domain makes the oscillation period temperature insensitive. ATPase activity is correlated to the frequency of phosphorylation oscillation in the single molecule of KaiC hexamer, which should be the origin of the observed ensemble-level correlation between the ATPase activity and the frequency of phosphorylation oscillation. Thus, the simulation results with the MM and SM models suggest that ATP hydrolysis stochastically occurring in each CI domain of individual KaiC hexamers is a key process for oscillatory behaviors of the ensemble of many KaiC hexamers.
著者
Keisuke Arikawa
出版者
The Biophysical Society of Japan
雑誌
Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日
vol.15, pp.58-74, 2018 (Released:2018-02-27)
参考文献数
50

We propose methods for directly analyzing structural compliance (SC) properties of elastic network models of proteins, and we also propose methods for extracting information about motion properties from the SC properties. The analysis of SC properties involves describing the relationships between the applied forces and the deformations. When decomposing the motion according to the magnitude of SC (SC mode decomposition), we can obtain information about the motion properties under the assumption that the lower SC mode motions or the softer motions occur easily. For practical applications, the methods are formulated in a general form. The parts where forces are applied and those where deformations are evaluated are separated from each other for enabling the analyses of allosteric interactions between the specified parts. The parts are specified not only by the points but also by the groups of points (the groups are treated as flexible bodies). In addition, we propose methods for quantitatively evaluating the properties based on the screw theory and the considerations of the algebraic structures of the basic equations expressing the SC properties. These methods enable quantitative discussions about the relationships between the SC mode motions and the motions estimated from two different conformations; they also help identify the key parts that play important roles for the motions by comparing the SC properties with those of partially constrained models. As application examples, lactoferrin and ATCase are analyzed. The results show that we can understand their motion properties through their lower SC mode motions or the softer motions.
著者
Shuya Ishii Madoka Suzuki Shin’ichi Ishiwata Masataka Kawai
出版者
The Biophysical Society of Japan
雑誌
Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日
vol.16, pp.28-40, 2019 (Released:2019-02-02)
参考文献数
77
被引用文献数
1

The majority of hypertrophic cardiomyopathy (HCM) is caused by mutations in sarcomere proteins. We examined tropomyosin (Tpm)’s HCM mutants in humans, V95A and D175N, with in vitro motility assay using optical tweezers to evaluate the effects of the Tpm mutations on the actomyosin interaction at the single molecular level. Thin filaments were reconstituted using these Tpm mutants, and their sliding velocity and force were measured at varying Ca2+ concentrations. Our results indicate that the sliding velocity at pCa ≥8.0 was significantly increased in mutants, which is expected to cause a diastolic problem. The velocity that can be activated by Ca2+ decreased significantly in mutants causing a systolic problem. With sliding force, Ca2+ activatable force decreased in V95A and increased in D175N, which may cause a systolic problem. Our results further demonstrate that the duty ratio determined at the steady state of force generation in saturating [Ca2+] decreased in V95A and increased in D175N. The Ca2+ sensitivity and cooperativity were not significantly affected by the mutations. These results suggest that the two mutants modulate molecular processes of the actomyosin interaction differently, but to result in the same pathology known as HCM.
著者
Hiroyuki Terashima Katsumi Imada
出版者
The Biophysical Society of Japan
雑誌
Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日
vol.15, pp.173-178, 2018 (Released:2018-08-22)
参考文献数
31

Type III secretion system (T3SS) is a protein translocator complex family including pathogenic injectisome or bacterial flagellum. The inejectisomal T3SS serves to deliver virulence proteins into host cell and the flagellar T3SS constructs the flagellar axial structure. Although earlier studies have provided many findings on the molecular mechanism of the Type III protein export, they were not sufficient to reveal energy transduction mechanism due to difficulties in controlling measurement conditions in vivo. Recently, we developed an in vitro flagellar Type III protein transport assay system using inverted membrane vesicles (IMVs), and analyzed protein export by using the in vitro method. We reproduced protein export of the flagellar T3SS, hook assembly and substrate specificity switch in IMV to a similar extent to what is seen in living cell. Furthermore, we demonstrated that ATP-hydrolysis energy can drive protein transport even in the absence of proton-motive force (PMF). In this mini-review, we will summarize our new in vitro Type III transport assay method and our findings on the molecular mechanism of Type III protein export.
著者
Akiko Higuchi Naoki Nonaka Kei Yura
出版者
The Biophysical Society of Japan
雑誌
Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日
vol.15, pp.94-103, 2018 (Released:2018-04-27)
参考文献数
50
被引用文献数
3

Membrane transporter proteins play important roles in transport of nutrients into the cell, in transport of waste out of the cell, in maintenance of homeostasis, and in signal transduction. Solute carrier (SLC) transporter is the superfamily, which has the largest number of genes (>400 in humans) in membrane transporter and consists of 52 families. SLC transporters carry a wide variety of substrates such as amino acids, peptides, saccharides, ions, neurotransmitters, lipids, hormones and related materials. Despite the apparent importance for the substrate transport, the information of sequence variation and three-dimensional structures have not been integrated to the level of providing new knowledge on the relationship to, for instance, diseases. We, therefore, built a new database named iMusta4SLC, which is available at http://cib.cf.ocha.ac.jp/slc/, that connected the data of structural properties and of pathogenic mutations on human SLC transporters. iMusta4SLC helps to investigate the structural features of pathogenic mutations on SLC transporters. With this database, we found that the mutations at the conserved arginine were frequently involved in diseases, and were located at a border between the membrane and the cytoplasm. Especially in SLC families 2 and 22, the conserved residues formed a large cluster at the border. In SLC2A1, one third of the reported pathogenic missense mutations were found in this conserved cluster.
著者
Ken H. Nagai
出版者
The Biophysical Society of Japan
雑誌
Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日
vol.15, pp.51-57, 2018 (Released:2018-02-09)
参考文献数
33
被引用文献数
1

Self-propelled rods, which propel by themselves in the direction from the tail to the head and align nematically through collision, have been well-investigated theoretically. Various phenomena including true long-range ordered phase with the Giant number fluctuations, and the collective motion composed of many vorices were predicted using the minimal mathematical models of self-propelled rods. Using filamentous bacteria and running microtubules, we found that the predicted phenomena by the minimal models occur in the real world. This strongly indicates that there exists the unified description of self-propelled rods independent of the details of the systems. The theoretically predicted phenomena and the experimental results concerning the phenomena are reviewed.
著者
Kazunori D. Yamada Hafumi Nishi Junichi Nakata Kengo Kinoshita
出版者
The Biophysical Society of Japan
雑誌
Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日
vol.13, pp.157-163, 2016 (Released:2016-07-14)
参考文献数
41
被引用文献数
2

Functional sites on proteins play an important role in various molecular interactions and reactions between proteins and other molecules. Thus, mutations in functional sites can severely affect the overall phenotype. Progress of genome sequencing projects has yielded a wealth of information on single nucleotide variants (SNVs), especially those with less than 1% minor allele frequency (rare variants). To understand the functional influence of genetic variants at a protein level, we investigated the relationship between SNVs and protein functional sites in terms of minor allele frequency and the structural position of variants. As a result, we observed that SNVs were less abundant at ligand binding sites, which is consistent with a previous study on SNVs and protein interaction sites. Additionally, we found that non-rare variants tended to be located slightly apart from enzyme active sites. Examination of non-rare variants revealed that most of the mutations resulted in moderate changes of the physico-chemical properties of amino acids, suggesting the existence of functional constraints. In conclusion, this study shows that the mapping of genetic variants on protein structures could be a powerful approach to evaluate the functional impact of rare genetic variations.
著者
Saeko Yanaka Takamasa Ueno Kouhei Tsumoto Kenji Sugase
出版者
The Biophysical Society of Japan
雑誌
BIOPHYSICS (ISSN:13492942)
巻号頁・発行日
vol.11, pp.103-106, 2015 (Released:2015-04-18)
参考文献数
7

Structural fluctuation on microsecond to millisecond time scales has been reported to play an important role in proteins that undergo significant structural change during their expression of function. In these proteins, the structural change was obvious in the crystal structures. However, protein motions in solution could contribute to the function of proteins, even if no significant structural difference is observed in crystal structure of different states while they function. In this review, we introduce our recent report on the stabilization mechanism of human leukocyte antigen, and the possibility of fluctuation contributing to several biophysical properties of proteins.