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1.
Eur Biophys J ; 53(1-2): 15-25, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38233601

ABSTRACT

The α7 nicotinic acetylcholine receptor is a member of the nicotinic acetylcholine receptor family and is composed of five α7 subunits arranged symmetrically around a central pore. It is localized in the central nervous system and immune cells and could be a target for treating Alzheimer's disease and schizophrenia. Acetylcholine is a ligand that opens the channel, although prolonged application rapidly decreases the response. Ivermectin was reported as one of the positive allosteric modulators, since the binding of Ivermectin to the channel enhances acetylcholine-evoked α7 currents. One research has suggested that tilting motions of the nicotinic acetylcholine receptor are responsible for channel opening and activation. To verify this hypothesis applies to α7 nicotinic acetylcholine receptor, we utilized a diffracted X-ray tracking method to monitor the stable twisting and tilting motion of nAChR α7 without a ligand, with acetylcholine, with Ivermectin, and with both of them. The results show that the α7 nicotinic acetylcholine receptor twists counterclockwise with the channel transiently opening, transitioning to a desensitized state in the presence of acetylcholine and clockwise without the channel opening in the presence of Ivermectin. We propose that the conformational transition of ACh-bound nAChR α7 may be due to the collective twisting of the five α7 subunits, resulting in the compression and movement, either downward or upward, of one or more subunits, thus manifesting tilting motions. These tilting motions possibly represent the transition from the resting state to channel opening and potentially to the desensitized state.


Subject(s)
Receptors, Nicotinic , alpha7 Nicotinic Acetylcholine Receptor , alpha7 Nicotinic Acetylcholine Receptor/chemistry , alpha7 Nicotinic Acetylcholine Receptor/metabolism , Acetylcholine/chemistry , Acetylcholine/metabolism , Ligands , Ivermectin/pharmacology , Receptors, Nicotinic/chemistry , Receptors, Nicotinic/metabolism , Allosteric Regulation
2.
Int J Mol Sci ; 22(10)2021 May 17.
Article in English | MEDLINE | ID: mdl-34067933

ABSTRACT

Serotonin receptors play important roles in neuronal excitation, emotion, platelet aggregation, and vasoconstriction. The serotonin receptor subtype 2A (5-HT2AR) is a Gq-coupled GPCR, which activate phospholipase C. Although the structures and functions of 5-HT2ARs have been well studied, little has been known about their real-time dynamics. In this study, we analyzed the intramolecular motion of the 5-HT2AR in living cells using the diffracted X-ray tracking (DXT) technique. The DXT is a very precise single-molecular analytical technique, which tracks diffraction spots from the gold nanocrystals labeled on the protein surface. Trajectory analysis provides insight into protein dynamics. The 5-HT2ARs were transiently expressed in HEK 293 cells, and the gold nanocrystals were attached to the N-terminal introduced FLAG-tag via anti-FLAG antibodies. The motions were recorded with a frame rate of 100 µs per frame. A lifetime filtering technique demonstrated that the unliganded receptors contain high mobility population with clockwise twisting. This rotation was, however, abolished by either a full agonist α-methylserotonin or an inverse agonist ketanserin. Mutation analysis revealed that the "ionic lock" between the DRY motif in the third transmembrane segment and a negatively charged residue of the sixth transmembrane segment is essential for the torsional motion at the N-terminus of the receptor.


Subject(s)
Receptor, Serotonin, 5-HT2A/metabolism , Receptor, Serotonin, 5-HT2A/physiology , Single Molecule Imaging/methods , Carrier Proteins/metabolism , Crystallography, X-Ray/methods , Gold , HEK293 Cells , Humans , Ions/metabolism , Ligands , Nanotechnology/methods , Receptors, Serotonin/metabolism , Receptors, Serotonin/physiology , X-Ray Diffraction/methods , X-Rays
3.
PLoS One ; 16(3): e0247969, 2021.
Article in English | MEDLINE | ID: mdl-33690686

ABSTRACT

Jinyunpelta sinensis is a basal ankylosaurine dinosaur excavated from the mid Cretaceous Liangtoutang Formation of Jinyun County, Zhejiang Province, China. In the present study, its dental microwear was observed using a confocal laser microscope. Jinyunpelta had steep wear facets that covered most of buccal surfaces of posterior dentary teeth. Observation of dental microwear on the wear facet revealed that scratch orientation varied according to its location within the wear facet: vertically (i.e. apicobasally) oriented scratches were dominant in the upper half of the wear facet, and horizontally (i.e. mesiolaterally) oriented ones were in the bottom of the facet. These findings indicated that Jinyunpelta adopted precise tooth occlusion and biphasal jaw movement (orthal closure and palinal lower jaw movement). The biphasal jaw movement was widely observed among nodosaurids, among ankylosaurids, it was previously only known from the Late Cretaceous North American taxa, and not known among Asian ankylosaurids. The finding of biphasal jaw movement in Jinyunpelta showed sophisticate feeding adaptations emerged among ankylosaurids much earlier (during Albian or Cenomanian) than previously thought (during Campanian). The Evolution of the biphasal jaw mechanism that contemporaneously occurred among two lineages of ankylosaurs, ankylosaurids and nodosaurids, showed high evolutionary plasticity of ankylosaur jaw mechanics.


Subject(s)
Dinosaurs/anatomy & histology , Tooth Wear/pathology , Adaptation, Physiological , Animals , Biological Evolution , China , Fossils/anatomy & histology , History, Ancient , Jaw/anatomy & histology , Mandible/anatomy & histology , Mastication/physiology , Paleodontology/methods , Tooth/anatomy & histology , Tooth Wear/veterinary
4.
J Phys Chem B ; 124(51): 11617-11624, 2020 12 24.
Article in English | MEDLINE | ID: mdl-33296594

ABSTRACT

Transient receptor potential vanilloid type 1 (TRPV1) channels are activated by heat, vanilloids, and extracellular protons. Cryo-EM has revealed various conformations of TRPV1, and these structures suggest an intramolecular twisting motion in response to ligand binding. However, limited experimental data support this observation. Here, we analyzed the intramolecular motion of TRPV1 using diffracted X-ray tracking (DXT). DXT analyzes trajectories of Laue spots generated from attached gold nanocrystals and provides picometer spatial and microsecond time scale information about the intramolecular motion. We observed that both an agonist and a competitive antagonist evoked a rotating bias in TRPV1, though these biases were in opposing directions. Furthermore, the rotational bias generated by capsaicin was reversed between the wild-type and the capsaicin-insensitive Y511A mutant. Our findings bolster the understanding of the mechanisms used for activation and modulation of TRP channels, and this knowledge can be exploited for pharmacological usage such as inhibitor design.


Subject(s)
Capsaicin , Hot Temperature , Capsaicin/pharmacology , Motion , Protons
5.
Biochem Biophys Res Commun ; 529(2): 306-313, 2020 08 20.
Article in English | MEDLINE | ID: mdl-32703428

ABSTRACT

G protein-coupled receptors (GPCRs) are seven-transmembrane proteins, which transmit extracellular signals inside cells via activating G proteins. GPCRs are involved in a wide variety of physiological functions, such as signal sensing, immune system processes, and neurotransmission. Although the structures and functions of GPCRs have been well studied, little has been known about their real-time dynamics on live cells. In this study, we used Diffracted X-ray Tracking (DXT) and Diffracted X-ray Blinking (DXB) techniques for analysis. These methods are very precise single-molecular analytical techniques that elucidate protein dynamics by analyzing the diffraction spots from the gold nanocrystals labeled on the protein surface. DXT tracks diffraction spot movements, whereas DXB analyzes continuation of signals by calculating the autocorrelation function of each pixel from the recorded data. Serotonin receptor subtype 2A (5-HT2A receptors) were transiently expressed on HEK 293 cells, and the gold nanocrystals were attached to the N-terminally introduced FLAG-tag via anti-FLAG antibodies. Fast- and mid-range motions were recorded by DXT with 100µs and 1.25 ms/frame rate, respectively. Slow-range motion was obtained using the DXB method with 100 ms/frame rate. An agonist interestingly suppressed the fluctuations of 5-HT2A receptors at the microsecond-ranged fast measurement. On the contrary, the motion was enhanced by the agonist in the hundred-millisecond-ranged slow time scale. These dual-natured data may suggest that we succeeded in extracting different modes of receptor's motion on live cells; microsecond ranged fluctuation on the cell membrane, and millisecond-ranged dynamic movement comprising interactions with intracellular signaling molecules.


Subject(s)
Receptor, Serotonin, 5-HT2A/analysis , Equipment Design , HEK293 Cells , Humans , Kinetics , Motion , Single Molecule Imaging/instrumentation , Single Molecule Imaging/methods , X-Ray Diffraction/instrumentation , X-Ray Diffraction/methods
6.
Integr Org Biol ; 2(1): obaa042, 2020.
Article in English | MEDLINE | ID: mdl-33791579

ABSTRACT

Body size is fundamental to the physiology and ecology of organisms. Crocodyliforms are no exception, and several methods have been developed to estimate their absolute body sizes from bone measurements. However, species-specific sizes, such as sexually mature sizes and the maximum sizes were not taken into account due to the challenging maturity assessment of osteological specimens. Here, we provide a vertebrae-based method to estimate absolute and species-specific body lengths in crocodylians. Lengths of cervical to anterior caudal centra were measured and relations between the body lengths (snout-vent and total lengths [TLs]) and lengths of either a single centrum or a series of centra were modeled for extant species. Additionally, states of neurocentral (NC) suture closure were recorded for the maturity assessment. Comparisons of TLs and timings of NC suture closure showed that most extant crocodylians reach sexual maturity before closure of precaudal NC sutures. Centrum lengths (CLs) of the smallest individuals with closed precaudal NC sutures within species were correlated with the species maximum TLs in extant taxa; therefore, the upper or lower limit of the species maximum sizes can be determined from CLs and states of NC suture closure. The application of the current method to noncrocodylian crocodyliforms requires similar numbers of precaudal vertebrae, body proportions, and timings of NC suture closure as compared to extant crocodylians.

7.
Methods Mol Biol ; 2070: 57-77, 2020.
Article in English | MEDLINE | ID: mdl-31625090

ABSTRACT

Directed in vitro evolution (IVE) is now a widely applied technology to obtain molecules that have designed new features of one's demands. We describe here experimental procedures for a cDNA display IVE to select peptide aptamers from a scaffold-based random peptide library. A three-finger (3-F) peptide library is exemplified, which has been shown its pluripotency to various target molecules. Peptide scaffolds including 3-F are refined through evolution, and they are mostly stabilized by disulfide bridges. To utilize such disulfide-containing protein library in IVE, we optimized the translation and folding conditions. Co-translational folding assisted by protein disulfide isomerase was found to have better efficiency than posttranslational refolding in the IVE. Linker is also a key element to make a tight genotype-phenotype linkage. Here, we introduced a whole procedure of IVE to use a newly designed puromycin linker, which was synthesized by a novel branching strategy. The improved linker enabled rapid and highly efficient ligation of mRNA and synthesis of protein fusions.


Subject(s)
DNA, Complementary , Directed Molecular Evolution , Peptide Library , Protein Engineering , DNA, Complementary/chemistry , DNA, Complementary/genetics , Disulfides/chemistry
8.
Syst Biol ; 68(6): 1034-1051, 2019 11 01.
Article in English | MEDLINE | ID: mdl-31135923

ABSTRACT

Network methods are widely used to represent and analyze biogeography. It is difficult, however, to convert occurrence data of fossil vertebrates to a biogeographical network, as most species were known from a single locality. A new method for creating a biogeographical network that can incorporate phylogenetic information is proposed in this study, which increases the number of edges in the network of fossil vertebrates and enables the application of various network methods. Using ancestral state reconstruction via maximum parsimony, the method first estimates the biogeographical regions of all internal nodes of a given phylogeny using biogeographical information on the terminal taxa. Then, each internal node in the phylogenetic tree is converted to an edge in the biogeographical network that connects the region(s), if unambiguously estimated, of its two descendants. The new method was applied to phylogenetic trees generated by a birth-death model. Under all conditions tested, an average of $CDATA[$CDATA[$>$$70% of the internal nodes in phylogenetic trees were converted into edges. Three network indices-link density, average link weight, and endemism index (EI)-were evaluated for their usefulness in comparing different biogeographical networks. The EI reflects the rate of dispersal; the other indices reflect nonbiogeographical parameters, the number of taxa and regions, which highlights the importance of evaluating network indices before applying them to biogeographical studies. Multiple Cretaceous biogeographical networks were constructed from the phylogenies of five tetrapod taxa: terrestrial crocodyliforms, terrestrial turtles, nonavian dinosaurs, avians, and pterosaurs. The networks of avians and pterosaurs showed similar topologies and a strong correlation, and unexpectedly high endemism indices. These similarities were probably a result of shared taphonomic biases (i.e., the Lagerstätten effect) for volant taxa with fragile skeletons. The crocodyliform network was partitioned into the Gondwanan and Laurasian continents. The dinosaur network was partitioned into three groups of continents: 1) North America, Asia, and Australia; 2) Europe and Africa; and 3) India, Madagascar, and South America. When Early and Late Cretaceous dinosaurs were analyzed separately, the dinosaur networks were divided into 1) North America, Asia, and Australia; and 2) Europe, Africa, India, and South America for the Early Cretaceous and 1) North America, Asia, and Europe; and 2) India, Madagascar, and South America for the Late Cretaceous. This partitioning of dinosaur and crocodyliform networks corroborates the results of previous biogeographical studies and indicates that the method introduced here can retrieve biogeographical signals from a source phylogeny when sufficient data are available for most targeted biogeographical regions.


Subject(s)
Classification/methods , Phylogeny , Animals , Fossils , Phylogeography
9.
Proc Natl Acad Sci U S A ; 116(7): 2618-2623, 2019 02 12.
Article in English | MEDLINE | ID: mdl-30692262

ABSTRACT

Terrestrial mammals have evolved various foot postures: flat-footed (plantigrady), tiptoed (digitigrady), and hooved (unguligrady) postures. Although the importance of foot posture on ecology and body size of mammalian species has been widely recognized, its evolutionary trajectory and influence on body size evolution across mammalian phylogeny remain untested. Taking a Bayesian phylogenetic approach combined with a comprehensive dataset of foot postures in 880 extant mammalian species, we investigated the evolutionary history of foot postures and rates of body size evolution, within the same posture and at transitions between postures. Our results show that the common ancestor of mammals was plantigrade, and transitions predominantly occurred only between plantigrady and digitigrady and between digitigrady and unguligrady. At the transitions between plantigrady and digitigrady and between digitigrady and unguligrady, rates of body size evolution are significantly elevated leading to the larger body masses of digitigrade species (∼1 kg) and unguligrade species (∼78 kg) compared with their respective ancestral postures [plantigrady (∼0.75 kg) and digitigrady]. Our results demonstrate the importance of foot postures on mammalian body size evolution and have implications for mammalian body size increase through time. In addition, we highlight a way forward for future studies that seek to integrate morphofunctional and macroevolutionary approaches.


Subject(s)
Biological Evolution , Body Size , Foot/anatomy & histology , Mammals/physiology , Animals , Bayes Theorem , Biomechanical Phenomena , Foot/physiology , Phylogeny
10.
Sci Rep ; 8(1): 17090, 2018 11 30.
Article in English | MEDLINE | ID: mdl-30504916

ABSTRACT

Single molecule dynamics studies have begun to use quantum probes. Single particle analysis using cryo-transmission electron microscopy has dramatically improved the resolution when studying protein structures and is shifting towards molecular motion observations. X-ray free-electron lasers are also being explored as routes for determining single molecule structures of biological entities. Here, we propose a new X-ray single molecule technology that allows observation of molecular internal motion over long time scales, ranging from milliseconds up to 103 seconds. Our method uses both low-dose monochromatic X-rays and nanocrystal labelling technology. During monochromatic X-ray diffraction experiments, the intensity of X-ray diffraction from moving single nanocrystals appears to blink because of Brownian motion in aqueous solutions. X-ray diffraction spots from moving nanocrystals were observed to cycle in and out of the Bragg condition. Consequently, the internal motions of a protein molecule labelled with nanocrystals could be extracted from the time trajectory using this diffracted X-ray blinking (DXB) approach. Finally, we succeeded in distinguishing the degree of fluctuation motions of an individual acetylcholine-binding protein (AChBP) interacting with acetylcholine (ACh) using a laboratory X-ray source.


Subject(s)
Motion , Proteins/chemistry , X-Ray Diffraction/methods , Acetylcholine/chemistry , Cryoelectron Microscopy/methods , Microscopy, Electron, Transmission/methods
11.
PLoS One ; 13(10): e0204719, 2018.
Article in English | MEDLINE | ID: mdl-30352053

ABSTRACT

Categorizing the archaeological remains of Sus scrofa as domesticated "pigs" or wild "boars" is often difficult because of their morphological and genetic similarities. For this purpose, we tested whether feeding ecological change of S. scrofa that accompanied their domestication can be detected based on the three-dimensional texture created on the tooth enamel surface by mastication. We scanned the lower tooth surface of one wild and one stall-fed populations of modern S. s. leucomystax and one wild population of S. s. riukiuanus by using a confocal laser microscope. The average body weight of S. s. leucomystax is twice as heavier as that of S. s. riukiuanus. The textures were quantified using the industrial "roughness" standard, ISO 25178, to prevent inter-observer errors and to distinguish small differences that were difficult to detect by two dimensional image observation. The values of parameters related to height and volume were significantly larger in the stall-fed population. Twenty parameters differed significantly between the stall-fed and wild population of S. s. leucomystax, which indicated that the feeding ecological difference affected the ISO parameters of the two boar populations. Six parameters also differed between the wild populations of S. s. leucomystax and S. s. riukiuanus. Surprisingly, no parameter differed between the populations of stall-fed S. s. leucomystax and wild S. s. riukiuanus. Consumption of hard nuts and/or agricultural fruits and crops by the wild population of S. s. riukiuanus may have produced a tooth surface texture similar to that of the stall-fed population of S. s. leucomystax. Further analysis of S. s. riukiuanus with a known diet is necessary to conclude whether ISO parameters reflect the dietary transition accompanying the domestication of Sus (e.g., wild, semi-domestic, and domestic). Until then, caution is needed in discriminating domesticated populations from wild populations that mainly feed on hard objects.


Subject(s)
Dental Enamel/anatomy & histology , Sus scrofa/anatomy & histology , Animals , Animals, Wild/anatomy & histology , Diet , Domestication , Female , Japan , Male , Mastication , Microscopy, Confocal , Species Specificity , Surface Properties , Sus scrofa/classification , Sus scrofa/physiology , Swine , Swine Diseases/pathology , Tooth Wear/pathology , Tooth Wear/veterinary
12.
R Soc Open Sci ; 5(3): 171774, 2018 Mar.
Article in English | MEDLINE | ID: mdl-29657781

ABSTRACT

Although two major clades of crocodylians (Alligatoroidea and Crocodyloidea) were split during the Cretaceous period, relatively few morphological and functional differences between them have been known. In addition, interaction of multiple morphofunctional systems that differentiated their ecology has barely been assessed. In this study, we examined the limb proportions of crocodylians to infer the differences of locomotor functions between alligatoroids and crocodyloids, and tested the correlation of locomotor and feeding morphofunctions. Our analyses revealed crocodyloids including Gavialis have longer stylopodia (humerus and femur) than alligatoroids, indicating that two groups may differ in locomotor functions. Fossil evidence suggested that alligatoroids have retained short stylopodia since the early stage of their evolution. Furthermore, rostral shape, an indicator of trophic function, is correlated with limb proportions, where slender-snouted piscivorous taxa have relatively long stylopodia and short overall limbs. In combination, trophic and locomotor functions might differently delimit the ecological opportunity of alligatoroids and crocodyloids in the evolution of crocodylians.

13.
PLoS One ; 12(11): e0188023, 2017.
Article in English | MEDLINE | ID: mdl-29186178

ABSTRACT

Dental microwear of four postcanine teeth of Exaeretodon argentinus was analyzed using both two dimensional (2D) and three dimensional (3D) methods to infer their masticatory jaw movements. Results of both methods were congruent, showing that linear microwear features (scratches) were well aligned and mostly directed to the antero-posterior direction in all four teeth examined. These findings support the palinal masticatory jaw movement, which was inferred in previous studies based on the observation of gross morphology of wear facets. In contrast, the lack of detection of lateral scratches confirmed the absence of the lateral jaw movement that was also proposed by a previous study. Considering previous microwear studies on cynodonts, palinal jaw movements observed in Exaeretodon evolved within cynognathian cynodonts from the fully orthal jaw movement of its basal member. Although there are currently only three studies of dental microwear of non-mammalian cynodonts including the present study, microwear analysis is a useful tool for the reconstruction of masticatory jaw movement and its future application to various cynodonts will shed light on the evolutionary process of jaw movement towards the mammalian condition in more detail.


Subject(s)
Fishes/physiology , Jaw/physiology , Mastication , Tooth Wear , Animals , Fossils
14.
ACS Comb Sci ; 18(2): 117-29, 2016 Feb 08.
Article in English | MEDLINE | ID: mdl-26812183

ABSTRACT

We describe a high performance platform based on cDNA display technology by developing a new modified puromycin linker-oligonucleotide. The linker consists of four major characteristics: a "ligation site" for hybridization and ligation of mRNA by T4 RNA ligase, a "puromycin arm" for covalent linkage of the protein, a "polyadenosine site" for a longer puromycin arm and purification of protein fusions (optional) using oligo-dT matrices, and a "reverse transcription site" for the formation of stable cDNA protein fusions whose cDNA is covalently linked to its encoded protein. The linker was synthesized by a novel branching strategy and provided >8-fold higher yield than previous linkers. This linker enables rapid and highly efficient ligation of mRNA (>90%) and synthesis of protein fusions (∼ 50-95%) in various cell-free expression systems. Overall, this new cDNA display method provides 10-200 fold higher end-usage fusions than previous methods and benefits higher diversity libraries crucial for directed protein/peptide evolution. With the increased efficiency, this system was able to reduce the time for one selection cycle to <8 h and is potentially amenable to high-throughput systems. We demonstrate the efficiency of this system for higher throughput selections of various biomolecular interactions and achieved 30-40-fold enrichment per selection cycle. Furthermore, a 4-fold higher enrichment of Flag-tag was obtained from a doped mixture compared with that of the previous cDNA display method. A three-finger protein library was evolved to isolate superior nanomolar range binding candidates for vascular endothelial growth factor. This method is expected to provide a beneficial impact to accelerated drug discovery and proteome analysis.


Subject(s)
DNA, Complementary/chemistry , Directed Molecular Evolution/methods , High-Throughput Screening Assays/methods , Recombinant Proteins/metabolism , Oligonucleotides/chemistry , Peptide Library , Peptides , Protein Conformation , Puromycin/chemistry , RNA Ligase (ATP) , Recombinant Proteins/chemistry , Viral Proteins
15.
PLoS One ; 11(1): e0145716, 2016.
Article in English | MEDLINE | ID: mdl-26790003

ABSTRACT

Dinosaurs had functionally digitigrade or sub-unguligrade foot postures. With their immediate ancestors, dinosaurs were the only terrestrial nonplantigrades during the Mesozoic. Extant terrestrial mammals have different optimal body sizes according to their foot posture (plantigrade, digitigrade, and unguligrade), yet the relationship of nonplantigrade foot posture with dinosaur body size has never been investigated, even though the body size of dinosaurs has been studied intensively. According to a large dataset presented in this study, the body sizes of all nonplantigrades (including nonvolant dinosaurs, nonvolant terrestrial birds, extant mammals, and extinct Nearctic mammals) are above 500 g, except for macroscelid mammals (i.e., elephant shrew), a few alvarezsauroid dinosaurs, and nondinosaur ornithodirans (i.e., the immediate ancestors of dinosaurs). When nonplantigrade tetrapods evolved from plantigrade ancestors, lineages with nonplantigrade foot posture exhibited a steady increase in body size following Cope's rule. In contrast, contemporaneous plantigrade lineages exhibited no trend in body size evolution and were largely constrained to small body sizes. This evolutionary pattern of body size specific to foot posture occurred repeatedly during both the Mesozoic and the Cenozoic eras. Although disturbed by the end-Cretaceous extinction, species of mid to large body size have predominantly been nonplantigrade animals from the Jurassic until the present; conversely, species with small body size have been exclusively composed of plantigrades in the nonvolant terrestrial tetrapod fauna.


Subject(s)
Body Size/physiology , Dinosaurs/anatomy & histology , Foot/anatomy & histology , Posture/physiology , Animals , Biological Evolution , Dinosaurs/classification , Dinosaurs/physiology , Foot/physiology , Fossils/anatomy & histology , Paleontology , Species Specificity
16.
Biosci Biotechnol Biochem ; 80(1): 158-61, 2016.
Article in English | MEDLINE | ID: mdl-26211734
17.
Sci Rep ; 4: 6384, 2014 Sep 16.
Article in English | MEDLINE | ID: mdl-25223459

ABSTRACT

We observed the dynamic three-dimensional (3D) single molecule behaviour of acetylcholine-binding protein (AChBP) and nicotinic acetylcholine receptor (nAChR) using a single molecule tracking technique, diffracted X-ray tracking (DXT) with atomic scale and 100 µs time resolution. We found that the combined tilting and twisting motions of the proteins were enhanced upon acetylcholine (ACh) binding. We present the internal motion maps of AChBP and nAChR in the presence of either ACh or α-bungarotoxin (αBtx), with views from two rotational axes. Our findings indicate that specific motion patterns represented as biaxial angular motion maps are associated with channel function in real time and on an atomic scale.


Subject(s)
Acetylcholine/chemistry , Bungarotoxins/chemistry , Carrier Proteins/chemistry , Receptors, Nicotinic/chemistry , Acetylcholine/metabolism , Animals , Aplysia/growth & development , Aplysia/metabolism , Binding Sites , Bungarotoxins/metabolism , Carrier Proteins/metabolism , Crystallography, X-Ray , Models, Molecular , Protein Conformation , Receptors, Nicotinic/metabolism , Torpedo/growth & development , Torpedo/metabolism
18.
Anal Chem ; 86(17): 8535-40, 2014 Sep 02.
Article in English | MEDLINE | ID: mdl-25079196

ABSTRACT

Immobilization of a protein in a functionally active form and correct orientation for high-throughput analysis is crucial for surface-based protein-molecular interaction studies and should aid progress in associated nanotechnologies. Here, we present a general method for controlled and oriented immobilization of proteins by a puromycin-linker for cDNA display technology. The utility and potential of this method was demonstrated by examining the interaction between the B domain of protein A and immunoglobulin G (IgG) by surface plasmon resonance. This study revealed that the mRNA fragment of the mRNA-protein fusion (i.e., mRNA display) interferes with the interaction between the protein (B domain) and its target molecule (IgG). This results in a reduction of the apparent affinity by ~10-fold. This method is expected to find wide appeal in the fields of surface-based studies of protein-protein interactions, drug screening, and single molecule analysis that require only a small amount of protein sample.


Subject(s)
Biotin/chemistry , Immunoglobulin G/chemistry , Puromycin/chemistry , Staphylococcal Protein A/chemistry , Surface Plasmon Resonance , Biotin/metabolism , Biotinylation , Cell-Free System , Immobilized Proteins/chemistry , Immobilized Proteins/metabolism , Immunoglobulin G/metabolism , Protein Biosynthesis , Protein Interaction Domains and Motifs , Protein Structure, Tertiary , Quartz Crystal Microbalance Techniques , RNA, Messenger/chemistry , RNA, Messenger/metabolism , Staphylococcal Protein A/metabolism
19.
J Recept Signal Transduct Res ; 34(3): 154-61, 2014 Jun.
Article in English | MEDLINE | ID: mdl-24308378

ABSTRACT

Directed evolution is a very popular strategy for improving biophysical properties and even for generating proteins with novel functions. Recent advances in combinatorial protein engineering mean it is now possible to develop protein scaffolds that could substitute for whole antibody-associated properties as emerging therapeutic proteins. In particular, disulfide-rich proteins are attractive templates for directed evolution in the search for novel molecules because they can regulate the activities of receptors, enzymes, and other molecules. Previously, we demonstrated that functional regulatory molecules against interleukin-6 receptor (IL-6R) could be obtained by directed evolution of the three-finger toxin (3F) scaffold. In the present study, trypsin was selected as a target for directed evolution to further explore the potential use of the 3F cDNA display library. After seven rounds of selection, the DNA sequences converged. The recombinant proteins produced by the selected candidates had inhibitory activity against trypsin (Ki of 33-450 nM). Three of the six groups had Ki values that were comparable to bovine pancreatic trypsin inhibitor and soybean trypsin inhibitor. Two of the candidates also had inhibitory effects against chymotrypsin and kallikrein. This study suggests that 3F protein is suitable for the preparation of high-diversity libraries that can be utilized to obtain protease inhibitors. In addition to our previous successful targeting of IL-6R, the technique developed in our studies may have wide applications in the generation of regulatory molecules for targets of interest, such as receptors, enzymes for research, diagnostic applications, and therapeutic uses.


Subject(s)
Directed Molecular Evolution/methods , Peptide Hydrolases/chemistry , Peptides/chemistry , Peptides/metabolism , Recombinant Proteins/biosynthesis , Serine Proteinase Inhibitors/biosynthesis , Serine Proteinase Inhibitors/chemistry , Gene Library , Peptides/genetics , Recombinant Proteins/genetics , Serine Proteinase Inhibitors/genetics
20.
Int J Pept ; 2012: 731293, 2012.
Article in English | MEDLINE | ID: mdl-22500178

ABSTRACT

Tarantula venom glands produce a large variety of bioactive peptides. Here we present the identification of venom components obtained by sequencing clones isolated from a cDNA library prepared from the venom glands of the Chilean common tarantula, Grammostola rosea. The cDNA sequences of about 1500 clones out of 4000 clones were analyzed after selection using several criteria. Forty-eight novel toxin-like peptides (GTx1 to GTx7, and GTx-TCTP and GTx-CRISP) were predicted from the nucleotide sequences. Among these peptides, twenty-four toxins are ICK motif peptides, eleven peptides are MIT1-like peptides, and seven are ESTX-like peptides. Peptides similar to JZTX-64, aptotoxin, CRISP, or TCTP are also obtained. GTx3 series possess a cysteine framework that is conserved among vertebrate MIT1, Bv8, prokineticins, and invertebrate astakines. GTx-CRISP is the first CRISP-like protein identified from the arthropod venom. Real-time PCR revealed that the transcripts for TCTP-like peptide are expressed in both the pereopodal muscle and the venom gland. Furthermore, a unique peptide GTx7-1, whose signal and prepro sequences are essentially identical to those of HaTx1, was obtained.

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