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ABSTRACT: The hepatitis B virus x protein (HBX) is expressed in HBV-infected liver cells and can interact with a wide range of cellular proteins. In order to understand such promiscuous behavior of HBX we expressed a truncated mini-HBX protein (named Tr-HBX) (residues 18-142) with 5 Cys → Ser mutations and characterized its structural features using circular dichroism (CD) spectropolarimetry, NMR spectroscopy as well as bioinformatics tools for predicting disorder in intrinsically unstructured proteins (IUPs). The secondary structural content of Tr-HBX from CD data suggests that Tr-HBX is only partially folded. The protein disorder prediction by IUPred reveals that the unstructured region encompasses its N-terminal ~30 residues of Tr-HBX. A two-dimensional (1)H-(15)N HSQC NMR spectrum exhibits fewer number of resonances than expected, suggesting that Tr-HBX is a hybrid type IUP where its folded C-terminal half coexists with a disordered N-terminal region. Many IUPs are known to be capable of having promiscuous interactions with a multitude of target proteins. Therefore the intrinsically disordered nature of Tr-HBX revealed in this study provides a partial structural basis for the promiscuous structure-function behavior of HBX.
Molecules and Cells 07/2012; 34(2):165-9. · 2.18 Impact Factor
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ABSTRACT: Intrinsically unfolded proteins (IUPs) do not obey the golden rule of structural biology, 3D structure = function, as they manifest their inherent functions without resorting to three-dimensional structures. Absence of a compact globular topology in these proteins strongly implies that their ligand recognition processes should involve factors other than spatially well-defined binding pockets. Heteronuclear multidimensional (HetMulD) NMR spectroscopy assisted with a stable isotope labeling technology is a powerful tool for quantitatively investigating detailed structural features in IUPs. In particular, it allows us to delineate the presence and locations of pre-structured motifs (PreSMos) on a per-residue basis. PreSMos are the transient local structural elements that presage target-bound conformations and act as specificity determinants for IUP recognition by target proteins. Here, we present a brief chronicle of HetMulD NMR studies on IUPs carried out over the past two decades along with a discussion on the functional significance of PreSMos in IUPs.
Current Protein and Peptide Science 10/2011; 13(1):34-54. · 2.89 Impact Factor
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ABSTRACT: Transcriptional activation domain (TAD) in virion protein 16 (VP16) of herpes simplex virus does not have any globular structure, yet exhibits a potent transcriptional activity. In order to probe the structural basis for the transcriptional activity of VP16 TAD, we have used NMR spectroscopy to investigate its detailed structural features. Results show that an unbound VP16 TAD is not merely "unstructured" but contains four short motifs (residues 424-433, 442-446, 465-467 and 472-479) with transient structural order. Pre-structured motifs in other intrinsically unfolded proteins (IUPs) were shown to be critically involved in target protein binding. The 472-479 motif was previously shown to bind to hTAF(II)31, whereas the hTAF(II)31-binding ability of other motifs found in this study has not been addressed. The VP16 TAD represents another IUP whose prestructured motifs mediate promiscuous binding to various target proteins.
BMB reports 08/2009; 42(7):411-7. · 1.72 Impact Factor
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ABSTRACT: Hypoxia-inducible factor 1alpha (HIF1alpha) is a transcription factor that plays a key role in the adaptation of cells to low oxygen stress and oxygen homeostasis. The oxygen-dependent degradation (ODD) domain of HIF1alpha responsible for the negative regulation of HIF1alpha in normoxia is intrinsically unfolded. Here, we carried out the backbone (1)H, (15)N, and (13)C resonance assignment of a proteolysis-resistant fragment (residues 404-477) in the HIF1alpha ODD domain using NMR spectroscopy. About 98% (344/352) of all the (1)HN, (15)N, (13)Calpha, (13)Cbeta, and (13)CO resonances were unambiguously assigned. The results will be useful for further investigation of the structural and dynamic states of the HIF1alpha ODD domain and its interaction with binding partners.
Molecules and Cells 05/2009; 27(4):493-6. · 2.18 Impact Factor
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ABSTRACT: The preS1 surface protein of the hepatitis B virus (HBV) is a key factor involved in initial viral entry into hepatocytes. It has been long postulated that an anti-HBV effect should be achievable using peptide fragments of the preS1. Recent reports demonstrated that several preS1-derived lipo-peptides in genotype D HBV exhibit nano to picomolar inhibitory activity against HBV infection. In this study, an acylated analog of a preS1 fragment, a 21-residue lipo-peptide (named 7524 BVS7) with a sequence of palmitoyl-GMGTNLSVPNPLGFFPDHQLDC-NH2, from genotype C HBV was produced base upon a previous structural study and was shown potently inhibits HBV infection with an IC(50) of approximately 20 nM.
BMB reports 10/2008; 41(9):640-4. · 1.72 Impact Factor
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ABSTRACT: The preS1 surface antigen of hepatitis B virus (HBV) is known to play an important role in the initial attachment of HBV to hepatocytes. We have characterized structural features of the full-length preS1 using heteronuclear NMR methods and discovered that this 119-residue protein is inherently unstructured without a unique tertiary structure under a nondenaturing condition. Yet, combination of various NMR parameters shows that the preS1 contains "pre-structured" domains broadly covering its functional domains. The most prominent domain is formed by residues 27-45 and overlaps with the putative hepatocyte-binding domain (HBD) encompassing residues 21-47, within which two well-defined pre-structured motifs, formed by Pro(32)-Ala(36) and Pro(41)-Phe(45) are found. Additional, somewhat less prominent, pre-structured motifs are also formed by residues 11-18, 22-25, 37-40, and 46-50. Overall results suggest that the preS1 is a natively unstructured protein (NUP) whose N-terminal 50 residues, populated with multiple pre-structured motifs, contribute critically to hepatocyte binding.
Protein Science 11/2007; 16(10):2108-17. · 2.80 Impact Factor
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ABSTRACT: This Chapter has attempted to deal with the issues on establishing a facial expression imitation system for natural and intuitive interactions with humans. Several real-time cognition abilities are implemented to a robotic system such as face detection, face tracking, and facial expression recognition. Moreover, a robotic system with facial components is developed, which is able to imitate human's facial expressions. A method of recognizing facial expressions is proposed through the use of an innovative rectangle feature. Using the AdaBoost algorithm, an expanded version of Viola and Jones' method has been suggested as a new approach. We deal with 7 facial expressions: neutral, happiness, anger, sadness, surprise, disgust, and fear. For each facial expression, we found five suitable rectangle features using the AdaBoost learning algorithm. These 35 rectangle features and 7 rectangle features were used to find new weak classifiers for facial expression recognition. A real-time performance rate can be achieved through constructing the strong classifier while extracting a few efficient weak classifiers by AdaBoost learning. In addition, an active vision system for social interaction with humans is developed. We proposed a high-speed bell-shaped velocity profiler to reduce the magnitude of jerking motion and used this method to control 12 actuators in real-time. We proved our distributed control structure and the proposed fast bell-shaped velocity profiler to be practical. Several basic algorithms, face detection and tracking, are implemented on the developed system. By directing the robot's gaze to the visual target, the person interacting with the robot can accurately use the robot's gaze as an indicator of what the robot is attending to. This greatly facilitates the interpretation and readability of the robot's behavior, as the robot reacts specifically to the thing that it is looking at. In order to implement visual attention, the basic functionality mentioned above, e.g. face detection, tracking and motor control, is needed. Finally, we introduced an artificial facial expression imitation system using a robot head. There are a number of real-time issues for developing the robotic system. In this Chapter, one solution for developing it is addressed. Our final goal of this research is that humans can easily perceive motor actions semantically and intuitively, regardless of what the robot intends. However, our research lacks a sound understanding of natural and intuitive social interactions among humans. Our future research will focus on perceiving the mental model of human to apply it to the robotic system. It is expected that the suitable mental model for the robots will convey robot's emotion by facial expressions.
09/2007; , ISBN: 978-3-902613-13-4
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ABSTRACT: We have applied NMR spectroscopy to determine the high-resolution structure of gaegurin 4, a 37-residue antimicrobial peptide from Rana rugosa, under varying hydrophobic conditions. Even in 100% H2O, gaegurin 4 contains a nascent turn near its C-terminal Rana box. Under a more hydrophobic condition it forms two amphipathic helices, one long encompassing residues 2-23 and the other consisting of residues 25-34, similar to what has been observed in cecropin A. Functional implication of the helix-breaking kink at Gly24 in gaegurin 4 was investigated by preparing several analogs. Based upon the current and previous results, we propose a novel seaanemone-like ion pore-forming model for gaegurin 4.
Biochemical and Biophysical Research Communications 02/2007; 352(3):592-7. · 2.48 Impact Factor
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ABSTRACT: We have determined the solution conformation of the major B cell epitope (residues 123-145, adrl23 hereafter) in the preS2 region of hepatitis B virus known to be associated with infection neutralization. The adrl23 shows an "L" shaped helix-turn-helix topology with two beta-turns formed by residues Ala(130)-Asp(133) and Asp(133)-Val(136) intervening the N- and C-terminal helices. The N-terminal alpha-helix consists of residues Ser(124)-Gln(129) whereas the C-terminal 3(10) helix is formed by residues Val(136)-Tyr(140). The beta-turns overlap partially with the putative "conformational" epitope. The overall topology of adrl23 is primarily maintained by hydrophobic interactions involving Phe(127), Leu(131), Leu(132), Val(136), and Tyr(140) that are clustered on one side of the molecule. An additional hydrophobic stabilization comes from Phe(141) that is buried inside the concave side of the molecule. A network of hydrogen bonds formed among Thr(125), His(128), and Arg(137) further contribute to the "boomerang-shaped" architecture of adrl23. The N-terminus of adrl23 is immobile due to a hydrogen bond between the N-terminal amide proton of Asn(123) and the hydroxyl oxygen of Thr(126). The side chains of Asp(133), Arg(135), Val(136), Leu(139), and Tyr(140) that were shown to be important for binding to a monoclonal antibody H8 mAb are surface exposed.
Antiviral Research 01/2007; 72(3):207-15. · 4.30 Impact Factor
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ABSTRACT: We have determined a high-resolution three-dimensional structure of alpha-conotoxin BuIA, a 13-residue peptide toxin isolated from Conus bullatus. Despite its unusual 4/4 disulfide bond layout alpha-conotoxin BuIA exhibits strong antagonistic activity at alpha6/alpha3beta2beta3, alpha3beta2, and alpha3beta4 nAChR subtypes like some alpha4/7 conotoxins. alpha-Conotoxin BuIA lacks the C-terminal beta-turn present within the second disulfide loop of alpha4/7 conotoxins, having only a "pseudo omega-shaped" molecular topology. Nevertheless, it contains a functionally critical two-turn helix motif, a feature ubiquitously found in alpha4/7 conotoxins. Such an aspect seems mainly responsible for similarities in the receptor recognition profile of alpha-conotoxin BuIA to alpha4/7 conotoxins. Structural comparison of alpha-conotoxin BuIA with alpha4/7 conotoxins and alpha4/3 conotoxin ImI suggests that presence of the second helical turn portion of the two-turn helix motif in alpha4/7 and alpha4/4 conotoxins may be important for binding to the alpha3 and/or alpha6 subunit of nAChR.
Biochemical and Biophysical Research Communications 12/2006; 349(4):1228-34. · 2.48 Impact Factor
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ABSTRACT: Robotic systems like humanoid frequently move to undesirable pose while being visually controlled at the boundary of its workspace, because the working environment is quite huge as compared with the robot's workspace. The main objective of this paper is to deal with problems occurring at the boundary of the robot's workspace. In addition, current typical problems on IBVS and PBVS, e.g., control in 2D and 3D space, task singularity, robustness to camera and robot calibration error, and robot singularity will be considered. To achieve the objective, the proposed two-stage visual servo system consists of exploring and positioning stages. In the exploring stage, given camera parameters, the target pose of the camera is estimated from the obtained images without the knowledge of the object. In the next positioning stage, a new hybrid control law that moves the camera equipped to a robot end-effector to around the target pose, which is estimated in the first stage and then positions it to the target pose more accurately using IBVS is proposed. Although the target pose is located out of the robot's workspace, the proposed visual servo system shows the proper behavior at the boundary of its workspace. Finally simulation and experimental results shows the feasibility of the proposed visual servo system
Intelligent Robots and Systems, 2006 IEEE/RSJ International Conference on; 11/2006
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ABSTRACT: alpha-Conotoxin OmIA from Conus omaria is the only alpha-conotoxin that shows a approximately 20-fold higher affinity to the alpha3beta2 over the alpha6beta2 subtype of nicotinic acetylcholine receptor. We have determined a three-dimensional structure of alpha-conotoxin OmIA by nuclear magnetic resonance spectroscopy. alpha-Conotoxin OmIA has an "omega-shaped" overall topology with His(5)-Asn(12) forming an alpha-helix. Structural features of alpha-conotoxin OmIA responsible for its selectivity are suggested by comparing its surface characteristics with other functionally related alpha4/7 subfamily conotoxins. Reduced size of the hydrophilic area in alpha-conotoxin OmIA seems to be associated with the reduced affinity towards the alpha6beta2 nAChR subtype.
Biochemical and Biophysical Research Communications 07/2006; 345(1):248-54. · 2.48 Impact Factor
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ABSTRACT: The p53−MDM2 interaction regulates p53-mediated cellular responses to DNA damage, and MDM2 is overexpressed in 7% of all cancers. Structure-based computational design was applied to this system to design libraries centered on a scaffold that projects side chain functionalities with distance and angular relationships equivalent to those seen in the MDM2 interacting motif of p53. A library of 173 such compounds was synthesized using solution phase parallel chemistry. The in vitro competitive ability of the compounds to block p53 peptide binding to MDM2 was determined using a fluorescence polarization competition assay. The most active compound bound with Kd = 12 μM, and its binding was characterized by 15N-1H HSQC NMR.
03/2006;
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2006 IEEE/RSJ International Conference on Intelligent Robots and Systems, IROS 2006, October 9-15, 2006, Beijing, China; 01/2006
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ABSTRACT: alpha-Conotoxin PIA is a novel nicotinic acetylcholine receptor (nAChR) antagonist isolated from Conus purpurascens that targets nAChR subtypes containing alpha6 and alpha3 subunits. alpha-conotoxin PIA displays 75-fold higher affinity for rat alpha6/alpha3beta2beta3 nAChRs than for rat alpha3beta2 nAChRs. We have determined the three-dimensional structure of alpha-conotoxin PIA by nuclear magnetic resonance spectroscopy. The alpha-conotoxin PIA has an "omega-shaped" overall topology as other alpha4/7 subfamily conotoxins. Yet, unlike other neuronally targeted alpha4/7-conotoxins, its N-terminal tail Arg1-Asp2-Pro3 protrudes out of its main molecular body because Asp2-Pro3-Cys4-Cys5 forms a stable type I beta-turn. In addition, a kink introduced by Pro15 in the second loop of this toxin provides a distinct steric and electrostatic environment from those in alpha-conotoxins MII and GIC. By comparing the structure of alpha-conotoxin PIA with other functionally related alpha-conotoxins we suggest structural features in alpha-conotoxin PIA that may be associated with its unique receptor recognition profile.
Biochemical and Biophysical Research Communications 01/2006; 338(4):1990-7. · 2.48 Impact Factor
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ABSTRACT: Mdm2 is a cellular antagonist of p53 that keeps a balanced cellular level of p53. The two proteins are linked by a negative regulatory feedback loop and physically bind to each other via a putative helix formed by residues 18-26 of p53 transactivation domain (TAD) and its binding pocket located within the N-terminal 100-residue domain of mdm2 (Kussie, P. H., Gorina, S., Marechal, V., Elenbaas, B., Moreau, J., Levine, A. J., and Pavletich, N. P. (1996) Science 274, 948-953). In a previous report we demonstrated that p53 TAD in the mdm2-freee state is mostly unstructured but contains two nascent turns in addition to a "preformed" helix that is the same as the putative helix mediating p53-mdm2 binding. Here, using heteronuclear multidimensional NMR methods, we show that the two nascent turn motifs in p53 TAD, turn I (residues 40-45) and turn II (residues 49-54), are also capable of binding to mdm2. In particular, the turn II motif has a higher mdm2 binding affinity ( approximately 20 mum) than the turn I and targets the same site in mdm2 as the helix. Upon mdm2 binding this motif becomes a well defined full helix turn whose hydrophobic face formed by the side chains of Ile-50, Trp-53, and Phe-54 inserts deeply into the helix binding pocket. Our results suggest that p53-mdm2 binding is subtler than previously thought and involves global contacts such as multiple "non-contiguous" minimally structured motifs instead of being localized to one small helix mini-domain in p53 TAD.
Journal of Biological Chemistry 12/2005; 280(46):38795-802. · 4.77 Impact Factor
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ABSTRACT: Socially intelligent robots are no longer an interesting topic of science fiction. In the robotics community, there is a growing interest in building personal robots, or in building robots that share the same workspace with humans. Natural interaction between humans and robots is therefore essential. To interact socially with humans, a robot must be able to do more than simply gather information about its surroundings; it must be able to express its states or emotions so that humans believe it has beliefs, desires, and intentions of its own. In the last decade, many researchers have focused on generating emotive facial expressions, which are known as the best cues for conveying the robot's state, intentions, feelings and emotions. This paper gives a brief overview of current robotic systems with emotive facial expressions and introduces the basic models and hardware of two different types of facial robotic systems.
Robot and Human Interactive Communication, 2005. ROMAN 2005. IEEE International Workshop on; 09/2005
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ABSTRACT: In this paper, we propose a method of selecting new types of rectangle features that are suitable for facial expression recognition. The basic concept in this paper is similar to Violar's approach, which is used for face detection. Instead of previous Haar-like rectangle features, we choose rectangle features for facial expression recognition among all possible rectangle types in a 3×3 matrix form using the AdaBoost algorithm. Also, the facial expression recognition system constituted with the proposed rectangle features is compared to that with previous rectangle features with regard to its capacity. The results show that the proposed approach has better performance in facial expression recognition in terms of simulation and experimental results.
Intelligent Robots and Systems, 2005. (IROS 2005). 2005 IEEE/RSJ International Conference on; 09/2005
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ABSTRACT: In recent decades, active vision systems have been studied widely because they can control the gaze direction of their mounted vision sensors and overcome many shortcomings of passive vision systems which have fixed vision sensors. Due to an increasing interest in humanoid robots and social robots, many researchers in the active vision area are focusing their research on developing active vision systems with socially interacting with humans. In this paper, we discuss an active vision system developed for interaction with humans, and we introduce a fast and simple system architecture which includes a high-speed serial communication bus (IEEE 1394a). In addition, we propose a distributed and jerkbounded control algorithm to ensure smooth system motion.
Control, Automation, Robotics and Vision Conference, 2004. ICARCV 2004 8th; 01/2005
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Proceedings of the IAPR Conference on Machine Vision Applications (IAPR MVA 2005), May 16-18, 2005, Tsukuba Science City, Japan; 01/2005
