1
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Ueda T. [Modulation of Aggregation and Immunogenicity of a Protein: Based on the Study of Hen Lysozyme]. YAKUGAKU ZASSHI 2024; 144:299-310. [PMID: 38432940 DOI: 10.1248/yakushi.23-00192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
This study focuses on the modulation of protein aggregation and immunogenicity. As a starting point for investigating long-range interactions within a non-native protein, the effects of perturbing denatured protein states on their aggregation, including the formation of amyloid fibrils, were evaluated. The effects of adducts, sugar modifications, and stabilization on protein aggregation were then examined. We also investigated how protein immunogenicity was affected by enhancing protein conformational stability and other factors.
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Affiliation(s)
- Tadashi Ueda
- Graduate School of Pharmaceutical Sciences, Kyushu University
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2
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Belchior DC, Quental MV, Pereira MM, Mendonça CM, Duarte IF, Freire MG. Performance of tetraalkylammonium-based ionic liquids as constituents of aqueous biphasic systems in the extraction of ovalbumin and lysozyme. Sep Purif Technol 2020. [DOI: 10.1016/j.seppur.2019.116019] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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3
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Zuk PJ, Cichocki B, Szymczak P. GRPY: An Accurate Bead Method for Calculation of Hydrodynamic Properties of Rigid Biomacromolecules. Biophys J 2018; 115:782-800. [PMID: 30144937 PMCID: PMC6127458 DOI: 10.1016/j.bpj.2018.07.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 07/08/2018] [Accepted: 07/16/2018] [Indexed: 10/28/2022] Open
Abstract
Two main problems that arise in the context of hydrodynamic bead modeling are an inaccurate treatment of bead overlaps and the necessity of using volume corrections when calculating intrinsic viscosity. We present a formalism based on the generalized Rotne-Prager-Yamakawa approximation that successfully addresses both of these issues. The generalized Rotne-Prager-Yamakawa method is shown to be highly effective for the calculation of transport properties of rigid biomolecules represented as assemblies of spherical beads of different sizes, both overlapping and nonoverlapping. We test the method on simple molecular shapes as well as real protein structures and compare its performance with other computational approaches.
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Affiliation(s)
- Pawel J Zuk
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland; Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey
| | - Bogdan Cichocki
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Piotr Szymczak
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland.
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4
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Niessen KA, Xu M, Paciaroni A, Orecchini A, Snell EH, Markelz AG. Moving in the Right Direction: Protein Vibrations Steering Function. Biophys J 2017; 112:933-942. [PMID: 28297652 DOI: 10.1016/j.bpj.2016.12.049] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 12/22/2016] [Accepted: 12/28/2016] [Indexed: 11/29/2022] Open
Abstract
Nearly all protein functions require structural change, such as enzymes clamping onto substrates, and ion channels opening and closing. These motions are a target for possible new therapies; however, the control mechanisms are under debate. Calculations have indicated protein vibrations enable structural change. However, previous measurements found these vibrations only weakly depend on the functional state. By using the novel technique of anisotropic terahertz microscopy, we find that there is a dramatic change to the vibrational directionality with inhibitor binding to lysozyme, whereas the vibrational energy distribution, as measured by neutron inelastic scattering, is only slightly altered. The anisotropic terahertz measurements provide unique access to the directionality of the intramolecular vibrations, and immediately resolve the inconsistency between calculations and previous measurements, which were only sensitive to the energy distribution. The biological importance of the vibrational directions versus the energy distribution is revealed by our calculations comparing wild-type lysozyme with a higher catalytic rate double deletion mutant. The vibrational energy distribution is identical, but the more efficient mutant shows an obvious reorientation of motions. These results show that it is essential to characterize the directionality of motion to understand and control protein dynamics to optimize or inhibit function.
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Affiliation(s)
- Katherine A Niessen
- Department of Physics, University at Buffalo, State University of New York, Buffalo, New York.
| | - Mengyang Xu
- Department of Physics, University at Buffalo, State University of New York, Buffalo, New York
| | | | - Andrea Orecchini
- Dipartimento di Fisica e Geologia, Università di Perugia, Perugia, Italy; CNR-IOM c/o Dipartimento di Fisica e Geologia, Università di Perugia, Perugia, Italy
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute and Department of Structural Biology, University at Buffalo, State University of New York, Buffalo, New York
| | - Andrea G Markelz
- Department of Physics, University at Buffalo, State University of New York, Buffalo, New York; Hauptman-Woodward Medical Research Institute and Department of Structural Biology, University at Buffalo, State University of New York, Buffalo, New York.
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5
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Ma FH, Wang X, Chen JL, Wen X, Sun H, Su XC. Deciphering the Multisite Interactions of a Protein and Its Ligand at Atomic Resolution by Using Sensitive Paramagnetic Effects. Chemistry 2017; 23:926-934. [DOI: 10.1002/chem.201604393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Fei-He Ma
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Xiao Wang
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Jia-Liang Chen
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Xin Wen
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Han Sun
- Department of Structural Biology; Leibniz-Institut für Molekulare Pharmakologie (FMP); Robert-Roessle-Str. 10 13125 Berlin Germany
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
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6
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Longo E, Hussain R, Siligardi G. Application of circular dichroism and magnetic circular dichroism for assessing biopharmaceuticals formulations photo-stability and small ligands binding properties. Int J Pharm 2015; 480:84-91. [PMID: 25596417 DOI: 10.1016/j.ijpharm.2015.01.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/13/2015] [Indexed: 10/24/2022]
Abstract
Synchrotron radiation circular dichroism (SRCD) is a powerful tool for photo-stability assessment of proteins. Recently our research has been interested in applying SRCD to develop screening methodologies for accelerated photo-stability assessment of monoclonal antibody formulations. Despite it was proven to be reliable and applicable within a wide range of salts and excipients containing solutions, the presence of far-UV (<260nm) strong absorbing species (e.g., sodium chloride, histidine, arginine) in common formulations completely prevent the analysis. Herein, we propose a new method based on CD coupled with magnetic CD (MCD) to address the problem and offer an additional versatile tool for monitoring the photo-stability. This is done by assessing the stability of the samples by looking at the near-UV band, as well as giving insights in the denaturation mechanism. We applied this method to four mAbs formulations and correlated the results with dynamic light scattering data. Finally, we applied MCD in ligand interaction to key proteins such as lysozyme, comparing the human with the hen enzyme in the binding of N,N',N''-triacetylchitotriose.
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Affiliation(s)
- Edoardo Longo
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Rohanah Hussain
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom.
| | - Giuliano Siligardi
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom.
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7
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Yuwen T, Skrynnikov NR. Proton-decoupled CPMG: a better experiment for measuring (15)N R2 relaxation in disordered proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:155-169. [PMID: 24120537 DOI: 10.1016/j.jmr.2013.08.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/15/2013] [Accepted: 08/16/2013] [Indexed: 06/02/2023]
Abstract
(15)N R2 relaxation is one of the most informative experiments for characterization of intrinsically disordered proteins (IDPs). Small changes in nitrogen R2 rates are often used to determine how IDPs respond to various biologically relevant perturbations such as point mutations, posttranslational modifications and weak ligand interactions. However collecting high-quality (15)N relaxation data can be difficult. Of necessity, the samples of IDPs are often prepared with low protein concentration and the measurement time can be limited because of rapid sample degradation. Furthermore, due to hardware limitations standard experiments such as (15)N spin-lock and CPMG can sample the relaxation decay only to ca. 150ms. This is much shorter than (15)N T2 times in disordered proteins at or near physiological temperature. As a result, the sampling of relaxation decay profiles in these experiments is suboptimal, which further lowers the precision of the measurements. Here we report a new implementation of the proton-decoupled (PD) CPMG experiment which allows one to sample (15)N R2 relaxation decay up to ca. 0.5-1s. The new experiment has been validated through comparison with the well-established spin-lock measurement. Using dilute samples of denatured ubiquitin, we have demonstrated that PD-CPMG produces up to 3-fold improvement in the precision of the data. It is expected that for intrinsically disordered proteins the gains may be even more substantial. We have also shown that this sequence has a number of favorable properties: (i) the spectra are recorded with narrow linewidth in nitrogen dimension; (ii) (15)N offset correction is small and easy to calculate; (iii) the experiment is immune to various spurious effects arising from solvent exchange; (iv) the results are stable with respect to pulse miscalibration and rf field inhomogeneity; (v) with minimal change, the pulse sequence can also be used to measure R2 relaxation of (15)N(ε) spins in arginine side chains. We anticipate that the new experiment will be a valuable addition to the NMR toolbox for studies of IDPs.
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Affiliation(s)
- Tairan Yuwen
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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8
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Moorman VR, Valentine KG, Wand AJ. The dynamical response of hen egg white lysozyme to the binding of a carbohydrate ligand. Protein Sci 2012; 21:1066-73. [PMID: 22593013 DOI: 10.1002/pro.2092] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 05/01/2012] [Accepted: 05/03/2012] [Indexed: 12/26/2022]
Abstract
It has become clear that the binding of small and large ligands to proteins can invoke significant changes in side chain and main chain motion in the fast picosecond to nanosecond timescale. Recently, the use of a "dynamical proxy" has indicated that changes in these motions often reflect significant changes in conformational entropy. These entropic contributions are sometimes of the same order as the total entropy of binding. Thus, it is important to understand the connections amongst motion between the manifold of states accessible to the native state of proteins, the corresponding entropy, and how this impacts the overall energetics of protein function. The interaction of proteins with carbohydrate ligands is central to a range of biological functions. Here, we examine a classic carbohydrate interaction with an enzyme: the binding of wild-type hen egg white lysozyme (HEWL) to the natural, competitive inhibitor chitotriose. Using NMR relaxation experiments, backbone amide and side chain methyl axial order parameters were obtained across apo and chitotriose-bound HEWL. Upon binding, changes in the apparent amplitude of picosecond to nanosecond main chain and side chain motions are seen across the protein. Indeed, binding of chitotriose renders a large contiguous fraction of HEWL effectively completely rigid. Changes in methyl flexibility are most pronounced closest to the binding site, but average to only a small overall change in the dynamics across the protein. The corresponding change in conformational entropy is unfavorable and estimated to be a significant fraction of the total binding entropy.
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Affiliation(s)
- Veronica R Moorman
- Graduate Group in Biochemistry & Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
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9
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Wang SC, Mirarefi P, Faraone A, Lee CT. Light-controlled protein dynamics observed with neutron spin echo measurements. Biochemistry 2011; 50:8150-62. [PMID: 21809812 DOI: 10.1021/bi200206z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A photoresponsive surfactant has been used as a means to control protein structure and dynamics with light illumination. This cationic azobenzene surfactant, azoTAB, which undergoes a reversible photoisomerization upon exposure to the appropriate wavelength of light, adopts a relatively hydrophobic, trans structure under visible light illumination and a relatively hydrophilic cis structure under UV light illumination. Small-angle neutron scattering (SANS) and neutron spin echo (NSE) spectroscopy were used to measure the tertiary structure and internal dynamics of lysozyme in the presence of the photosurfactant, respectively. The SANS-based in vitro structures indicate that under visible light the photosurfactant induces partial unfolding that principally occurs away from the active site near the hinge region connecting the α and β domains. Upon UV exposure, however, the protein refolds to a nativelike structure. At the same time, enhanced internal dynamics of lysozyme were detected with the surfactant in the trans form through NSE measurements of the Q-dependent effective diffusion coefficient (D(eff)) of the protein. In contrast, the D(eff) values of lysozyme in the presence of cis azoTAB largely agree with the rigid-body calculation as well as those measured for pure lysozyme, suggesting that the native protein is dormant on the nanosecond time and nanometer length scales. Lysozyme internal motions were modeled by assuming a protein of two (α and β domains) or three (α and β domains and the hinge region) domains connects by either soft linkers or rigid, freely rotating bonds. Protein dynamics were also tracked with Fourier transform infrared spectroscopy through hydrogen-deuterium exchange kinetics, which further demonstrated enhanced protein flexibility induced by the trans form of the surfactant relative to the native protein. Ensemble-averaged intramolecular fluorescent resonance energy transfer measurements similarly demonstrated the enhanced dynamics of lysozyme with the trans form of the photosurfactant. Previous results have shown a significant increase in protein activity in the presence of azoTAB in the trans conformation. Combined, these results provide insight into a unique light-based method of controlling protein structure, dynamics, and function and strongly support the relevance of large domain motions for the activity of proteins.
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Affiliation(s)
- Shao-Chun Wang
- Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
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10
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Zabara A, Amar-Yuli I, Mezzenga R. Tuning in-meso-crystallized lysozyme polymorphism by lyotropic liquid crystal symmetry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:6418-6425. [PMID: 21506575 DOI: 10.1021/la200710p] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Lipid-based lyotropic liquid crystals (LLCs) show great potential for applications in fields as diverse as food technology, cosmetics, pharmaceutics, or structural biology. Recently, these systems have provided a viable alternative to the difficult process of membrane protein crystallization, owing to their similarities with cell membranes. Nonetheless, the process of in-meso crystallization of proteins still remains poorly understood. In this study, we demonstrate that in-meso crystal morphologies of lysozyme (LSZ), a model hydrophilic protein, can be controlled by both the composition and symmetry of the mesophase, inferring a possible general influence of the LLC space group on the protein crystal polymorphism. Lysozyme was crystallized in-meso from three common LLC phases (lamellar, inverse hexagonal, and inverse bicontinuous cubic) composed of monolinolein and water. Different mixing ratios of mesophase to crystallization buffer were used in order to tune crystallization both in the bulk mesophase and in excess water conditions. Two distinct mechanisms of crystallization were shown to take place depending on available water in the mesophases. In the bulk mesophases, protein nuclei form and grow within structural defects of the mesophase and partially dehydrate the system inducing order-to-order transitions of the liquid crystalline phase toward stable symmetries in conditions of lower hydration. The formed protein crystals eventually macrophase separate from the mesophase allowing the system to reach its final symmetry. On the other hand, when excess water is available, protein molecules diffuse from the water channels into the excess water, where the crystallization process can take place freely, and with little to no effect on the structure and symmetry of the lyotropic liquid crystals.
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Affiliation(s)
- Alexandru Zabara
- ETH Zurich, Food & Soft Materials Science, Institute of Food, Nutrition & Health Schmelzbergstrasse 9, LFO E23, 8092 Zürich, Switzerland
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11
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Libster D, Aserin A, Garti N. Interactions of biomacromolecules with reverse hexagonal liquid crystals: Drug delivery and crystallization applications. J Colloid Interface Sci 2011; 356:375-86. [DOI: 10.1016/j.jcis.2011.01.047] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Revised: 01/13/2011] [Accepted: 01/14/2011] [Indexed: 11/26/2022]
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12
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Gao G, Yan Y, Pispas S, Yao P. Sustained and Extended Release with Structural and Activity Recovery of Lysozyme from Complexes with Sodium (Sulfamate Carboxylate) Isoprene/Ethylene Oxide Block Copolymer. Macromol Biosci 2010; 10:139-46. [DOI: 10.1002/mabi.200900186] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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13
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Mishraki T, Libster D, Aserin A, Garti N. Lysozyme entrapped within reverse hexagonal mesophases: Physical properties and structural behavior. Colloids Surf B Biointerfaces 2010; 75:47-56. [DOI: 10.1016/j.colsurfb.2009.08.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Revised: 08/06/2009] [Accepted: 08/06/2009] [Indexed: 11/12/2022]
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14
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Kawasaki T, Toyoda M, Okahata Y. Pulse Frequency-dependent Regulation of Lysozyme Reactivity under Pulsed Ultrasound Irradiation. CHEM LETT 2009. [DOI: 10.1246/cl.2009.536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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15
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Kawasaki T, Toyoda M, Hoshino Y, Okahata Y. Pulsed Ultrasound Effect on DNA Polymerase Reaction Monitored on a QCM. CHEM LETT 2009. [DOI: 10.1246/cl.2009.538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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16
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Goto T, Ohkuri T, Shioi S, Abe Y, Imoto T, Ueda T. Crystal structures of K33 mutant hen lysozymes with enhanced activities. J Biochem 2008; 144:619-23. [PMID: 18776207 DOI: 10.1093/jb/mvn108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using random mutagenesis, we previously obtained K33N mutant lysozyme that showed a large lytic halo on the plate coating Micrococcus luteus. In order to examine the effects of mutation of K33N on enzyme activity, we prepared K33N and K33A mutant lysozymes from yeast. It was found that the activities of both the mutant lysozymes were higher than those of the wild-type lysozyme based on the results of the activity measurements against M. luteus (lytic activity) and glycol chitin. Moreover, 3D structures of K33N and K33A mutant lysozyme were solved by X-ray crystallographic analyses. The side chain of K33 in the wild-type lysozyme hydrogen bonded with N37 involved in the substrate-binding region, and the orientation of the side chain of N37 in K33 mutant lysozymes were different in the wild-type lysozyme. These results suggest that the enhancement of activity in K33N mutant lysozyme was due to an alteration in the orientation of the side chain of N37. On the other hand, K33N lysozyme was less stable than the wild-type lysozyme. Lysozyme may sacrifice its enzyme activity to acquire the conformational stability at position 33.
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Affiliation(s)
- Takashi Goto
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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17
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Gao G, Yao P. Structure and activity transition of lysozyme on interacting with and releasing from polyelectrolyte with different hydrophobicity. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/pola.22799] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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18
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Wang SC, Lee CT. Enhanced Enzymatic Activity through Photoreversible Conformational Changes. Biochemistry 2007; 46:14557-66. [DOI: 10.1021/bi701073d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shao-Chun Wang
- Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211
| | - C. Ted Lee
- Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211
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19
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Jarymowycz VA, Stone MJ. Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences. Chem Rev 2007; 106:1624-71. [PMID: 16683748 DOI: 10.1021/cr040421p] [Citation(s) in RCA: 342] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Virginia A Jarymowycz
- Department of Chemistry and Interdisciplinary Biochemistry Program, Indiana University, Bloomington, Indiana 47405-0001, USA
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20
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Yoshida Y, Tanaka M, Ohkuri T, Tanaka Y, Imoto T, Ueda T. Analysis of internal motions of RNase T1 complexed with a productive substrate involving 15N NMR relaxation measurements. J Biochem 2006; 140:43-8. [PMID: 16877767 DOI: 10.1093/jb/mvj123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The backbone dynamics of RNase T1 in the presence of exo-guanosine 2',3'-cyclophosphorothioate (exo-cGPS isomer), which is a productive substrate, and in the presence of 3'-guanylic acid (3'GMP), which is an nonproductive substrate, were examined using (15)N nuclear magnetic resonance. Although the X-ray crystal structure suggests that the modes of binding of these substrates to the active-site cleft are very similar, the order parameters in a number of regions in RNase T1 complexed with exo-cGPS isomer were different from those with 3'GMP. Moreover, the chemical exchange in line width observed for RNase T1 complexed with exo-cGPS isomer was also different from that observed for RNase T1 complexed with 3'GMP. From these results, we concluded that the internal motions in RNase T1 complexed with a productive substrate were not always identical to those in RNase T1 complexed with a nonproductive substrate.
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Affiliation(s)
- Yuichiro Yoshida
- Department of Immunology, Department of Pharmaceutical Synthetic Chemistry, and NMR Section, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582
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21
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Wirmer J, Schlörb C, Klein-Seetharaman J, Hirano R, Ueda T, Imoto T, Schwalbe H. Modulation of compactness and long-range interactions of unfolded lysozyme by single point mutations. Angew Chem Int Ed Engl 2005; 43:5780-5. [PMID: 15523735 DOI: 10.1002/anie.200460907] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Julia Wirmer
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University Frankfurt, Marie-Curie-Strasse 11, 60439 Frankfurt, Germany
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22
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Zhu H, Liu K, Cerny J, Imoto T, Moudgil KD. Insertion of the dibasic motif in the flanking region of a cryptic self-determinant leads to activation of the epitope-specific T cells. THE JOURNAL OF IMMUNOLOGY 2005; 175:2252-60. [PMID: 16081793 DOI: 10.4049/jimmunol.175.4.2252] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Efficient induction of self tolerance is critical for avoiding autoimmunity. The T cells specific for the well-processed and -presented (dominant) determinants of a native self protein are generally tolerized in the thymus, whereas those potentially directed against the inefficiently processed and presented (cryptic) self epitopes escape tolerance induction. We examined whether the crypticity of certain determinants of mouse lysozyme-M (ML-M) could be attributed to the nonavailability of a proteolytic site, and whether it could be reversed to immunodominance by engraftment of a novel cleavage site in the flanking region of the epitope. Using site-directed mutagenesis, we created the dibasic motif (RR or RK; R = arginine, K = lysine), a target of intracellular proteases, in the region adjoining one of the three cryptic epitopes (46-61, 66-79, or 105-119) of ML-M. Interestingly, the mutated lysozyme proteins, but not unmutated ML-M, were immunogenic in mice. The T cell response to the altered lysozyme was attributable to the efficient processing and presentation of the previously cryptic epitope, and this response was both epitope and MHC haplotype specific. In addition, the anti-self T cell response was associated with the generation of autoantibodies against self lysozyme. However, the results using one of three mutated lysozymes suggested that the naturally processed, dibasic motif-marked epitope may not always correspond precisely to the cryptic determinant within a synthetic peptide. This is the first report describing the circumvention of self tolerance owing to the targeted reversal of crypticity to dominance in vivo of a specific epitope within a native self Ag.
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Affiliation(s)
- Hui Zhu
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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23
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Hill JJ, Shalaev EY, Zografi G. Thermodynamic and dynamic factors involved in the stability of native protein structure in amorphous solids in relation to levels of hydration. J Pharm Sci 2005; 94:1636-67. [PMID: 15965985 DOI: 10.1002/jps.20333] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The internal, dynamical fluctuations of protein molecules exhibit many of the features typical of polymeric and bulk small molecule glass forming systems. The response of a protein's internal molecular mobility to temperature changes is similar to that of other amorphous systems, in that different types of motions freeze out at different temperatures, suggesting they exhibit the alpha-beta-modes of motion typical of polymeric glass formers. These modes of motion are attributed to the dynamic regimes that afford proteins the flexibility for function but that also develop into the large-scale collective motions that lead to unfolding. The protein dynamical transition, T(d), which has the same meaning as the T(g) value of other amorphous systems, is attributed to the temperature where protein activity is lost and the unfolding process is inhibited. This review describes how modulation of T(d) by hydration and lyoprotectants can determine the stability of protein molecules that have been processed as bulk, amorphous materials. It also examines the thermodynamic, dynamic, and molecular factors involved in stabilizing folded proteins, and the effects typical pharmaceutical processes can have on native protein structure in going from the solution state to the solid state.
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Affiliation(s)
- John J Hill
- ICOS Corporation, 22021 20th Avenue SE, Bothell, WA 98021, USA.
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24
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Yoshida M, Aizawa T, Nakamura T, Shitara K, Hayakawa Y, Matsubara K, Miura K, Kouno T, Clark KD, Strand MR, Mizuguchi M, Demura M, Nitta K, Kawano K. The Gly-Gly Linker Region of the Insect Cytokine Growth-blocking Peptide Is Essential for Activity. J Biol Chem 2004; 279:51331-7. [PMID: 15385535 DOI: 10.1074/jbc.m409382200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Growth-blocking peptide (GBP) is a 25-amino acid cytokine isolated from the lepidopteran insect Pseudaletia separata. GBP exhibits various biological activities such as regulation of larval growth of insects, proliferation of a few kinds of cultured cells, and stimulation of a class of insect immune cells called plasmatocytes. The tertiary structure of GBP consists of a well structured core domain and disordered N and C termini. Our previous studies revealed that, in addition to the structured core, specific residues in the unstructured N-terminal region (Glu1 and Phe3) are also essential for the plasmatocyte-stimulating activity. In this study, a number of deletion, insertion, and site-directed mutants targeting the unstructured N-terminal residues of GBP were constructed to gain more detailed insight into the mode of interaction between the N-terminal region and GBP receptor. Alteration of the backbone length of the linker region between the core structure and N-terminal domain reduced plasmatocyte-stimulating activity. The substitutions of Gly5 or Gly6 in this linker region with more bulky residues, such as Phe and Pro, also remarkably reduced this activity. We conclude that the interaction of GBP with its receptor depends on the relative position of the N-terminal domain to the core structure, and therefore the backbone flexibility of Gly residues in the linker region is necessary for adoption of a proper conformation suited to receptor binding. Additionally, antagonistic experiments using deletion mutants confirmed that not only the core domain but also the N-terminal region of GBP are required for "receptor-binding," and furthermore Phe3 is a binding determinant of the N-terminal domain.
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Affiliation(s)
- Masanobu Yoshida
- Faculty of Pharmaceutical Sciences, Toyama Medical and Pharmaceutical University, Toyama 930-0194, Japan
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25
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Wirmer J, Schlörb C, Klein-Seetharaman J, Hirano R, Ueda T, Imoto T, Schwalbe H. Modulation of Compactness and Long-Range Interactions of Unfolded Lysozyme by Single Point Mutations. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200460907] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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26
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Takeshita K, Hashimoto Y, Thujihata Y, So T, Ueda T, Iomoto T. Determination of the complete cDNA sequence, construction of expression systems, and elucidation of fibrinolytic activity for Tapes japonica lysozyme. Protein Expr Purif 2004; 36:254-62. [PMID: 15249048 DOI: 10.1016/j.pep.2004.05.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2004] [Revised: 04/22/2004] [Indexed: 11/20/2022]
Abstract
The lysozyme of the marine bivalve, Tapes japonica (13.8 kDa), belongs to the invertebrate lysozyme family and displays both chitinase and isopeptidase activities. We determined the complete cDNA sequence and constructed effective expression systems for this enzyme using Escherichia coli (BL21) and Pichia pastoris. The native and recombinant proteins indicated lysozyme activity and isopeptidase activity, including the proteolysis of d-dimer, a plasminolytic product of stabilized polymeric fibrin. These results will be utilized for the structural and functional study of invertebrate lysozymes, and for the development of applications for thrombosis therapies.
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Affiliation(s)
- Kouhei Takeshita
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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27
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Niccolai N, Spiga O, Bernini A, Scarselli M, Ciutti A, Fiaschi I, Chiellini S, Molinari H, Temussi PA. NMR studies of protein hydration and TEMPOL accessibility. J Mol Biol 2003; 332:437-47. [PMID: 12948493 DOI: 10.1016/s0022-2836(03)00852-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding the mechanisms of the interaction between a protein surface and its outer molecular environment is of primary relevance for the rational design of new drugs and engineered proteins. Protein surface accessibility is emerging as a new dimension of Structural Biology, since NMR methods have been developed to follow how molecules, even those different from physiological ligands, preferentially approach specific regions of the protein surface. Hen egg-white lysozyme, a paradigmatic example of the state of the art of protein structure and dynamics, has been selected as a model system to study protein surface accessibility. Bound water and soluble spin-labels have been used to investigate the interaction of this enzyme, both free and bound to the inhibitor (NAG)(3), with its molecular environment. No tightly bound water molecules were found inside the enzyme active site, which, conversely, appeared as the most exposed to visits from the soluble paramagnetic probe TEMPOL. From the presented set of data, an integrated view of lysozyme surface accessibility towards water and TEMPOL molecules is obtained.
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Affiliation(s)
- Neri Niccolai
- Biomolecular Structure Research Center and Department of Molecular Biology, University of Siena, via A. Fiorentina, I-53100, Siena, Italy.
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28
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Abstract
I have pursued research on lysozymes for 42 years. During that time, I made Several new findings, some of them by chance. My enjoyment of the following areas is reviewed: the story of tryptophan; protease digestion mechanisms; peptide mapping with RP-HPLC; gene engineering; renaturation of protein; catalytic residues; fluctuation and function; stabilization; folding; antigenecity; tolerance; and various lysozymes.
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Affiliation(s)
- Taiji Imoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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29
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Obita T, Iwura T, Su'etsugu M, Yoshida Y, Tanaka Y, Katayama T, Ueda T, Imoto T. Determination of the secondary structure in solution of the Escherichia coli DnaA DNA-binding domain. Biochem Biophys Res Commun 2002; 299:42-8. [PMID: 12435387 DOI: 10.1016/s0006-291x(02)02590-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
DnaA protein binds specifically to a group of binding sites collectively called as DnaA boxes within the bacterial replication origin to induce local unwinding of duplex DNA. The DNA-binding domain of DnaA, domain IV, comprises the C-terminal 94 amino acid residues of the protein. We overproduced and purified a protein containing only this domain plus a methionine residue. This protein was stable as a monomer and maintained DnaA box-specific binding activity. We then analyzed its solution structure by CD spectrum and heteronuclear multi-dimensional NMR experiments. We established extensive assignments of the 1H, 13C, and 15N nuclei, and revealed by obtaining combined analyses of chemical shift index and NOE connectivities that DnaA domain IV contains six alpha-helices and no beta-sheets, consistent with results of CD analysis. Mutations known to reduce DnaA box-binding activity were specifically located in or near two of the alpha-helices. These findings indicate that the DNA-binding fold of DnaA domain IV is unique among origin-binding proteins.
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Affiliation(s)
- Takayuki Obita
- Department of Immunology, Kyushu University Graduate School of Pharmaceutical Sciences, 3-1-1 Maidashi, Higashi-ku, 812-8582, Fukuoka, Japan
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30
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Tada M, Kobashigawa Y, Mizuguchi M, Miura K, Kouno T, Kumaki Y, Demura M, Nitta K, Kawano K. Stabilization of protein by replacement of a fluctuating loop: structural analysis of a chimera of bovine alpha-lactalbumin and equine lysozyme. Biochemistry 2002; 41:13807-13. [PMID: 12427044 DOI: 10.1021/bi020360u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Equine lysozyme is a calcium-binding lysozyme and an evolutional intermediate between non-calcium binding c-type lysozyme and alpha-lactalbumin. We constructed a chimeric protein by substituting the fluctuating loop of bovine alpha-lactalbumin with the D-helix of equine lysozyme. The substitution affects the protection factors not only in the fluctuating loop but also in the antiparallel beta-sheet, the A- and B-helices, and the loop between the B-helix and the beta-sheet. Amide protons in these regions of the chimera are more protected from exchange than are those of bovine alpha-lactalbumin. We used model-free analysis based on 15N nuclear magnetic resonance relaxation measurements to investigate the dynamics of the main chain of the chimera and showed that the fluctuating loop of the chimera is as rigid as three major helices. When we analyzed the chemical shift deviations and backbone HN-H(alpha) scalar coupling constants, we found that the chimera showed an alpha-helical tendency in residues around the fluctuating loop. Our results suggest that the replacement of a highly fluctuating loop in a protein with a rigid structural element in a homologous one may be useful to stabilize the protein structure.
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Affiliation(s)
- Masahito Tada
- Faculty of Pharmaceutical Sciences, Toyama Medical and Pharmaceutical University, Toyama, Japan
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31
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Imoto T. [Foundation of the bases for protein research and its application to the pharmaceutical science field]. YAKUGAKU ZASSHI 2002; 122:537-46. [PMID: 12187769 DOI: 10.1248/yakushi.122.537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This paper reviews the results of basic research conducted by the author's group to determine appropriate methods to develop protein-based drugs. These include production strategies, elucidation of physiologic function, improving existing pharmaceuticals, de novo design, and protein reconstruction. The antigenicity of modified proteins and methods to induce antigenic protein tolerance are also described.
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Affiliation(s)
- Taiji Imoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi 3-1-1 Higashi-ku, Fukuoka 812-8582, Japan
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32
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Yun S, Jang DS, Kim DH, Choi KY, Lee HC. 15N NMR relaxation studies of backbone dynamics in free and steroid-bound Delta 5-3-ketosteroid isomerase from Pseudomonas testosteroni. Biochemistry 2001; 40:3967-73. [PMID: 11300777 DOI: 10.1021/bi0023192] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The backbone dynamics of Delta(5)-3-ketosteroid isomerase (KSI) from Pseudomonas testosteroni has been studied in free enzyme and its complex with a steroid ligand, 19-nortestosterone hemisuccinate (19-NTHS), by (15)N relaxation measurements. The relaxation data were analyzed using the model-free formalism to extract the model-free parameters (S(2), tau(e), and R(ex)) and the overall rotational correlation time (tau(m)). The rotational correlation times were 19.23 +/- 0.08 and 17.08 +/- 0.07 ns with the diffusion anisotropies (D( parallel)/D( perpendicular)) of 1.26 +/- 0.03 and 1.25 +/- 0.03 for the free and steroid-bound KSI, respectively. The binding of 19-NTHS to free KSI causes a slight increase in the order parameters (S(2)) for a number of residues, which are located mainly in helix A1 and strand B4. However, the majority of the residues exhibit reduced order parameters upon ligand binding. In particular, strands B3, B5, and B6, which have most of the residues involved in the dimer interaction, have the reduced order parameters in the steroid-bound KSI, indicating the increased high-frequency (pico- to nanosecond) motions in the intersubunit region of this homodimeric enzyme. Our results differ from those of previous studies on the backbone dynamics of monomeric proteins, in which high-frequency internal motions are typically restricted upon ligand binding.
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Affiliation(s)
- S Yun
- Department of Chemistry, Center for Biofunctional Molecules, and Division of Molecular and Life Sciences, Pohang Universtity of Science and Technology, Pohang, 790-784 Korea
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33
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Wintrode PL, Arnold FH. Temperature adaptation of enzymes: lessons from laboratory evolution. ADVANCES IN PROTEIN CHEMISTRY 2001; 55:161-225. [PMID: 11050934 DOI: 10.1016/s0065-3233(01)55004-4] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- P L Wintrode
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, Pasadena 91125, USA
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34
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Ohmura T, Ueda T, Ootsuka K, Saito M, Imoto T. Stabilization of hen egg white lysozyme by a cavity-filling mutation. Protein Sci 2001; 10:313-20. [PMID: 11266617 PMCID: PMC2373952 DOI: 10.1110/ps.37401] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Stabilization of a protein using cavity-filling strategy has hardly been successful because of unfavorable van der Waals contacts. We succeeded in stabilizing lysozymes by cavity-filling mutations. The mutations were checked by a simple energy minimization in advance. It was shown clearly that the sum of free energy change caused by the hydrophobicity and the cavity size was correlated very well with protein stability. We also considered the aromatic-aromatic interaction. It is reconfirmed that the cavity-filling mutation in a hydrophobic core is a very useful method to stabilize a protein when the mutation candidate is selected carefully.
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Key Words
- cavity-filling mutation
- lysozyme
- stability
- aromatic-aromatic interaction
- hel, hen egg white lysozyme
- vdw, van der waals
- dsc, differential scanning calorimetry
- wt, the wild-type lysozyme
- ll mutant, a mutant lysozyme where met12 is mutated to leu
- fl mutant, a mutant lysozyme where met12 is mutated to phe
- lf mutant, a double mutant lysozyme where met12 is mutated to leu and leu56 is mutated to phe
- ff mutant, a double mutant lysozyme where met12 is mutated to phe and leu56 is mutated to phe
- gc, glycol chitin
- (nag)3, trimer of n-acetyl-glucosamine
- md, molecular dynamics
- gdn-hcl, guanidine-hydrochloride
- rmsd, root-mean-square deviation
- rmsf, root-mean-square fluctuation calculated by molecular dynamics simulation
- b-rmsf, root-mean-square fluctuation calculated by b-factor of crystallographic data
- vc, the volume of the cavity was defined to be the volume contained within the cavity surface which was the area swept out by a sphere of radius 1.2 å as it rolls over the cavity surface
- csa, the cavity surface area, that is, the area swept out by a sphere of radius 1.2 å as it rolls over the cavity surface
- gtm, gibbs free energy calculated from δδtm
- δδgvc, the differences in free energy change with changes of cavity volume
- δδgcsa, the differences in free energy change with changes of cavity surface
- δgtr, the virtual free energy of transfer of residues from the exterior to the interior of globular protein.
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Affiliation(s)
- T Ohmura
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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35
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Hoofnagle AN, Resing KA, Goldsmith EJ, Ahn NG. Changes in protein conformational mobility upon activation of extracellular regulated protein kinase-2 as detected by hydrogen exchange. Proc Natl Acad Sci U S A 2001; 98:956-61. [PMID: 11158577 PMCID: PMC14691 DOI: 10.1073/pnas.98.3.956] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Changes in protein mobility accompany changes in conformation during the trans-activation of enzymes; however, few studies exist that validate or characterize this behavior. In this study, amide hydrogen/deuterium exchange/mass spectrometry was used to probe the conformational flexibility of extracellular signal-regulated protein kinase-2 before and after activation by phosphorylation. The exchange data indicated that extracellular regulated protein kinase-2 activation caused altered backbone flexibility in addition to the conformational changes previously established by x-ray crystallography. The changes in flexibility occurred in regions involved in substrate binding and turnover, suggesting their importance in enzyme regulation.
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Affiliation(s)
- A N Hoofnagle
- Department of Chemistry and Biochemistry, and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA.
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36
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Tsujihata Y, So T, Chijiiwa Y, Hashimoto Y, Hirata M, Ueda T, Imoto T. Mutant mouse lysozyme carrying a minimal T cell epitope of hen egg lysozyme evokes high autoantibody response. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2000; 165:3606-11. [PMID: 11034362 DOI: 10.4049/jimmunol.165.7.3606] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Self proteins including foreign T cell epitope induce autoantibodies. We evaluated the relationship between the size of foreign Ag introduced into self protein and the magnitude of autoantibody production. Mouse lysozyme (ML) was used as a model self protein, and we prepared three different ML derivatives carrying T cell epitope of hen egg white lysozyme (HEL) 107-116, i.e, heterodimer of ML and HEL (ML-HEL), chimeric lysozyme that has residue 1-82 of ML and residue 83-130 of HEL in its sequence (chiMH), and mutant ML that has triple mutations rendering the most potent T cell epitope of HEL (sequence 107-116). Immunization of BALB/c mice with these three ML derivatives induced anti-ML autoantibody responses, whereas native ML induced no detectable response. In particular, mutML generated a 10(4) times higher autoantibody titer than did ML-HEL. Anti-HEL107-116 T cell-priming activities were almost similar among the ML derivatives. The heterodimerization of mutant ML and HEL led to significant reduction of the autoantibody response, whereas the mixture did not. These results show that size of the nonself region in modified self Ag has an important role in determining the magnitude of the autoantibody response, and that decrease in the foreign region in a modified self protein may cause high-titered autoantibody response.
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MESH Headings
- Animals
- Autoantibodies/biosynthesis
- Autoantibodies/metabolism
- Binding Sites, Antibody
- Chickens
- Dose-Response Relationship, Immunologic
- Enzyme-Linked Immunosorbent Assay
- Epitopes, T-Lymphocyte/administration & dosage
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/metabolism
- Female
- Immunoglobulin G/biosynthesis
- Immunoglobulin G/metabolism
- Injections, Subcutaneous
- Lymphocyte Activation/genetics
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C3H
- Mice, Inbred C57BL
- Muramidase/administration & dosage
- Muramidase/genetics
- Muramidase/immunology
- Ovum/immunology
- Peptide Fragments/administration & dosage
- Peptide Fragments/genetics
- Peptide Fragments/immunology
- Recombinant Fusion Proteins/administration & dosage
- Recombinant Fusion Proteins/immunology
- Recombinant Proteins/administration & dosage
- Recombinant Proteins/immunology
- T-Lymphocytes/immunology
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Affiliation(s)
- Y Tsujihata
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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37
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Mine S, Ueda T, Hashimoto Y, Imoto T. Analysis of the internal motion of free and ligand-bound human lysozyme by use of 15N NMR relaxation measurement: a comparison with those of hen lysozyme. Protein Sci 2000; 9:1669-84. [PMID: 11045614 PMCID: PMC2144705 DOI: 10.1110/ps.9.9.1669] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Human lysozyme has a structure similar to that of hen lysozyme and differs in amino acid sequence by 51 out of 129 residues with one insertion at the position between 47 and 48 in hen lysozyme. The backbone dynamics of free or (NAG)3-bound human lysozyme has been determined by measurements of 15N nuclear relaxation. The relaxation data were analyzed using the Lipari-Szabo formalism and were compared with those of hen lysozyme, which was already reported (Mine S et al.. 1999, J Mol Biol 286:1547-1565). In this paper, it was found that the backbone dynamics of free human and hen lysozymes showed very similar behavior except for some residues, indicating that the difference in amino acid sequence did not affect the behavior of entire backbone dynamics, but the folded pattern was the major determinant of the internal motion of lysozymes. On the other hand, it was also found that the number of residues in (NAG)3-bound human and hen lysozymes showed an increase or decrease in the order parameters at or near active sites on the binding of (NAG)3, indicating the increase in picosecond to nanosecond. These results suggested that the immobilization of residues upon binding (NAG)3 resulted in an entropy penalty and that this penalty was compensated by mobilizing other residues. However, compared with the internal motions between both ligand-bound human and hen lysozymes, differences in dynamic behavior between them were found at substrate binding sites, reflecting a subtle difference in the substrate-binding mode or efficiency of activity between them.
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Affiliation(s)
- S Mine
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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38
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Vergani B, Kintrup M, Hillen W, Lami H, Piémont E, Bombarda E, Alberti P, Doglia SM, Chabbert M. Backbone dynamics of Tet repressor alpha8intersectionalpha9 loop. Biochemistry 2000; 39:2759-68. [PMID: 10704228 DOI: 10.1021/bi9912591] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A set of single Trp mutants of class B Tet repressor (TetR), in which Trp residues are located from positions 159 to 167, has been engineered to investigate the dynamics of the loop joining the alpha-helices 8 and 9. The fluorescence anisotropy decay of most mutants can be described by the sum of three exponential components. The longest rotational correlation time, 30 ns at 10 degrees C, corresponds to the overall rotation of the protein. The shortest two components, on the subnanosecond and nanosecond time scale, are related to internal motions of the protein. The initial anisotropy, in the 0.16-0.22 range, indicates the existence of an additional ultrafast motion on the picosecond time scale. Examination of physical models for underlying motions indicates that librational motions of the Trp side chain within the rotameric chi(1) x chi(2) potential wells contribute to the picosecond depolarization process, whereas the subnanosecond and nanosecond depolarization processes are related to backbone dynamics. In the absence of inducer, the order parameters of these motions, about 0.90 and 0.80 for most positions, indicate limited flexibility of the loop backbone. Anhydrotetracycline binding to TetR induces an increased mobility of the loop on the nanosecond time scale. This suggests that entropic factors might play a role in the mechanism of allosteric transition.
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Affiliation(s)
- B Vergani
- Laboratoire de Pharmacologie et Physicochimie, Centre National de la Recherche Scientifique UMR 7034, Faculté de Pharmacie, Université Louis Pasteur de Strasbourg, 74 route du Rhin, 67401 Illkirch, France
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39
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Abstract
Direct measurement of the thermodynamics of biomolecular interactions is now relatively easy. Interpretation of these thermodynamics in simple molecular terms is not. Recent work shows how the multiplicity of weak noncovalent interactions, and the inevitable enthalpy/entropy compensation that these interactions engender, lead to difficulties in teasing out the different components.
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Affiliation(s)
- A Cooper
- Chemistry Department, Glasgow University Glasgow, G12 8QQ, UK.
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