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Pachetti M, D'Amico F, Pascolo L, Pucciarelli S, Gessini A, Parisse P, Vaccari L, Masciovecchio C. UV Resonance Raman explores protein structural modification upon fibrillation and ligand interaction. Biophys J 2021; 120:4575-4589. [PMID: 34474016 PMCID: PMC8553600 DOI: 10.1016/j.bpj.2021.08.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 06/28/2021] [Accepted: 08/10/2021] [Indexed: 11/30/2022] Open
Abstract
Amyloids are proteinaceous deposits considered an underlying pathological hallmark of several degenerative diseases. The mechanism of amyloid formation and its inhibition still represent challenging issues, especially when protein structure cannot be investigated by classical biophysical techniques as for the intrinsically disordered proteins (IDPs). In this view, the need to find an alternative way for providing molecular and structural information regarding IDPs prompted us to set a novel, to our knowledge, approach focused on UV Resonance Raman (UVRR) spectroscopy. To test its applicability, we study the fibrillation of hen-egg white lysozyme (HEWL) and insulin as well as their interaction with resveratrol, employing also intrinsic fluorescence spectroscopy, Fourier transform infrared (FTIR) spectroscopy, and atomic force microscopy (AFM). The increasing of the β-sheet structure content at the end of protein fibrillation probed by FTIR occurs simultaneously with a major solvent exposure of tryptophan (Trp) and tyrosine (Tyr) residues of HEWL and insulin, respectively, as revealed by UVRR and intrinsic fluorescence spectroscopy. However, because the latter technique is successfully used when proteins naturally contain Trp residues, it shows poor performances in the case of insulin, and the information regarding its tertiary structure is exclusively provided by UVRR spectroscopy. The presence of an increased concentration of resveratrol induces mild changes in the secondary structure of both protein fibrils while remodeling HEWL fibril length and promoting the formation of amorphous aggregates in the case of insulin. Although the intrinsic fluorescence spectra of proteins are hidden by resveratrol signal, UVRR Trp and Tyr bands are resonantly enhanced, showing a good sensitivity to the presence of resveratrol and marking a modification in the noncovalent interactions in which they are involved. Our findings demonstrate that UVRR is successfully employed in the study of aggregation-prone proteins and of their interaction with ligands, especially in the case of Trp-lacking proteins.
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Affiliation(s)
- Maria Pachetti
- Elettra - Sincrotrone Trieste, Trieste, Italy; Department of Physics, University of Trieste, Trieste, Italy; Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy.
| | | | - Lorella Pascolo
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Stefania Pucciarelli
- University of Camerino, School of Biosciences and Veterinary Medicine, Camerino, Italy
| | | | - Pietro Parisse
- Elettra - Sincrotrone Trieste, Trieste, Italy; Istituto Officina dei Materiali - CNR (IOM-CNR), Trieste, Italy
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Martínez-Archundia M, Hernández Mojica TG, Correa-Basurto J, Montaño S, Camacho-Molina A. Molecular dynamics simulations reveal structural differences among wild-type NPC1 protein and its mutant forms. J Biomol Struct Dyn 2019; 38:3527-3532. [DOI: 10.1080/07391102.2019.1664324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- M. Martínez-Archundia
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de fármacos, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, México
| | - T. G. Hernández Mojica
- Departamento de Genética, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Secretaría de Salud, Mexico City, México, Facultad de Ciencias Químico Biológicas
| | - J. Correa-Basurto
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de fármacos, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, México
| | - S. Montaño
- Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, México
| | - A. Camacho-Molina
- Departamento de Genética, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Secretaría de Salud, Mexico City, México, Facultad de Ciencias Químico Biológicas
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3
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A Bacillus pumilus originated β-N-acetylglucosaminidase for chitin combinatory hydrolysis and exploration of its thermostable mechanism. Int J Biol Macromol 2019; 132:1282-1289. [DOI: 10.1016/j.ijbiomac.2019.04.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 04/08/2019] [Accepted: 04/08/2019] [Indexed: 11/23/2022]
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4
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Antagonistic role of Klotho-derived peptides dynamics in the pancreatic cancer treatment through obstructing WNT-1 and Frizzled binding. Biophys Chem 2018; 240:107-117. [PMID: 30014891 DOI: 10.1016/j.bpc.2018.07.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 06/29/2018] [Accepted: 07/05/2018] [Indexed: 12/14/2022]
Abstract
Klotho is an anti-aging protein that is engaged in the suppression of canonical WNT signaling. In this study, we investigated the expression pattern of human WNTs and Klotho in the pancreatic cancer. In the cancerous cells, WNT-1 exhibited much higher expression as compared to other WNTs, while no WNT expression was detected in the normal tissue. In contrast, Klotho expression was significantly low in the cancerous tissue. Based on these observations, we intended to explore Klotho binding to WNT-1 and cystein-rich domains (CRDs) of Frizzled (FZD) homologs through molecular docking and dynamics simulation assays. Interestingly, similar region of WNT-1 was detected in binding with Klotho and CRDs of FZD-1/2. FZD-CRDs were grasped by the association of peripheral hydrophobic residues of WNT-1 U-shaped cavity. Subsequently, WNT-1-bound Klotho-peptides were isolated and reevaluated for their binding abilities against WNT-1 and FZD-CRDs., The conformational readjustements of these complexes were deeply analyzed by calculating the size of WNT-1 U-shaped cavity. In comparison to apo-WNT-1, cavity opening was markedly enhanced (8.2 Å to 15.64 Å, 32.89 Å and 35.11 Å) in WNT-1-a, WNT-1-c and WNT-1-e complexes, respectively. Thus Klotho-derived peptides may facilitate distinct conformational changes in the WNT-1-FZD associated region. As a result, aberrant loss of FZD binding may lead to augment WNT signaling. Overall, current study opens up new avenues in the pancreatic cancer therapeutics through antagonizing WNT-1 by Klotho.
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Mäntele W. The analysis of protein conformation by infrared spectroscopy: an introduction of the editor to a scientific dispute. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 138:964-966. [PMID: 25466222 DOI: 10.1016/j.saa.2014.11.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 11/01/2014] [Indexed: 06/04/2023]
Affiliation(s)
- Werner Mäntele
- Institute of Biophysics, Physics Department, Johann Wolfgang Goethe-Universität Frankfurt, Max von Laue-Straße 1, 60438 Frankfurt am Main, Germany.
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6
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Fort KL, Silveira JA, Pierson NA, Servage KA, Clemmer DE, Russell DH. From Solution to the Gas Phase: Factors That Influence Kinetic Trapping of Substance P in the Gas Phase. J Phys Chem B 2014; 118:14336-44. [DOI: 10.1021/jp5103687] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kyle L. Fort
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Joshua A. Silveira
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Nicholas A. Pierson
- Department
of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Kelly A. Servage
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E. Clemmer
- Department
of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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Kamal MZ, Ahmad S, Molugu TR, Vijayalakshmi A, Deshmukh MV, Sankaranarayanan R, Rao NM. In vitro evolved non-aggregating and thermostable lipase: structural and thermodynamic investigation. J Mol Biol 2011; 413:726-41. [PMID: 21925508 DOI: 10.1016/j.jmb.2011.09.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Revised: 08/02/2011] [Accepted: 09/02/2011] [Indexed: 11/27/2022]
Abstract
Rational and in vitro evolutionary approaches to improve either protein stability or aggregation resistance were successful, but empirical rules for simultaneous improvement of both stability and aggregation resistance under denaturing conditions are still to be ascertained. We have created a robust variant of a lipase from Bacillus subtilis named "6B" using multiple rounds of in vitro evolution. T(m) and optimum activity temperature of 6B is 78 °C and 65 °C, respectively, which is ~22 °C and 30 °C higher than that of wild-type lipase. Most significantly, 6B does not aggregate upon heating. Physical basis of remarkable thermostability and non-aggregating behavior of 6B was explored using X-ray crystallography, NMR and differential scanning calorimetry. Our structural investigations highlight the importance of tightening of mobile regions of the molecule such as loops and helix termini to attain higher thermostability. Accordingly, NMR studies suggest a very rigid structure of 6B lipase. Further investigation suggested that reduction/perturbation of the large hydrophobic patches present in the wild-type protein structure, decreased propensity of amino acid sequence for aggregation and absence of aggregation-prone intermediate during thermal unfolding of 6B can account for its resistance to aggregation. Overall, our study suggest that better anchoring of the loops with the rest of the protein molecule through mutations particularly on the sites that perturb/disturb the exposed hydrophobic patches can simultaneously increase protein stability and aggregation resistance.
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Affiliation(s)
- Md Zahid Kamal
- Centre for Cellular and Molecular Biology (Council of Scientific and Industrial Research), Hyderabad 500007, India
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8
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Feng YW, Ooishi A, Honda S. Aggregation factor analysis for protein formulation by a systematic approach using FTIR, SEC and design of experiments techniques. J Pharm Biomed Anal 2011; 57:143-52. [PMID: 21920692 DOI: 10.1016/j.jpba.2011.08.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Revised: 08/24/2011] [Accepted: 08/25/2011] [Indexed: 11/19/2022]
Abstract
A simple systematic approach using Fourier transform infrared (FTIR) spectroscopy, size exclusion chromatography (SEC) and design of experiments (DOE) techniques was applied to the analysis of aggregation factors for protein formulations in stress and accelerated testings. FTIR and SEC were used to evaluate protein conformational and storage stabilities, respectively. DOE was used to determine the suitable formulation and to analyze both the main effect of single factors and the interaction effect of combined factors on aggregation. Our results indicated that (i) analysis at a low protein concentration is not always applicable to high concentration formulations; (ii) an investigation of interaction effects of combined factors as well as main effects of single factors is effective for improving conformational stability of proteins; (iii) with the exception of pH, the results of stress testing with regard to aggregation factors would be available for suitable formulation instead of performing time-consuming accelerated testing; (iv) a suitable pH condition should not be determined in stress testing but in accelerated testing, because of inconsistent effects of pH on conformational and storage stabilities. In summary, we propose a three-step strategy, using FTIR, SEC and DOE techniques, to effectively analyze the aggregation factors and perform a rapid screening for suitable conditions of protein formulation.
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Affiliation(s)
- Yan Wen Feng
- National Institute of Advanced Industrial Science and Technology, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
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9
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Stability and folding dynamics of polyglutamic acid. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:673-85. [PMID: 21274709 DOI: 10.1007/s00249-011-0673-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 12/21/2010] [Accepted: 12/31/2010] [Indexed: 10/18/2022]
Abstract
The thermal stability and folding dynamics of polyglutamic acid were studied by equilibrium circular dichroism (CD), Fourier-transform infrared (FTIR), and time-resolved temperature-jump infrared (IR) spectroscopy. Polyglutamic acid (PGA) forms α-helical peptides in aqueous solution and is an ideal model system to study the helix-coil transition. Melting curves were monitored with CD and FTIR as a function of pD. At low pD, PGA aggregates at temperatures above 323 K, whereas at pD >5, unfolding and refolding are reversible. At pD 5.4, a helix-coil transition occurs with a transition temperature T(m) of 307 K. At slightly higher pD of 6.2, the peptide conformation is already in a coil structure and only small conformational changes occur upon heating. We determined the equilibrium constant for the reversible helix-coil transition at pD 5.4. The dynamics of this transition was measured at single IR wavelengths after a nanosecond laser-excited temperature jump of ∆T ~ 10 K. Relaxation constants decreased with increasing peptide temperature. Folding and unfolding rates as well as activation energies were extracted based on a two-state model. Our study shows how equilibrium and time-resolved infrared spectroscopic data can be combined to characterize a structural transition and to analyze folding mechanisms.
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Meuvis J, Gerard M, Desender L, Baekelandt V, Engelborghs Y. The Conformation and the Aggregation Kinetics of α-Synuclein Depend on the Proline Residues in Its C-Terminal Region. Biochemistry 2010; 49:9345-52. [DOI: 10.1021/bi1010927] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jessika Meuvis
- Laboratory of Biomolecular Dynamics, Katholieke Universiteit Leuven, Celestijnenlaan 200G, B-3001 Leuven, Belgium
| | - Melanie Gerard
- Laboratory of Biochemistry, Katholieke Universiteit Leuven Campus Kortrijk, Etienne Sabbelaan 53, B-8500 Kortrijk, Belgium
| | - Linda Desender
- Laboratory of Biochemistry, Katholieke Universiteit Leuven Campus Kortrijk, Etienne Sabbelaan 53, B-8500 Kortrijk, Belgium
| | - Veerle Baekelandt
- Laboratory for Neurobiology and Gene Therapy, Katholieke Universiteit Leuven, Kapucijnenvoer 33, B-3000 Leuven, Belgium
| | - Yves Engelborghs
- Laboratory of Biomolecular Dynamics, Katholieke Universiteit Leuven, Celestijnenlaan 200G, B-3001 Leuven, Belgium
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11
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Korkmaz-Ozkan F, Köster S, Kühlbrandt W, Mäntele W, Yildiz O. Correlation between the OmpG secondary structure and its pH-dependent alterations monitored by FTIR. J Mol Biol 2010; 401:56-67. [PMID: 20561532 DOI: 10.1016/j.jmb.2010.06.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 06/01/2010] [Accepted: 06/08/2010] [Indexed: 11/16/2022]
Abstract
The channel activity of the outer-membrane protein G (OmpG) from Escherichia coli is pH-dependent. To investigate the role of the histidine pair His231/His261 in triggering channel opening and closing, we mutated both histidines to alanines and cysteines. Fourier transform infrared spectra revealed that the OmpG mutants stay-independent of pH-in an open conformation. Temperature ramp experiments indicate that the mutants are as stable as the open state of wild-type OmpG. The X-ray structure of the alanine-substituted OmpG mutant obtained at pH 6.5 confirms the constitutively open conformation. Compared to previous structures of the wild-type protein in the open and closed conformation, the mutant structure shows a difference in the extracellular loop L6 connecting beta-strands S12 and S13. A deletion of amino acids 220-228, which are thought to block the channel at low pH in wild-type OmpG, indicates conformational changes, which might be triggered by His231/His261.
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Affiliation(s)
- Filiz Korkmaz-Ozkan
- Institute of Biophysics, Goethe-University, Max-von-Laue-Str. 1, D-60438 Frankfurt am Main, Germany
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12
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Infrared spectroscopic study of the structural and functional properties of the Na+/H+ antiporter MjNhaP1 from Methanococcus jannaschii. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:730-7. [DOI: 10.1016/j.bbabio.2009.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Revised: 04/02/2009] [Accepted: 04/02/2009] [Indexed: 11/23/2022]
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13
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Dzafić E, Klein O, Screpanti E, Hunte C, Mäntele W. Flexibility and dynamics of NhaA Na+/H+-antiporter of Escherichia coli studied by Fourier transform infrared spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2009; 72:102-109. [PMID: 18930435 DOI: 10.1016/j.saa.2008.08.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 08/15/2008] [Accepted: 08/20/2008] [Indexed: 05/26/2023]
Abstract
NhaA (41,355Da) is a Na(+)/H(+) antiporter of Escherichia coli which plays a central role in regulation of intracellular pH, cellular Na(+) content, and cell volume [E. Padan, S. Schuldiner, J. Exp. Biol. 196 (1994) 443]. Its activity is strongly regulated by pH and increases over 3 orders of magnitude between pH 7 and 8 [A. Rothman, Y. Gerchman, E. Padan, S. Schuldiner, Biochemistry 36 (1997) 14572]. Protein dynamics and flexibility in the activated and inactivated state, respectively, was analysed by probing accessibility in (1)H/(2)H exchange experiments for the wild type and the mutant G338S which is constitutively active independent of pH [A. Rimon, Y. Gerchman, Z. Kariv, E. Padan, J. Biol. Chem. 273 (1998) 26470]. This was studied by ATR-FTIR difference spectroscopy using a home built microvolume (<5 microl) perfusion chamber [E. Agić, O. Klein, W. Mäntele, Proceedings of the 10th European Conference on the Spectroscopy of Biological Molecules, vol. 93, 2003, ISBN 9634826148; S. Gourion-Arsiquaud, S. Chevance, P. Bouyer, L. Garnier, J.-L. Montillet, A. Bondon, C. Berthomieu, Biochemistry 44 (2005) 8652]. The solution or suspension of the target protein is contained in a chamber with sample volumes of below 5 microl. It is in contact with the ATR crystal and separated from the flowing effector molecules by a dialysis membrane. The flow-ATR unit is characterised by high stability, fast response, and high sensitivity for the IR spectroscopic detection of binding-induced conformational changes and reactions. On the basis of (1)H-(2)H exchange of NhaA followed in the amide I and amide II region of the IR spectrum, it is concluded that the accessible fraction of the polypeptide chain of NhaA increases by more than 10% in the active state. For the mutant, no changes in accessibility were observed for different pH values. The increase of Na(+) concentration increases the extent of exchange. The stability of the wild type protein in the active and inactive form was analysed by measuring the temperature profiles of the IR spectra. A decrease of the structural stability of the protein with activation was observed. Together with the results from (1)H/(2)H exchange, the inactive state represents a more compact form whereas activation induces a more open conformation of the protein.
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Affiliation(s)
- E Dzafić
- Institut für Biophysik, Johann Wolfgang Goethe-Universität, Max-von-Laue-Strasse 1, D-60438 Frankfurt am Main, Germany.
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Korkmaz F, Köster S, Yildiz Ö, Mäntele W. The Role of Lipids for the Functional Integrity of Porin: An FTIR Study Using Lipid and Protein Reporter Groups. Biochemistry 2008; 47:12126-34. [DOI: 10.1021/bi801224y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Filiz Korkmaz
- Institute of Biophysics, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 1, D-60438 Frankfurt am Main, Germany, and Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, D-60438 Frankfurt am Main, Germany
| | - Stefan Köster
- Institute of Biophysics, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 1, D-60438 Frankfurt am Main, Germany, and Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, D-60438 Frankfurt am Main, Germany
| | - Özkan Yildiz
- Institute of Biophysics, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 1, D-60438 Frankfurt am Main, Germany, and Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, D-60438 Frankfurt am Main, Germany
| | - Werner Mäntele
- Institute of Biophysics, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 1, D-60438 Frankfurt am Main, Germany, and Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, D-60438 Frankfurt am Main, Germany
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15
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Fabian H, Huser H, Narzi D, Misselwitz R, Loll B, Ziegler A, Böckmann RA, Uchanska-Ziegler B, Naumann D. HLA-B27 Subtypes Differentially Associated with Disease Exhibit Conformational Differences in Solution. J Mol Biol 2008; 376:798-810. [DOI: 10.1016/j.jmb.2007.12.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Revised: 11/23/2007] [Accepted: 12/05/2007] [Indexed: 10/22/2022]
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16
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Huang LT, Gromiha MM, Ho SY. Sequence analysis and rule development of predicting protein stability change upon mutation using decision tree model. J Mol Model 2007; 13:879-90. [PMID: 17394029 DOI: 10.1007/s00894-007-0197-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2006] [Accepted: 03/01/2007] [Indexed: 11/26/2022]
Abstract
Understanding the mechanism of the protein stability change is one of the most challenging tasks. Recently, the prediction of protein stability change affected by single point mutations has become an interesting topic in molecular biology. However, it is desirable to further acquire knowledge from large databases to provide new insights into the nature of them. This paper presents an interpretable prediction tree method (named iPTREE-2) that can accurately predict changes of protein stability upon mutations from sequence based information and analyze sequence characteristics from the viewpoint of composition and order. Therefore, iPTREE-2 based on a regression tree algorithm exhibits the ability of finding important factors and developing rules for the purpose of data mining. On a dataset of 1859 different single point mutations from thermodynamic database, ProTherm, iPTREE-2 yields a correlation coefficient of 0.70 between predicted and experimental values. In the task of data mining, detailed analysis of sequences reveals the possibility of the compositional specificity of residues in different ranges of stability change and implies the existence of certain patterns. As building rules, we found that the mutation residues in wild type and in mutant protein play an important role. The present study demonstrates that iPTREE-2 can serve the purpose of predicting protein stability change, especially when one requires more understandable knowledge.
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Affiliation(s)
- Liang-Tsung Huang
- Institute of Information Engineering and Computer Science, Feng-Chia University, Taichung, Taiwan
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17
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Shamsir MS, Dalby AR. Beta-sheet containment by flanking prolines: molecular dynamic simulations of the inhibition of beta-sheet elongation by proline residues in human prion protein. Biophys J 2007; 92:2080-9. [PMID: 17172295 PMCID: PMC1861792 DOI: 10.1529/biophysj.106.092320] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Accepted: 11/16/2006] [Indexed: 12/30/2022] Open
Abstract
Previous molecular dynamic simulations have reported elongation of the existing beta-sheet in prion proteins. Detailed examination has shown that these elongations do not extend beyond the proline residues flanking these beta-sheets. In addition, proline has also been suggested to possess a possible structural role in preserving protein interaction sites by preventing invasion of neighboring secondary structures. In this work, we have studied the possible structural role of the flanking proline residues by simulating mutant structures with alternate substitution of the proline residues with valine. Simulations showed a directional inhibition of elongation, with the elongation progressing in the direction of valine including evident inhibition of elongation by existing proline residues. This suggests that the flanking proline residues in prion proteins may have a containment role and would confine the beta-sheet within a specific length.
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Affiliation(s)
- Mohd S Shamsir
- Biology Department, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor
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18
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Abstract
Porcine pancreatic lipase was modified with Z-proline via the constitution of amide bonds between the free amino groups of lipase and the carboxyl groups of Z-proline, which were activated by 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC). Different amounts of Z-proline were bound to lipase. Modification degree was determined by 2,4,6-trinitrobenzene sulphonic acid (TNBS), by means of the decrease in free amino groups on lipase. The reason for choosing Z-proline was its unique structural characteristics, protected amino groups, and its effect on protein conformation by reducing the flexibility of the lipase molecule, thus achieving stabilization against changes in pH and temperature. After the modification, porcine pancreatic lipase was found to have new physicochemical characteristics, such as optimum alkaline pH stability and thermal stability at elevated temperatures.
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Affiliation(s)
- Serap Evran
- Department of Biochemistry, Faculty of Science, Ege University, Izmir, Turkey.
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19
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Huang LT, Gromiha MM, Hwang SF, Ho SY. Knowledge acquisition and development of accurate rules for predicting protein stability changes. Comput Biol Chem 2006; 30:408-15. [PMID: 17000135 DOI: 10.1016/j.compbiolchem.2006.06.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2006] [Revised: 06/19/2006] [Accepted: 06/19/2006] [Indexed: 11/22/2022]
Abstract
Knowing the mechanisms by which protein stability change is one of the most important and valuable tasks in molecular biology. The conventional methods of predicting protein stability changes mainly focus on improving prediction accuracy. However, it is desirable to extract domain knowledge from large databases that is beneficial to accurate prediction of the protein stability change. This paper presents an interpretable prediction tree method (named iPTREE) that produces explanatory rules to explore hidden knowledge accompanied with high prediction accuracy and consequently analyzes the factors influencing the protein stability changes. To evaluate iPTREE and the knowledge upon protein stability changes, a thermodynamic dataset consisting of 1615 mutants led by single point mutation from ProTherm is adopted. Being as a predictor for protein stability changes, the rule-based approach can achieve a prediction accuracy of 87%, which is better than other methods based on artificial neural networks (ANN) and support vector machines (SVM). Besides, these methods lack the ability in biological knowledge discovery. The human-interpretable rules produced by iPTREE reveal that temperature is a factor of concern in predicting protein stability changes. For example, one of interpretable rules with high support is as follows: if the introduced residue type is Alanine and temperature is between 4 degrees C and 40 degrees C, then the stability change will be negative (destabilizing). The present study demonstrates that iPTREE can easily be used in the application of protein stability changes where one requires more understandable knowledge.
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Affiliation(s)
- Liang-Tsung Huang
- Institute of Information Engineering and Computer Science, Feng Chia University, Taichung 407, Taiwan
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20
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Sukumaran S, Hauser K, Maier E, Benz R, Mäntele W. Structure-function correlation of outer membrane protein porin from Paracoccus denitrificans. Biopolymers 2006; 82:344-8. [PMID: 16345000 DOI: 10.1002/bip.20422] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Porins from outer membrane of Gram-negative bacteria have a highly stable structure. Our previous studies on porin from Paracoccus denitrificans showed that the outer membrane protein porin is extremely stable toward heat, pH, and chemical denaturants. The major question we have addressed in this paper is whether the high stability of porin is a consequence of the beta-barrel structure and whether it is required for its function. To explain this we have analyzed two cases: first, we used porin wild-type and mutants and compared their structure and function; second, we compared the activity of porin preheated to different temperatures. Structural changes were monitored by infrared spectroscopy. We observed that the structural stability of porin is not equivalent to functional activity as minor alteration in the structure can result in drastic differences in the activity of porins.
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Affiliation(s)
- S Sukumaran
- Institut für Biophysik, Johann Wolfgang Goethe-Universität, Max von Laue-Strasse 1, 60438 Frankfurt am Main, Germany
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21
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Tremmel S, Beyermann M, Oschkinat H, Bienert M, Naumann D, Fabian H. 13C-Labeled Tyrosine Residues as Local IR Probes for Monitoring Conformational Changes in Peptides and Proteins. Angew Chem Int Ed Engl 2005; 44:4631-5. [PMID: 15977271 DOI: 10.1002/anie.200500547] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sandra Tremmel
- Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.
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Tremmel S, Beyermann M, Oschkinat H, Bienert M, Naumann D, Fabian H. 13C-markierte Tyrosinreste als lokale IR-Sonden zur Analyse konformativer Änderungen in Peptiden und Proteinen. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200500547] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Sukumaran S, Hauser K, Rauscher A, Mäntele W. Thermal stability of outer membrane protein porin fromParacoccus denitrificans: FT-IR as a spectroscopic tool to study lipid-protein interaction. FEBS Lett 2005; 579:2546-50. [PMID: 15862288 DOI: 10.1016/j.febslet.2005.03.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2005] [Revised: 03/15/2005] [Accepted: 03/15/2005] [Indexed: 10/25/2022]
Abstract
Lipid protein interactions play a key role in the stability and function of various membrane proteins. Earlier we have reported the extreme thermal stability of porin from Paracoccus denitrificans reconstituted into liposomes. Here, we used Fourier transform infrared spectroscopy for a label free analysis of the global secondary structural changes and local changes in the tyrosine microenvironment. Our results show that a mixed lipid system (non-uniform bilayer) optimizes the thermal stability of porin as compared to the porin in pure lipids (uniform bilayer) or detergent micelles. This is in line with the fact that the bacterial outer membrane is a dynamic system made up of lipids of varying chain lengths, head groups and the barrel wall height contacting the membrane is uneven.
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Affiliation(s)
- Suja Sukumaran
- Institut für Biophysik, Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany
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Zandomeneghi G, Krebs MRH, McCammon MG, Fändrich M. FTIR reveals structural differences between native beta-sheet proteins and amyloid fibrils. Protein Sci 2004; 13:3314-21. [PMID: 15537750 PMCID: PMC2287307 DOI: 10.1110/ps.041024904] [Citation(s) in RCA: 518] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The presence of beta-sheets in the core of amyloid fibrils raised questions as to whether or not beta-sheet-containing proteins, such as transthyretin, are predisposed to form such fibrils. However, we show here that the molecular structure of amyloid fibrils differs more generally from the beta-sheets in native proteins. This difference is evident from the amide I region of the infrared spectrum and relates to the distribution of the phi/psi dihedral angles within the Ramachandran plot, the average number of strands per sheet, and possibly, the beta-sheet twist. These data imply that amyloid fibril formation from native beta-sheet proteins can involve a substantial structural reorganization.
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