1
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Berner F, Kovermann M. Including the Ensemble of Unstructured Conformations in the Analysis of Protein's Native State by High-Pressure NMR Spectroscopy. Angew Chem Int Ed Engl 2024; 63:e202401343. [PMID: 38656763 DOI: 10.1002/anie.202401343] [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] [Received: 01/19/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024]
Abstract
The analysis of pressure induced changes in the chemical shift of proteins allows statements on structural fluctuations proteins exhibit at ambient pressure. The inherent issue of separating general pressure effects from structural related effects on the pressure dependence of chemical shifts has so far been addressed by considering the characteristics of random coil peptides on increasing pressure. In this work, chemically and pressure denatured states of the cold shock protein B from Bacillus subtilis (BsCspB) have been assigned in 2D 1H-15N HSQC NMR spectra and their dependence on increasing hydrostatic pressure has been evaluated. The pressure denatured polypeptide chain has been used to separate general from structural related effects on 1H and 15N chemical shifts of native BsCspB and the implications on the interpretation of pressure induced changes in the chemical shift regarding the structure of BsCspB are discussed. It has been found that the ensemble of unstructured conformations of BsCspB shows different responses to increasing pressure than random coil peptides do. Thus, the approach used for considering the general effects that arise when hydrostatic pressure increases changes the structural conclusions that are drawn from high pressure NMR spectroscopic experiments that rely on the analysis of chemical shifts.
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Affiliation(s)
- Frederic Berner
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
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2
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Munte CE, Kalbitzer HR. Solution structure and pressure response of thioredoxin-1 of Plasmodium falciparum. PLoS One 2024; 19:e0301579. [PMID: 38635664 PMCID: PMC11025842 DOI: 10.1371/journal.pone.0301579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/19/2024] [Indexed: 04/20/2024] Open
Abstract
We present here the solution structures of the protein thioredoxin-1 from Plasmodium falciparum (PfTrx-1), in its reduced and oxidized forms. They were determined by high-resolution NMR spectroscopy at 293 K on uniformly 13C-, 15N-enriched, matched samples allowing to identification of even small structural differences. PfTrx-1 shows an α/β-fold with a mixed five-stranded β-sheet that is sandwiched between 4 helices in a β1 α1 β2 α2 β3 α3 β4 β5 α4 topology. The redox process of the CGPC motif leads to significant structural changes accompanied by larger chemical shift changes from residue Phe25 to Ile36, Thr70 to Thr74, and Leu88 to Asn91. By high-field high-pressure NMR spectroscopy, rare conformational states can be identified that potentially are functionally important and can be used for targeted drug development. We performed these experiments in the pressure range from 0.1 MPa to 200 MPa. The mean combined, random-coil corrected B1* values of reduced and oxidized thioredoxin are quite similar with -0.145 and -0.114 ppm GPa-1, respectively. The mean combined, random-coil corrected B2* values in the reduced and oxidized form are 0.179 and 0.119 ppm GPa-2, respectively. The mean ratios of the pressure coefficients B2/B1 are -0.484 and -0.831 GPa-1 in the reduced and oxidized form respectively. They differ at some points in the structure after the formation of the disulfide bond between C30 and C33. The thermodynamical description of the pressure dependence of chemical shifts requires the assumption of at least three coexisting conformational states of PfTrx-1. These three conformational states were identified in the reduced as well as in the oxidized form of the protein, therefore, they represent sub-states of the two main oxidation states of PfTrx-1.
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Affiliation(s)
- Claudia Elisabeth Munte
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Regensburg, Germany
| | - Hans Robert Kalbitzer
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Regensburg, Germany
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3
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Derewenda ZS. C-H Groups as Donors in Hydrogen Bonds: A Historical Overview and Occurrence in Proteins and Nucleic Acids. Int J Mol Sci 2023; 24:13165. [PMID: 37685972 PMCID: PMC10488043 DOI: 10.3390/ijms241713165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Hydrogen bonds constitute a unique type of non-covalent interaction, with a critical role in biology. Until fairly recently, the canonical view held that these bonds occur between electronegative atoms, typically O and N, and that they are mostly electrostatic in nature. However, it is now understood that polarized C-H groups may also act as hydrogen bond donors in many systems, including biological macromolecules. First recognized from physical chemistry studies, C-H…X bonds were visualized with X-ray crystallography sixty years ago, although their true significance has only been recognized in the last few decades. This review traces the origins of the field and describes the occurrence and significance of the most important C-H…O bonds in proteins and nucleic acids.
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Affiliation(s)
- Zygmunt Stanislaw Derewenda
- Department of Molecular Physiology and Biological Physics, School of Medicine, University of Virginia, Charlottesville, VA 22903-2628, USA
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4
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Chiliveri SC, Shen Y, Baber JL, Ying J, Sagar V, Wistow G, Anfinrud P, Bax A. Experimental NOE, Chemical Shift, and Proline Isomerization Data Provide Detailed Insights into Amelotin Oligomerization. J Am Chem Soc 2023; 145:18063-18074. [PMID: 37548612 PMCID: PMC10436275 DOI: 10.1021/jacs.3c05710] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Indexed: 08/08/2023]
Abstract
Amelotin is an intrinsically disordered protein (IDP) rich in Pro residues and is involved in hydroxyapatite mineralization. It rapidly oligomerizes under physiological conditions of pH and pressure but reverts to its monomeric IDP state at elevated pressure. We identified a 105-residue segment of the protein that becomes ordered upon oligomerization, and we used pressure-jump NMR spectroscopy to measure long-range NOE contacts that exist exclusively in the oligomeric NMR-invisible state. The kinetics of oligomerization and dissociation were probed at the residue-specific level, revealing that the oligomerization process is initiated in the C-terminal half of the segment. Using pressure-jump NMR, the degree of order in the oligomer at the sites of Pro residues was probed by monitoring changes in cis/trans equilibria relative to the IDP state after long-term equilibration under oligomerizing conditions. Whereas most Pro residues revert to trans in the oligomeric state, Pro-49 favors a cis configuration and three Pro residues retain an unchanged cis fraction, pointing to their local lack of order in the oligomeric state. NOE contacts and secondary 13C chemical shifts in the oligomeric state indicate the presence of an 11-residue α-helix, preceded by a small intramolecular antiparallel β-sheet, with slower formation of long-range intermolecular interactions to N-terminal residues. Although none of the models generated by AlphaFold2 for the amelotin monomer was consistent with experimental data, subunits of a hexamer generated by AlphaFold-Multimer satisfied intramolecular NOE and chemical shift data and may provide a starting point for developing atomic models for the oligomeric state.
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Affiliation(s)
- Sai Chaitanya Chiliveri
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Yang Shen
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - James L. Baber
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Jinfa Ying
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Vatsala Sagar
- Section
on Molecular Structure and Function, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Graeme Wistow
- Section
on Molecular Structure and Function, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Philip Anfinrud
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Ad Bax
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
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5
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Photopolymerized silk fibroin gel for advanced burn wound care. Int J Biol Macromol 2023; 233:123569. [PMID: 36758758 DOI: 10.1016/j.ijbiomac.2023.123569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/24/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023]
Abstract
The future of burn wound treatment lies in developing bioactive dressings for faster and more effective healing and regeneration. Silk fibroin (SF) hydrogels have proven regenerative abilities and are being explored as a burn wound dressing. However, unfavorable gelation conditions limit the processability and clinical application. Herein a white light-responsive photopolymerization technique was adapted for gelation via photooxidation of tyrosine. To render the gel suitable for application to irregular and non-planar burn surfaces, SF gel-incorporated dressing (SFD) was fabricated. The mild gelation conditions using white light afforded the loading of drugs for local delivery. The moisture balance ability of the dressing was confirmed by the favorable measures of swelling capacity (106 ± 1 %) and moisture retention (≈10 h). The in vitro cytocompatibility of the gel was confirmed using HaCaT cells. Finally, in vivo performance of the SFD was tested on a second-degree burn in a rodent model. The gross analysis and histological assessment revealed scarless healing in SFD-treated groups. Overall, the SFD developed in this work is shown to be a promising candidate for advanced burn wound care.
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Kovács D, Bodor A. The influence of random-coil chemical shifts on the assessment of structural propensities in folded proteins and IDPs. RSC Adv 2023; 13:10182-10203. [PMID: 37006359 PMCID: PMC10065145 DOI: 10.1039/d3ra00977g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/15/2023] [Indexed: 04/03/2023] Open
Abstract
In studying secondary structural propensities of proteins by nuclear magnetic resonance (NMR) spectroscopy, secondary chemical shifts (SCSs) serve as the primary atomic scale observables. For SCS calculation, the selection of an appropriate random coil chemical shift (RCCS) dataset is a crucial step, especially when investigating intrinsically disordered proteins (IDPs). The scientific literature is abundant in such datasets, however, the effect of choosing one over all the others in a concrete application has not yet been studied thoroughly and systematically. Hereby, we review the available RCCS prediction methods and to compare them, we conduct statistical inference by means of the nonparametric sum of ranking differences and comparison of ranks to random numbers (SRD-CRRN) method. We try to find the RCCS predictors best representing the general consensus regarding secondary structural propensities. The existence and the magnitude of resulting differences on secondary structure determination under varying sample conditions (temperature, pH) are demonstrated and discussed for globular proteins and especially IDPs.
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Affiliation(s)
- Dániel Kovács
- ELTE, Eötvös Loránd University, Institute of Chemistry, Analytical and BioNMR Laboratory Pázmány Péter sétány 1/A Budapest 1117 Hungary
- Eötvös Loránd University, Hevesy György PhD School of Chemistry Pázmány Péter sétány 1/A Budapest 1117 Hungary
| | - Andrea Bodor
- ELTE, Eötvös Loránd University, Institute of Chemistry, Analytical and BioNMR Laboratory Pázmány Péter sétány 1/A Budapest 1117 Hungary
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7
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Zhang C, Dai D, Zhao G, Lu W, Fan J. Origin of proton induced fluorescence quenching of colloidal carbon dots: reshaping of Schrödinger wavefunctions and huge red shift of transition energy. NANOTECHNOLOGY 2022; 33:205503. [PMID: 35108697 DOI: 10.1088/1361-6528/ac512b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
The fluorescence quenching by protons is a universal phenomenon but the mechanism remains unclear. Here, we take the fluorescent amide-terminated carbon dots as a prototype to study the proton fluorescence quenching mechanism by using both experiments and time-dependent density functional theory calculations. The study reveals that when an approached proton is captured by the weakly negatively charged fluorophore group of the colloidal carbon dot, it will substantially change the electron wavefunctions owing to the strong proton-electron interaction, and this leads to highly diminished energy gap and resultant fluorescence quenching in the visible spectral region. The protons generated by hydrolysis of various types of metal ions also exhibit fruitful fluorescence quenching and the quenching efficiency is roughly proportional to the hydrolysis constant of the metal ion. This fluorescence quenching mechanism is quite distinct from the conventional ones involving electron or energy transfer.
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Affiliation(s)
- Chengyu Zhang
- College of Artificial Intelligence, Nanjing Agricultural University, Nanjing 210031, People's Republic of China
| | - Dejian Dai
- College of Artificial Intelligence, Nanjing Agricultural University, Nanjing 210031, People's Republic of China
| | - Guo Zhao
- College of Artificial Intelligence, Nanjing Agricultural University, Nanjing 210031, People's Republic of China
| | - Wei Lu
- College of Artificial Intelligence, Nanjing Agricultural University, Nanjing 210031, People's Republic of China
| | - Jiyang Fan
- School of Physics, Southeast University, Nanjing 211189, People's Republic of China
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8
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Carvalho IC, Mansur AAP, Carvalho SM, Mansur HS. Nanotheranostics through Mitochondria-targeted Delivery with Fluorescent Peptidomimetic Nanohybrids for Apoptosis Induction of Brain Cancer Cells. Nanotheranostics 2021; 5:213-239. [PMID: 33614399 PMCID: PMC7893535 DOI: 10.7150/ntno.54491] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/26/2021] [Indexed: 01/23/2023] Open
Abstract
Overview: Malignant brain tumors remain one of the greatest challenges faced by health professionals and scientists among the utmost lethal forms of cancer. Nanotheranostics can play a pivotal role in developing revolutionary nanoarchitectures with multifunctional and multimodal capabilities to fight cancer. Mitochondria are vital organelles to eukaryotic cells, which have been recognized as a significant target in cancer therapy where, by damaging the mitochondria, it will cause irreparable cell death or apoptosis. Methods: We designed and produced novel hybrid nanostructures comprising a fluorescent semiconductor core (AgInS2, AIS) and cysteine-modified carboxymethylcellulose (termed thiomer, CMC_Cys) conjugated with mitochondria-targeting peptides (KLA) forming a macromolecular shell for combining bioimaging and for inducing brain cancer cell (U-87 MG) death. Results: The optical and physicochemical properties of the nanoconjugates demonstrated suitability as photoluminescent nanostructures for cell bioimaging and intracellular tracking. Additionally, the results proved a remarkable killing activity towards glioblastoma cells of cysteine-bearing CMC conjugates coupled with KLA peptides through the half-maximal effective concentration values, approximately 70-fold higher compared to the conjugate analogs without Cys residues. Moreover, these thiomer-based pro-apoptotic drug nanoconjugates displayed higher lethality against U-87 MG cancer cells than doxorubicin, a model drug in chemotherapy, although extremely toxic. Remarkably, these peptidomimetic nanohybrids demonstrated a relative "protective effect" regarding healthy cells while maintaining high killing activity towards malignant brain cells. Conclusion: These findings pave the way for developing hybrid nanoarchitectures applied as targeted multifunctional platforms for simultaneous imaging and therapy against cancer while minimizing the high systemic toxicity and side-effects of conventional drugs in anticancer chemotherapy.
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Affiliation(s)
| | | | | | - Herman S. Mansur
- Center of Nanoscience, Nanotechnology, and Innovation - CeNano2I, Department of Metallurgical and Materials Engineering, Federal University of Minas Gerais - UFMG, Av. Antônio Carlos, 6627 - Belo Horizonte/MG, Brazil
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9
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Liu Q, He QT, Lyu X, Yang F, Zhu ZL, Xiao P, Yang Z, Zhang F, Yang ZY, Wang XY, Sun P, Wang QW, Qu CX, Gong Z, Lin JY, Xu Z, Song SL, Huang SM, Guo SC, Han MJ, Zhu KK, Chen X, Kahsai AW, Xiao KH, Kong W, Li FH, Ruan K, Li ZJ, Yu X, Niu XG, Jin CW, Wang J, Sun JP. DeSiphering receptor core-induced and ligand-dependent conformational changes in arrestin via genetic encoded trimethylsilyl 1H-NMR probe. Nat Commun 2020; 11:4857. [PMID: 32978402 PMCID: PMC7519161 DOI: 10.1038/s41467-020-18433-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 08/12/2020] [Indexed: 01/11/2023] Open
Abstract
Characterization of the dynamic conformational changes in membrane protein signaling complexes by nuclear magnetic resonance (NMR) spectroscopy remains challenging. Here we report the site-specific incorporation of 4-trimethylsilyl phenylalanine (TMSiPhe) into proteins, through genetic code expansion. Crystallographic analysis revealed structural changes that reshaped the TMSiPhe-specific amino-acyl tRNA synthetase active site to selectively accommodate the trimethylsilyl (TMSi) group. The unique up-field 1H-NMR chemical shift and the highly efficient incorporation of TMSiPhe enabled the characterization of multiple conformational states of a phospho-β2 adrenergic receptor/β-arrestin-1(β-arr1) membrane protein signaling complex, using only 5 μM protein and 20 min of spectrum accumulation time. We further showed that extracellular ligands induced conformational changes located in the polar core or ERK interaction site of β-arr1 via direct receptor transmembrane core interactions. These observations provided direct delineation and key mechanism insights that multiple receptor ligands were able to induce distinct functionally relevant conformational changes of arrestin.
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Affiliation(s)
- Qi Liu
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong, 250012, China
| | - Qing-Tao He
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, 250012, Shandong, China
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Xiaoxuan Lyu
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
| | - Fan Yang
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong, 250012, China
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Zhong-Liang Zhu
- School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Peng Xiao
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, 250012, Shandong, China
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Zhao Yang
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong, 250012, China
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Feng Zhang
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
| | - Zhao-Ya Yang
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, 250012, Shandong, China
| | - Xiao-Yan Wang
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
| | - Peng Sun
- Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, 30 Xiaohongshan Road, Wuchang District, Wuhan, Hubei, 430071, China
| | - Qian-Wen Wang
- Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, 30 Xiaohongshan Road, Wuchang District, Wuhan, Hubei, 430071, China
| | - Chang-Xiu Qu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, 250012, Shandong, China
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Zheng Gong
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, 250012, Shandong, China
| | - Jing-Yu Lin
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong, 250012, China
| | - Zhen Xu
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
| | - Shao-le Song
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
| | - Shen-Ming Huang
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Sheng-Chao Guo
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, 250012, Shandong, China
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Ming-Jie Han
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xiqi Road, Airport Economic Zone, Dongli District, Tianjin, 300308, China
| | - Kong-Kai Zhu
- School of Biological Science and Technology, University of Jinan, 336 Nanxinzhuangxi Road, Shizhong District, Jinan, 250022, China
| | - Xin Chen
- Department of Medicinal Chemistry, School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Alem W Kahsai
- Duke University, School of Medicine, Durham, NC, 27705, USA
| | - Kun-Hong Xiao
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Wei Kong
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Fa-Hui Li
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
| | - Ke Ruan
- Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, 443 Huangshan Road, Hefei, Anhui, 230027, China
| | - Zi-Jian Li
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Xiao Yu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong, 250012, China
| | - Xiao-Gang Niu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing, 100084, China
| | - Chang-Wen Jin
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing, 100084, China
| | - Jiangyun Wang
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China.
- College of Life Sciences and School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jin-Peng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, 250012, Shandong, China.
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China.
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10
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Beck Erlach M, Koehler J, Munte CE, Kremer W, Crusca E, Kainosho M, Kalbitzer HR. Pressure dependence of side chain 1H and 15N-chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH 2. JOURNAL OF BIOMOLECULAR NMR 2020; 74:381-399. [PMID: 32572797 PMCID: PMC7508751 DOI: 10.1007/s10858-020-00326-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
For interpreting the pressure induced shifts of resonance lines of folded as well as unfolded proteins the availability of data from well-defined model systems is indispensable. Here, we report the pressure dependence of 1H and 15N chemical shifts of the side chain atoms in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx is one of the 20 canonical amino acids) measured at 800 MHz proton frequency. As observed earlier for other nuclei the chemical shifts of the side chain nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The pressure response is described by a second degree polynomial with the pressure coefficients B1 and B2 that are dependent on the atom type and type of amino acid studied. A number of resonances could be assigned stereospecifically including the 1H and 15N resonances of the guanidine group of arginine. In addition, stereoselectively isotope labeled SAIL amino acids were used to support the stereochemical assignments. The random-coil pressure coefficients are also dependent on the neighbor in the sequence as an analysis of the data shows. For Hα and HN correction factors for different amino acids were derived. In addition, a simple correction of compression effects in thermodynamic analysis of structural transitions in proteins was derived on the basis of random-coil pressure coefficients.
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Affiliation(s)
- Markus Beck Erlach
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany
| | - Joerg Koehler
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany
| | - Claudia E Munte
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany
| | - Werner Kremer
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany
| | - Edson Crusca
- Physics Institute of São Carlos, University of São Paulo, São Carlos, 13566-590, Brazil
| | - Masatsune Kainosho
- Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo, 192-0397, Japan
| | - Hans Robert Kalbitzer
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany.
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11
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Luminescent switch of polysaccharide-peptide-quantum dot nanostructures for targeted-intracellular imaging of glioblastoma cells. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112759] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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12
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Carvalho IC, Mansur AA, Carvalho SM, Florentino RM, Mansur HS. L-cysteine and poly-L-arginine grafted carboxymethyl cellulose/Ag-In-S quantum dot fluorescent nanohybrids for in vitro bioimaging of brain cancer cells. Int J Biol Macromol 2019; 133:739-753. [DOI: 10.1016/j.ijbiomac.2019.04.140] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 12/13/2022]
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13
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Zamora WJ, Campanera JM, Luque FJ. Development of a Structure-Based, pH-Dependent Lipophilicity Scale of Amino Acids from Continuum Solvation Calculations. J Phys Chem Lett 2019; 10:883-889. [PMID: 30741551 DOI: 10.1021/acs.jpclett.9b00028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Lipophilicity is a fundamental property to characterize the structure and function of proteins, motivating the development of lipophilicity scales. We report a versatile strategy to derive a pH-adapted scale that relies on theoretical estimates of distribution coefficients from conformational ensembles of amino acids. This is accomplished by using an accurately parametrized version of the IEFPCM/MST continuum solvation model as an effective way to describe the partitioning between n-octanol and water, in conjunction with a formalism that combines partition coefficients of neutral and ionic species of residues and the corresponding p Ka values of ionizable groups. Two weighting schemes are considered to derive solvent-like and protein-like scales, which have been calibrated by comparison with other experimental scales developed in different chemical/biological environments and pH conditions as well as by examining properties such as the retention time of small peptides and the recognition of antigenic peptides. A straightforward extension to nonstandard residues is enabled by this efficient methodological strategy.
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Affiliation(s)
- William J Zamora
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Science, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), Campus Torribera , University of Barcelona , 08921 Santa Coloma de Gramenet , Spain
| | - Josep M Campanera
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Science, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), Campus Torribera , University of Barcelona , 08921 Santa Coloma de Gramenet , Spain
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Science, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), Campus Torribera , University of Barcelona , 08921 Santa Coloma de Gramenet , Spain
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14
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Borcherds WM, Daughdrill GW. Using NMR Chemical Shifts to Determine Residue-Specific Secondary Structure Populations for Intrinsically Disordered Proteins. Methods Enzymol 2018; 611:101-136. [PMID: 30471686 PMCID: PMC8130511 DOI: 10.1016/bs.mie.2018.09.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Protein disorder is a pervasive phenomenon in biology and a natural consequence of polymer evolution that facilitates cell signaling by organizing sites for posttranslational modifications and protein-protein interactions into arrays of short linear motifs that can be rearranged by RNA splicing. Disordered proteins are missing the long-range nonpolar interactions that form tertiary structures, but they often contain regions with residual secondary structure that are stabilized by protein binding. NMR spectroscopy is uniquely suited to detect residual secondary structure in a disordered protein and it can provide atomic resolution data on the structure and dynamics of disordered protein interaction sites. Here we describe how backbone chemical shifts are used for assigning residual secondary structure in disordered proteins and discuss some of the tools available for estimating secondary structure populations with a focus on disordered proteins containing different levels of alpha helical secondary structure which are stabilized by protein binding.
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Affiliation(s)
- Wade M Borcherds
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, United States.
| | - Gary W Daughdrill
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, United States.
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15
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Roche J, Royer CA, Roumestand C. Monitoring protein folding through high pressure NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:15-31. [PMID: 29157491 DOI: 10.1016/j.pnmrs.2017.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/31/2017] [Accepted: 05/31/2017] [Indexed: 06/07/2023]
Abstract
High-pressure is a well-known perturbation method used to destabilize globular proteins. It is perfectly reversible, which is essential for a proper thermodynamic characterization of a protein equilibrium. In contrast to other perturbation methods such as heat or chemical denaturant that destabilize protein structures uniformly, pressure exerts local effects on regions or domains of a protein containing internal cavities. When combined with NMR spectroscopy, hydrostatic pressure offers the possibility to monitor at a residue level the structural transitions occurring upon unfolding and to determine the kinetic properties of the process. High-pressure NMR experiments can now be routinely performed, owing to the recent development of commercially available high-pressure sample cells. This review summarizes recent advances and some future directions of high-pressure NMR techniques for the characterization at atomic resolution of the energy landscape of protein folding.
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Affiliation(s)
- Julien Roche
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Christian Roumestand
- Centre de Biochimie Structural INSERM U1054, CNRS UMMR 5058, Université de Montpellier, Montpellier 34090, France.
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16
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Beck Erlach M, Koehler J, Crusca E, Munte CE, Kainosho M, Kremer W, Kalbitzer HR. Pressure dependence of side chain 13C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH 2. JOURNAL OF BIOMOLECULAR NMR 2017; 69:53-67. [PMID: 28913741 DOI: 10.1007/s10858-017-0134-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
For evaluating the pressure responses of folded as well as intrinsically unfolded proteins detectable by NMR spectroscopy the availability of data from well-defined model systems is indispensable. In this work we report the pressure dependence of 13C chemical shifts of the side chain atoms in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx, one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of a number of nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The size of the polynomial pressure coefficients B 1 and B 2 is dependent on the type of atom and amino acid studied. For HN, N and Cα the first order pressure coefficient B 1 is also correlated to the chemical shift at atmospheric pressure. The first and second order pressure coefficients of a given type of carbon atom show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure also are weakly correlated. The downfield shifts of the methyl resonances suggest that gauche conformers of the side chains are not preferred with pressure. The valine and leucine methyl groups in the model peptides were assigned using stereospecifically 13C enriched amino acids with the pro-R carbons downfield shifted relative to the pro-S carbons.
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Affiliation(s)
- Markus Beck Erlach
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany
| | - Joerg Koehler
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany
| | - Edson Crusca
- Institute of Chemistry, São Paulo State University (UNESP), Araraquara, 14800-060, Brazil
| | - Claudia E Munte
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany
- Physics Institute of São Carlos, University of São Paulo, São Carlos, 13566-590, Brazil
| | - Masatsune Kainosho
- Graduate School of Science and Technology, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo, 192-0397, Japan
| | - Werner Kremer
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany
| | - Hans Robert Kalbitzer
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany.
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17
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Zamora WJ, Curutchet C, Campanera JM, Luque FJ. Prediction of pH-Dependent Hydrophobic Profiles of Small Molecules from Miertus–Scrocco–Tomasi Continuum Solvation Calculations. J Phys Chem B 2017; 121:9868-9880. [DOI: 10.1021/acs.jpcb.7b08311] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- William J. Zamora
- Departament de Nutrició, Ciències de l’Alimentació i Gastronomia, and Institut de Biomedicina (IBUB), Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica, and Institut de Biomedicina (IBUB), Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Avgda. Diagonal 643, 08028 Barcelona, Spain
| | - Carles Curutchet
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica, and Institut de Biomedicina (IBUB), Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Avgda. Diagonal 643, 08028 Barcelona, Spain
| | - Josep M. Campanera
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica, and Institut de Biomedicina (IBUB), Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Avgda. Diagonal 643, 08028 Barcelona, Spain
| | - F. Javier Luque
- Departament de Nutrició, Ciències de l’Alimentació i Gastronomia, and Institut de Biomedicina (IBUB), Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain
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18
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Sastre S, Casasnovas R, Muñoz F, Frau J. Isodesmic reaction for accurate theoretical pKa calculations of amino acids and peptides. Phys Chem Chem Phys 2017; 18:11202-12. [PMID: 27052591 DOI: 10.1039/c5cp07053h] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Theoretical and quantitative prediction of pKa values at low computational cost is a current challenge in computational chemistry. We report that the isodesmic reaction scheme provides semi-quantitative predictions (i.e. mean absolute errors of 0.5-1.0 pKa unit) for the pKa1 (α-carboxyl), pKa2 (α-amino) and pKa3 (sidechain groups) of a broad set of amino acids and peptides. This method fills the gaps of thermodynamic cycles for the computational pKa calculation of molecules that are unstable in the gas phase or undergo proton transfer reactions or large conformational changes from solution to the gas phase. We also report the key criteria to choose a reference species to make accurate predictions. This method is computationally inexpensive and makes use of standard density functional theory (DFT) and continuum solvent models. It is also conceptually simple and easy to use for researchers not specialized in theoretical chemistry methods.
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Affiliation(s)
- S Sastre
- Department de Química, Universitat de les Illes Balears, Palma de Mallorca 07122, Spain.
| | - R Casasnovas
- Institute of Neuroscience and Medicine INM-9, Institute for Advanced Simulations IAS-5. Computational Biomedicine, Forschungszentrum Jülich 52428, Germany
| | - F Muñoz
- Department de Química, Universitat de les Illes Balears, Palma de Mallorca 07122, Spain. and Instituto de Investigación Sanitaria de Palma (IdISPa), 07010, Palma, Spain
| | - J Frau
- Department de Química, Universitat de les Illes Balears, Palma de Mallorca 07122, Spain. and Instituto de Investigación Sanitaria de Palma (IdISPa), 07010, Palma, Spain
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19
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Schummel PH, Haag A, Kremer W, Kalbitzer HR, Winter R. Cosolvent and Crowding Effects on the Temperature and Pressure Dependent Conformational Dynamics and Stability of Globular Actin. J Phys Chem B 2016; 120:6575-86. [DOI: 10.1021/acs.jpcb.6b04738] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Paul Hendrik Schummel
- Physical
Chemistry I − Biophysical Chemistry, Faculty of Chemistry and
Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, D-44227 Dortmund, Germany
| | - Andreas Haag
- Institute
of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance
in Chemistry and Biomedicine (CMRCB), University of Regensburg, Universitätsstrasse
31, D-93047 Regensburg, Germany
| | - Werner Kremer
- Institute
of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance
in Chemistry and Biomedicine (CMRCB), University of Regensburg, Universitätsstrasse
31, D-93047 Regensburg, Germany
| | - Hans Robert Kalbitzer
- Institute
of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance
in Chemistry and Biomedicine (CMRCB), University of Regensburg, Universitätsstrasse
31, D-93047 Regensburg, Germany
| | - Roland Winter
- Physical
Chemistry I − Biophysical Chemistry, Faculty of Chemistry and
Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, D-44227 Dortmund, Germany
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20
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Frach R, Kibies P, Böttcher S, Pongratz T, Strohfeldt S, Kurrmann S, Koehler J, Hofmann M, Kremer W, Kalbitzer HR, Reiser O, Horinek D, Kast SM. The Chemical Shift Baseline for High-Pressure NMR Spectra of Proteins. Angew Chem Int Ed Engl 2016; 55:8757-60. [DOI: 10.1002/anie.201602054] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Roland Frach
- Physikalische Chemie III, Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Patrick Kibies
- Physikalische Chemie III, Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Saraphina Böttcher
- Physikalische Chemie III, Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Tim Pongratz
- Physikalische Chemie III, Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Steven Strohfeldt
- Physikalische Chemie III, Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Simon Kurrmann
- Institut für Biophysik und physikalische Biochemie, Fakultät für Biologie und Vorklin. Medizin; Universität Regensburg; Germany
| | - Joerg Koehler
- Institut für Biophysik und physikalische Biochemie, Fakultät für Biologie und Vorklin. Medizin; Universität Regensburg; Germany
| | - Martin Hofmann
- Institut für Organische Chemie, Fakultät für Chemie und Pharmazie; Universität Regensburg; Germany
| | - Werner Kremer
- Institut für Biophysik und physikalische Biochemie, Fakultät für Biologie und Vorklin. Medizin; Universität Regensburg; Germany
| | - Hans Robert Kalbitzer
- Institut für Biophysik und physikalische Biochemie, Fakultät für Biologie und Vorklin. Medizin; Universität Regensburg; Germany
| | - Oliver Reiser
- Institut für Organische Chemie, Fakultät für Chemie und Pharmazie; Universität Regensburg; Germany
| | - Dominik Horinek
- Institut für Physikalische und Theoretische Chemie, Fakultät für Chemie und Pharmazie; Universität Regensburg; Germany
| | - Stefan M. Kast
- Physikalische Chemie III, Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
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21
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Frach R, Kibies P, Böttcher S, Pongratz T, Strohfeldt S, Kurrmann S, Koehler J, Hofmann M, Kremer W, Kalbitzer HR, Reiser O, Horinek D, Kast SM. Die Basislinie der chemischen Verschiebung in Hochdruck-NMR-Spektren von Proteinen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Roland Frach
- Physikalische Chemie III, Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Patrick Kibies
- Physikalische Chemie III, Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Saraphina Böttcher
- Physikalische Chemie III, Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Tim Pongratz
- Physikalische Chemie III, Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Steven Strohfeldt
- Physikalische Chemie III, Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Simon Kurrmann
- Institut für Biophysik und physikalische Biochemie, Fakultät für Biologie und Vorklin. Medizin; Universität Regensburg; Deutschland
| | - Joerg Koehler
- Institut für Biophysik und physikalische Biochemie, Fakultät für Biologie und Vorklin. Medizin; Universität Regensburg; Deutschland
| | - Martin Hofmann
- Institut für Organische Chemie, Fakultät für Chemie und Pharmazie; Universität Regensburg; Deutschland
| | - Werner Kremer
- Institut für Biophysik und physikalische Biochemie, Fakultät für Biologie und Vorklin. Medizin; Universität Regensburg; Deutschland
| | - Hans Robert Kalbitzer
- Institut für Biophysik und physikalische Biochemie, Fakultät für Biologie und Vorklin. Medizin; Universität Regensburg; Deutschland
| | - Oliver Reiser
- Institut für Organische Chemie, Fakultät für Chemie und Pharmazie; Universität Regensburg; Deutschland
| | - Dominik Horinek
- Institut für Physikalische und Theoretische Chemie, Fakultät für Chemie und Pharmazie; Universität Regensburg; Deutschland
| | - Stefan M. Kast
- Physikalische Chemie III, Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
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22
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Erlach MB, Koehler J, Crusca E, Kremer W, Munte CE, Kalbitzer HR. Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH2. JOURNAL OF BIOMOLECULAR NMR 2016; 65:65-77. [PMID: 27335085 DOI: 10.1007/s10858-016-0030-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 03/21/2016] [Indexed: 06/06/2023]
Abstract
For a better understanding of nuclear magnetic resonance (NMR) detected pressure responses of folded as well as unstructured proteins the availability of data from well-defined model systems are indispensable. In this work we report the pressure dependence of chemical shifts of the backbone atoms (1)H(α), (13)C(α) and (13)C' in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of these nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The polynomial pressure coefficients B 1 and B 2 are dependent on the type of amino acid studied. The coefficients of a given nucleus show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure are also weakly correlated.
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Affiliation(s)
- Markus Beck Erlach
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany
| | - Joerg Koehler
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany
| | - Edson Crusca
- Physics Institute of São Carlos, University of São Paulo, São Carlos, 13566-590, Brazil
| | - Werner Kremer
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany
| | - Claudia E Munte
- Physics Institute of São Carlos, University of São Paulo, São Carlos, 13566-590, Brazil
| | - Hans Robert Kalbitzer
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany.
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23
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Abstract
Proteins usually exist in multiple conformational states in solution. High pressure NMR spectroscopy is a well-suited method to identify these states. In addition, these states can be characterized by their thermodynamic parameters, the free enthalpies at ambient pressure, the partial molar volumes, and the partial molar compressibility that can be obtained from the analysis of the high pressure NMR data. Two main types of states of proteins exist, functional states and folding states. There is a strong link between these two types, the functional states represent essential folding states (intermediates), other folding states may have no functional meaning (optional folding states). In this chapter, this concept is tested on the Ras protein, an important proto-oncogen in humans where all substates required by theory can be identified experimentally by high pressure NMR spectroscopy. Finally, we show how these data can be used to develop allosteric inhibitors of proteins.
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24
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Norouzy A, Assaf KI, Zhang S, Jacob MH, Nau WM. Coulomb Repulsion in Short Polypeptides. J Phys Chem B 2014; 119:33-43. [DOI: 10.1021/jp508263a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Amir Norouzy
- Department of Life Sciences
and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Khaleel I. Assaf
- Department of Life Sciences
and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Shuai Zhang
- Department of Life Sciences
and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Maik H. Jacob
- Department of Life Sciences
and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Werner M. Nau
- Department of Life Sciences
and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
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25
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Koehler J, Beck Erlach M, Crusca E, Kremer W, Munte CE, Meier A, Kalbitzer HR. Pressure response of amide one-bond J-couplings in model peptides and proteins. JOURNAL OF BIOMOLECULAR NMR 2014; 60:45-50. [PMID: 25117742 DOI: 10.1007/s10858-014-9850-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 07/30/2014] [Indexed: 06/03/2023]
Abstract
The pressure dependence of the one-bond indirect spin-spin coupling constants (1)J(N-H) was studied in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (with Xxx being one of the 20 proteinogenic amino acids). The response of the (1)J(N-H) coupling constants is amino acid type specific, with an average increase of its magnitude by 0.6 Hz at 200 MPa. The variance of the pressure response is rather large, the largest pressure effect is observed for asparagine where the coupling constant becomes more negative by -2.9 Hz at 200 MPa. The size of the J-coupling constant at high pressure is positively correlated with its low pressure value and the β-propensity, and negatively correlated with the amide proton shift and the first order nitrogen pressure coefficient and the electrostatic solvation free energy.
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Affiliation(s)
- Joerg Koehler
- Centre of Magnetic Resonance in Chemistry and Biomedicine (CMRCB), Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93047, Regensburg, Germany
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26
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Beck Erlach M, Koehler J, Moeser B, Horinek D, Kremer W, Kalbitzer HR. Relationship between Nonlinear Pressure-Induced Chemical Shift Changes and Thermodynamic Parameters. J Phys Chem B 2014; 118:5681-90. [DOI: 10.1021/jp502664a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Markus Beck Erlach
- Institute of Biophysics
and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry
and Biophysics, University of Regensburg, 93040 Regensburg, Germany
| | - Joerg Koehler
- Institute of Biophysics
and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry
and Biophysics, University of Regensburg, 93040 Regensburg, Germany
| | - Beate Moeser
- Institute of Physical
and Theoretical Chemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Dominik Horinek
- Institute of Physical
and Theoretical Chemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Werner Kremer
- Institute of Biophysics
and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry
and Biophysics, University of Regensburg, 93040 Regensburg, Germany
| | - Hans Robert Kalbitzer
- Institute of Biophysics
and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry
and Biophysics, University of Regensburg, 93040 Regensburg, Germany
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Linser R, Sarkar R, Krushelnitzky A, Mainz A, Reif B. Dynamics in the solid-state: perspectives for the investigation of amyloid aggregates, membrane proteins and soluble protein complexes. JOURNAL OF BIOMOLECULAR NMR 2014; 59:1-14. [PMID: 24595988 DOI: 10.1007/s10858-014-9822-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/26/2014] [Indexed: 06/03/2023]
Abstract
Aggregates formed by amyloidogenic peptides and proteins and reconstituted membrane protein preparations differ significantly in terms of the spectral quality that they display in solid-state NMR experiments. Structural heterogeneity and dynamics can both in principle account for that observation. This perspectives article aims to point out challenges and limitations, but also potential opportunities in the investigation of these systems.
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Affiliation(s)
- Rasmus Linser
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA
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Shim YS, Yoon WJ, Ha J, Seo D, Lee KW, Lee WY, Kwon KI, Kang TS, Lee JH, Kim HJ, Kwak HJ, Lee SP, Kim SJ, Yun WK, Lee J, Hwang JB. Method validation of 16 types of structural amino acids using an automated amino acid analyzer. Food Sci Biotechnol 2013. [DOI: 10.1007/s10068-013-0252-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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29
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Kitahara R, Hata K, Li H, Williamson MP, Akasaka K. Pressure-induced chemical shifts as probes for conformational fluctuations in proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 71:35-58. [PMID: 23611314 DOI: 10.1016/j.pnmrs.2012.12.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 12/18/2012] [Indexed: 06/02/2023]
Affiliation(s)
- Ryo Kitahara
- College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
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Koehler J, Beck Erlach M, Crusca E, Kremer W, Munte CE, Kalbitzer HR. Pressure Dependence of 15N Chemical Shifts in Model Peptides Ac-Gly-Gly-X-Ala-NH2. MATERIALS 2012. [PMCID: PMC5449040 DOI: 10.3390/ma5101774] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
High pressure NMR spectroscopy has developed into an important tool for studying conformational equilibria of proteins in solution. We have studied the amide proton and nitrogen chemical shifts of the 20 canonical amino acids X in the random-coil model peptide Ac-Gly-Gly-X-Ala-NH2, in a pressure range from 0.1 to 200 MPa, at a proton resonance frequency of 800 MHz. The obtained data allowed the determination of first and second order pressure coefficients with high accuracy at 283 K and pH 6.7. The mean first and second order pressure coefficients <B115N> and <B215N> for nitrogen are 2.91 ppm/GPa and −2.32 ppm/GPa2, respectively. The corresponding values <B11H> and <B21H> for the amide protons are 0.52 ppm/GPa and −0.41 ppm/GPa2. Residual dependent 1J1H15N-coupling constants are shown.
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Affiliation(s)
- Joerg Koehler
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Regensburg 93040, Germany; E-Mails: (J.K.); (M.B.E.); (W.K.)
| | - Markus Beck Erlach
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Regensburg 93040, Germany; E-Mails: (J.K.); (M.B.E.); (W.K.)
| | - Edson Crusca
- Physics Institute of São Carlos, University of São Paulo, São Carlos 13566-590, Brazil; E-Mails: (E.C.); (C.E.M.)
| | - Werner Kremer
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Regensburg 93040, Germany; E-Mails: (J.K.); (M.B.E.); (W.K.)
| | - Claudia E. Munte
- Physics Institute of São Carlos, University of São Paulo, São Carlos 13566-590, Brazil; E-Mails: (E.C.); (C.E.M.)
| | - Hans Robert Kalbitzer
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Regensburg 93040, Germany; E-Mails: (J.K.); (M.B.E.); (W.K.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +49-941-943-2594; Fax: +49-941-943-2479
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31
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Chen WQ, Heymann G, Kursula P, Rosner M, Hengstschläger M, Huppertz H, Lubec G. Effects of Gigapascal Level Pressure on Protein Structure and Function. J Phys Chem B 2012; 116:1100-10. [DOI: 10.1021/jp207864c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wei-Qiang Chen
- Department of Pediatrics, Medical University of Vienna, Währinger Gürtel 18, 1090 Vienna, Austria
| | - Gunter Heymann
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52; 6020 Innsbruck, Austria
| | - Petri Kursula
- Department of Biochemistry, University of Oulu, PL3000; 90014 Oulu, Finland
- Centre for Structural Systems Biology (CSSB-HZI), German Electron Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Margit Rosner
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090 Vienna, Austria
| | - Markus Hengstschläger
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090 Vienna, Austria
| | - Hubert Huppertz
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52; 6020 Innsbruck, Austria
| | - Gert Lubec
- Department of Pediatrics, Medical University of Vienna, Währinger Gürtel 18, 1090 Vienna, Austria
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32
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Sieber T, Scholz R, Spoerner M, Schumann F, Kalbitzer HR, Dobner T. Intrinsic disorder in the common N-terminus of human adenovirus 5 E1B-55K and its related E1BN proteins indicated by studies on E1B-93R. Virology 2011; 418:133-43. [DOI: 10.1016/j.virol.2011.07.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 07/13/2011] [Accepted: 07/18/2011] [Indexed: 10/17/2022]
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Kremer W, Arnold M, Munte CE, Hartl R, Erlach MB, Koehler J, Meier A, Kalbitzer HR. Pulsed pressure perturbations, an extra dimension in NMR spectroscopy of proteins. J Am Chem Soc 2011; 133:13646-51. [PMID: 21774550 DOI: 10.1021/ja2050698] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The introduction of multidimensional NMR spectroscopy was a breakthrough in biological NMR methodology because it allowed the unequivocal correlation of different spin states of the system. The introduction of large pressure perturbations in the corresponding radio frequency (RF) pulse sequences adds an extra structural dimension into these experiments. We have developed a microprocessor-controlled pressure jump unit that is able to introduce fast, strong pressure changes at any point in the pulse sequences. Repetitive pressure changes of 80 MPa in the sample tube are thus feasible in less than 30 ms. Two general forms of these experiments are proposed here, the pressure perturbation transient state spectroscopy (PPTSS) and the pressure perturbation state correlation spectroscopy (PPSCS). PPTSS can be used to measure the rate constants and the activation energies and activation volumes for the transition between different conformational states including the folded and unfolded state of proteins, for polymerization-depolymerization processes, and for ligand binding at atomic resolution. PPSCS spectroscopy correlates the NMR parameters of different pressure-induced states of the system, thus allowing the measurement of properties of a given pressure induced state such as a folding intermediate in a different state, for example, the folded state. Selected examples for PPTSS and PPSCS spectroscopy are presented in this Article.
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Affiliation(s)
- Werner Kremer
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Universitätsstrasse 31, D-93047 Regensburg, Germany
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Wishart DS. Interpreting protein chemical shift data. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 58:62-87. [PMID: 21241884 DOI: 10.1016/j.pnmrs.2010.07.004] [Citation(s) in RCA: 184] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 07/29/2010] [Indexed: 05/12/2023]
Affiliation(s)
- David S Wishart
- Department of Biological Sciences, National Institute for Nanotechnology (NINT), Edmonton, AB, Canada T6G 2E8.
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35
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Vermeer LS, Réat V, Hemminga MA, Milon A. Structural properties of a peptide derived from H+-V-ATPase subunit a. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:1204-12. [DOI: 10.1016/j.bbamem.2009.02.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 02/10/2009] [Accepted: 02/11/2009] [Indexed: 10/21/2022]
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36
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Gronwald W, Bomke J, Maurer T, Domogalla B, Huber F, Schumann F, Kremer W, Fink F, Rysiok T, Frech M, Kalbitzer HR. Structure of the Leech Protein Saratin and Characterization of Its Binding to Collagen. J Mol Biol 2008; 381:913-27. [DOI: 10.1016/j.jmb.2008.06.034] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Revised: 06/09/2008] [Accepted: 06/11/2008] [Indexed: 11/25/2022]
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37
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Kremer W, Kachel N, Kuwata K, Akasaka K, Kalbitzer HR. Species-specific differences in the intermediate states of human and Syrian hamster prion protein detected by high pressure NMR spectroscopy. J Biol Chem 2007; 282:22689-98. [PMID: 17519231 DOI: 10.1074/jbc.m701884200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human (huPrP) and Syrian hamster (ShaPrP) prion proteins have barriers for mutual infectivity, although they fold into almost an identical structure. The pressure responses of huPrP and ShaPrP characterized by high pressure NMR spectroscopy show differences in their excited states, as monitored by pressure-induced chemical shifts and intensity changes of individual residues in the (15)N/(1)H HSQC spectra. Both proteins fluctuate rapidly between two well folded (native) conformations N(1) and N(2) and less frequently between N and the excited states I(1) and I(2) with local disorder that may present structural intermediates on the way to PrP(Sc). These four structural states can be observed in the hamster and human PrP. At ambient pressure, less than 5 molecules of 10,000 are in the intermediate state I(2). From the structural point of view, the different states are mutually different, particularly in positions strategically important for generating species barriers for infection. The results point to the notion that excited state conformers are important for infection and that their structural differences may crucially determine species barriers for infection.
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Affiliation(s)
- Werner Kremer
- Institute for Biophysics and Physical Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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38
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LeMaster DM, Hernández G. Residue cluster additivity of thermodynamic stability in the hydrophobic core of mesophile vs. hyperthermophile rubredoxins. Biophys Chem 2007; 125:483-9. [PMID: 17118523 DOI: 10.1016/j.bpc.2006.10.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2006] [Revised: 10/27/2006] [Accepted: 10/27/2006] [Indexed: 11/23/2022]
Abstract
The branched sidechain residues 24 and 33 in the hydrophobic core of rubredoxin differ between the Clostridium pasteurianum (Cp) and Pyrococcus furiosus (Pf) sequences. Their X-ray structures indicate that these two sidechains are in van der Waals contact with each other, while neither appears to significantly interact with the other nonconserved residues. The simultaneous interchange of residues 24 and 33 between the Cp and Pf rubredoxin sequences yield a complementary pair of hybrid proteins for which the sum of their thermodynamic stabilities equals that of the parental rubredoxins. The 1.2 kcal/mol change arising from this two residues interchange accounts for 21% of the differential thermodynamic stability between the mesophile and hyperthermophile proteins. The additional interchange of the sole nonconserved aromatic residue in the hydrophobic core yields a 0.78 kcal/mol deviation from thermodynamic additivity.
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Affiliation(s)
- David M LeMaster
- Wadsworth Center, New York State Department of Health, New York 12201-0509, USA
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39
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Kachel N, Kremer W, Zahn R, Kalbitzer HR. Observation of intermediate states of the human prion protein by high pressure NMR spectroscopy. BMC STRUCTURAL BIOLOGY 2006; 6:16. [PMID: 16846506 PMCID: PMC1557509 DOI: 10.1186/1472-6807-6-16] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Accepted: 07/17/2006] [Indexed: 11/30/2022]
Abstract
Background Prions as causative agents of transmissible spongiform encephalopathies (TSEs) in humans and animals are composed of the infectious isomer, PrPSc, of the cellular prion protein, PrPC. The conversion and thus the propensity of PrPC to adopt alternative folds leads to the species-specific propagation of the disease. High pressure is a powerful tool to study the physico-chemical properties of proteins as well as the dynamics and structure of folding intermediates. Results Conformational intermediates of the human prion protein huPrPC were characterized by a combination of hydrostatic pressure (up to 200 MPa) with two-dimensional NMR spectroscopy. All pressure effects showed to be reversible and there is virtually no difference in the overall pressure response between the folded core of the N-terminal truncated huPrPC(121–230) and the full-length huPrPC(23–230). The only significant differences in the pressure response of full-length and truncated PrP suggest that E168, H187, T192, E207, E211 and Y226 are involved in a transient interaction with the unfolded N-terminus. High-pressure NMR spectroscopy indicates that the folded core of the human prion protein occurs in two structural states N1and N2 in solution associated with rather small differences in free enthalpies (3.0 kJ/mol). At atmospheric pressure approximately 29% of the protein are already in the pressure favored conformation N2. There is a second process representing two possible folding intermediates I1 and I2 with corresponding average free enthalpies of 10.8 and 18.6 kJ/mol. They could represent preaggregation states of the protein that coexist at ambient pressure with a very small population of approximately 1.2% and less than 0.1%. Further the pressure response of the N-terminus indicates that four different regions are in a fast equilibrium with non-random structural states whose populations are shifted by pressure. Conclusion We identified pressure stabilized folding intermediates of the human prion protein. The regions reflecting most strongly the transition to the intermediate states are the β1/α1-loop and the solvent exposed side of α3. The most pressure-sensitive region (representing mainly intermediate I1) is the loop between β-strand 1 and α-helix 1 (residue 139–141), indicating that this region might be the first entry point for the infectious conformer to convert the cellular protein.
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Affiliation(s)
- Norman Kachel
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, Universitätsstr. 31, 93053 Regensburg, Germany
| | - Werner Kremer
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, Universitätsstr. 31, 93053 Regensburg, Germany
| | - Ralph Zahn
- Institute of Molecular Biology and Biophysics, ETH Hönggerberg, CH-8093 Zürich, Switzerland
- Alicon AG, Wagistrasse 23, 8952 Zürich-Schlieren, Switzerland
| | - Hans Robert Kalbitzer
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, Universitätsstr. 31, 93053 Regensburg, Germany
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40
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Affiliation(s)
- Kazuyuki Akasaka
- School of biology-Oriented Science and Technology, Kinki University, 930 Nishimitani, Kinokawa-shi, Wakayama 649-6493, Japan.
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41
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Li H, Akasaka K. Conformational fluctuations of proteins revealed by variable pressure NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:331-45. [PMID: 16448868 DOI: 10.1016/j.bbapap.2005.12.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2005] [Revised: 12/12/2005] [Accepted: 12/13/2005] [Indexed: 11/19/2022]
Abstract
With the high-resolution variable-pressure NMR spectroscopy, one can study conformational fluctuations of proteins in a much wider conformational space than hitherto explored by NMR and other spectroscopic techniques. This is because a protein in solution generally exists as a dynamic mixture of conformers mutually differing in partial molar volume, and pressure can select the population of a conformer according to its relative volume. In this review, we describe how variable-pressure NMR can be used to probe conformational fluctuations of proteins in a wide conformational space from the folded to the fully unfolded structures, with actual examples. Furthermore, the newly emerging technique "NMR snapshots" expresses amply fluctuating protein structures as changes in atomic coordinates. Finally, the concept of conformational fluctuation is extended to include intermolecular association leading to amyloidosis.
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Affiliation(s)
- Hua Li
- RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan
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42
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Epand RM, Rychnovsky SD, Belani JD, Epand RF. Role of chirality in peptide-induced formation of cholesterol-rich domains. Biochem J 2006; 390:541-8. [PMID: 15929726 PMCID: PMC1198934 DOI: 10.1042/bj20050649] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The chiral specificity of the interactions of peptides that induce the formation of cholesterol-rich domains has not been extensively investigated. Both the peptide and most lipids are chiral, so there is a possibility that interactions between peptide and lipid could require chiral recognition. On the other hand, in our models with small peptides, the extent of folding of the peptide to form a specific binding pocket is limited. We have determined that replacing cholesterol with its enantiomer, ent-cholesterol, alters the modulation of lipid organization by peptides. The phase-transition properties of SOPC (1-stearoyl-2-oleoylphosphatidylcholine):cholesterol [in a 6:4 ratio with 0.2 mol% PtdIns(4,5)P2] are not significantly altered when ent-cholesterol replaces cholesterol. However, in the presence of 10 mol% of a 19-amino-acid, N-terminally myristoylated fragment (myristoyl-GGKLSKKKKGYNVNDEKAK-amide) of the protein NAP-22 (neuronal axonal membrane protein), the lipid mixture containing cholesterol undergoes separation into cholesterol-rich and cholesterol-depleted domains. This does not occur when ent-cholesterol replaces cholesterol. In another example, when N-acetyl-Leu-Trp-Tyr-Ile-Lys-amide (N-acetyl-LWYIK-amide) is added to SOPC:cholesterol (7:3 ratio), there is a marked increase in the transition enthalpy of the phospholipid, indicating separation of a cholesterol-depleted domain of SOPC. This phenomenon completely disappears when ent-cholesterol replaces cholesterol. The all-D-isomer of N-acetyl-LWYIK-amide also induces the formation of cholesterol-rich domains with natural cholesterol, but does so to a lesser extent with ent-cholesterol. Thus specific peptide chirality is not required for interaction with cholesterol-containing membranes. However, a specific chirality of membrane lipids is required for peptide-induced formation of cholesterol-rich domains.
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Affiliation(s)
- Richard M Epand
- Department of Biochemistry, McMaster University, 1200 Main Street West, Hamilton, Ontario, Canada L8N 3Z5.
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43
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LeMaster DM, Hernández G. Additivity in Both Thermodynamic Stability and Thermal Transition Temperature for Rubredoxin Chimeras via Hybrid Native Partitioning. Structure 2005; 13:1153-63. [PMID: 16084387 DOI: 10.1016/j.str.2005.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2005] [Revised: 04/17/2005] [Accepted: 05/06/2005] [Indexed: 11/23/2022]
Abstract
Given any operational definition of pairwise interaction, the set of residues that differ between two structurally homologous proteins can be uniquely partitioned into subsets of clusters for which no such interactions occur between clusters. Although hybrid protein sequences that preserve such clustering are consistent with tertiary structures composed of only parental native-like interactions, the stability of such predicted structures will depend upon the physical robustness of the assumed interaction potential. A simple distance cutoff criterion was applied to the most thermostable protein known to predict such a seven-residue cluster in the metal binding site region of Pyrococcus furiosus rubredoxin and a mesophile homolog. Both conformational stability and thermal transition temperature measurements demonstrate that 39% of the differential stability arises from these seven residues.
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Affiliation(s)
- David M LeMaster
- Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, New York 12201, USA
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44
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LeMaster DM, Tang J, Paredes DI, Hernández G. Contribution of the multi-turn segment in the reversible thermal stability of hyperthermophile rubredoxin: NMR thermal chemical exchange analysis of sequence hybrids. Biophys Chem 2005; 116:57-65. [PMID: 15911082 DOI: 10.1016/j.bpc.2005.01.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2004] [Revised: 01/27/2005] [Accepted: 01/31/2005] [Indexed: 11/21/2022]
Abstract
Pyrococcus furiosus (Pf) rubredoxin is the most thermostable protein characterized to date. Reflecting the complications arising from irreversible denaturation of this protein, predictions of which structural regions confer differential thermal stability have utilized kinetic stability measurements, hydrogen exchange protection factors, long range hydrogen bond NMR spin couplings, and molecular dynamics simulations, and have primarily implicated the three-stranded beta-sheet and the adjacent metal binding site. Herein, NMR chemical exchange experiments demonstrate reversible two-state unfolding at the thermal transition temperature (T(m)) for hybrids of Pf and the mesophile Clostridium pasteurianum (Cp) rubredoxins which interchange residues 14-33, the so-called multi-turn segment. This complementary pair of hybrid rubredoxins exhibits largely additive incremental thermal stabilizations vs. the parental proteins. Both stabilization free energy measurements as well as incremental T(m) values indicate that a minimum of 37% of the total differential thermal stability resides in this multi-turn segment. Such a proportionality between DeltaDeltaG and incremental T(m) values is predicted for hybrid pairs exhibiting thermodynamic additivity in which the differential stability is predominantly enthalpic.
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Affiliation(s)
- David M LeMaster
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, University at Albany-SUNY, Empire State Plaza, Albany, NY 12201-0509, USA
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Hattori M, Li H, Yamada H, Akasaka K, Hengstenberg W, Gronwald W, Kalbitzer HR. Infrequent cavity-forming fluctuations in HPr from Staphylococcus carnosus revealed by pressure- and temperature-dependent tyrosine ring flips. Protein Sci 2005; 13:3104-14. [PMID: 15557257 PMCID: PMC2287304 DOI: 10.1110/ps.04877104] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Infrequent structural fluctuations of a globular protein is seldom detected and studied in detail. One tyrosine ring of HPr from Staphylococcus carnosus, an 88-residue phosphocarrier protein with no disulfide bonds, undergoes a very slow ring flip, the pressure and temperature dependence of which is studied in detail using the on-line cell high-pressure nuclear magnetic resonance technique in the pressure range from 3 MPa to 200 MPa and in the temperature range from 257 K to 313 K. The ring of Tyr6 is buried sandwiched between a beta-sheet and alpha-helices (the water-accessible area is less than 0.26 nm2), its hydroxyl proton being involved in an internal hydrogen bond. The ring flip rates 10(1)-10(5) s(-1) were determined from the line shape analysis of H(delta1, delta2) and H(epsilon1,epsilon2) of Tyr6, giving an activation volume DeltaV++ of 0.044 +/- 0.008 nm3 (27 mL mol(-1)), an activation enthalpy DeltaH++ of 89 +/- 10 kJ mol(-1), and an activation entropy DeltaS++ of 16 +/- 2 JK(-1) mol(-1). The DeltaV++) and DeltaH++ values for HPr found previously for Tyr and Phe ring flips of BPTI and cytochrome c fall within the range of DeltaV(double dagger) of 28 to 51 mL mol(-1) and DeltaH++ of 71 to 155 kJ mol(-1). The fairly common DeltaV++ and DeltaH++ values are considered to represent the extra space or cavity required for the ring flip and the extra energy required to create a cavity, respectively, in the core part of a globular protein. Nearly complete cold denaturation was found to take place at 200 MPa and 257 K independently from the ring reorientation process.
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Affiliation(s)
- Mineyuki Hattori
- Department of Molecular Science, Graduate School of Science and Technology, Kobe University, Japan
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46
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Bracken C, Iakoucheva LM, Romero PR, Dunker AK. Combining prediction, computation and experiment for the characterization of protein disorder. Curr Opin Struct Biol 2005; 14:570-6. [PMID: 15465317 DOI: 10.1016/j.sbi.2004.08.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Several computational and experimental methods exist for identifying disordered residues within proteins. Computational algorithms can now identify these disordered sequences and predict their occurrence within genomes with relatively high accuracy. Recent advances in NMR and mass spectroscopy permit faster and more detailed studies of disordered states at atomic resolutions. Combining prediction, computation and experimentation is proposed to accelerate and enhance the characterization of intrinsically disordered protein.
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Affiliation(s)
- Clay Bracken
- Department of Biochemistry, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA.
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Epand RF, Sayer BG, Epand RM. Induction of raft-like domains by a myristoylated NAP-22 peptide and its Tyr mutant. FEBS J 2005; 272:1792-803. [PMID: 15794765 DOI: 10.1111/j.1742-4658.2005.04612.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The N-terminally myristoylated, 19-amino acid peptide, corresponding to the amino terminus of the neuronal protein NAP-22 (NAP-22 peptide) is a naturally occurring peptide that had been shown by fluorescence to cause the sequestering of a Bodipy-labeled PtdIns(4,5)P2 in a cholesterol-dependent manner. The present work, using differential scanning calorimetry (DSC), extends the observation that formation of a PtdIns(4,5)P2-rich domain is cholesterol dependent and shows that it also leads to the formation of a cholesterol-depleted domain. The PtdIns(4,5)P2 used in the present work is extracted from natural sources and does not contain any label and has the native acyl chain composition. Peptide-induced formation of a cholesterol-depleted domain is abolished when the sole aromatic amino acid, Tyr11 is replaced with a Leu. Despite this, the modified peptide can still sequester PtdIns(4,5)P2 into domains, probably because of the presence of a cluster of cationic residues in the peptide. Cholesterol and PtdIns(4,5)P2 also modulate the insertion of the peptide into the bilayer as revealed by 1H NOESY MAS/NMR. The intensity of cross peaks between the aromatic protons of the Tyr residue and the protons of the lipid indicate that in the presence of cholesterol there is a change in the nature of the interaction of the peptide with the membrane. These results have important implications for the mechanism by which NAP-22 affects actin reorganization in neurons.
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Affiliation(s)
- Raquel F Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada.
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Epand RM, Sayer BG, Epand RF. Caveolin scaffolding region and cholesterol-rich domains in membranes. J Mol Biol 2005; 345:339-50. [PMID: 15571726 DOI: 10.1016/j.jmb.2004.10.064] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Revised: 10/20/2004] [Accepted: 10/20/2004] [Indexed: 12/30/2022]
Abstract
A protein that constitutes a good marker for a type of cholesterol-rich domain in biological membranes is caveolin. A segment of this protein has a sequence that corresponds to a cholesterol recognition/interaction amino acid consensus (CRAC) motif; this motif has been suggested to cause the incorporation of proteins into cholesterol-rich domains. We have studied the interaction of two peptides containing the CRAC motif of caveolin-1 by differential scanning calorimetry, fluorescence, circular dichroism and magic angle spinning NMR. These peptides promote the segregation of cholesterol into domains from mixtures of the sterol with phosphatidylcholine, as shown by depletion of cholesterol from a portion of the membrane and enrichment of cholesterol in another domain. Cholesterol passes its solubility limit in the cholesterol-rich domain, resulting in the formation of cholesterol crystallites, suggesting that not all of the cholesterol recruited to this domain is bound to the peptide. NMR studies show that the peptides insert somewhat more deeply into membranes when cholesterol is present, but their strongest interaction takes place with the interfacial region of the membrane. We conclude that the peptides we studied containing CRAC sequences are more effective in promoting the formation of cholesterol-rich domains than are shorter peptides of this region of caveolin, which although they contain several aromatic amino acids, they have no CRAC motif. The presence or absence of a CRAC motif, however, is not a sufficient criterion to determine the extent to which a protein will promote the segregation of cholesterol in membranes.
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Affiliation(s)
- Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada, L8N 3Z5.
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Abstract
NMR is one of the few experimental methods that can provide detailed insights into the structure and dynamics of unfolded and partly folded states of proteins. Mapping the protein folding landscape is of central importance to understanding the mechanism of protein folding. In addition, it is now recognized that many proteins are intrinsically unstructured in their functional states, while partly folded states of several cellular proteins have been implicated in amyloid disease. NMR is uniquely suited to characterize the structures present in the conformational ensemble and probe the dynamics of the polypeptide chain in unfolded and partially folded protein states.
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Affiliation(s)
- H Jane Dyson
- Department of Molecular Biology and Skaggs Institute for Chemical Research, Scripps Research Institute, La Jolla, California 92037, USA
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Epand RM, Epand RF, Sayer BG, Datta G, Chaddha M, Anantharamaiah GM. Two Homologous Apolipoprotein AI Mimetic Peptides. J Biol Chem 2004; 279:51404-14. [PMID: 15358763 DOI: 10.1074/jbc.m408581200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two related 18-amino acid, class A, amphipathic helical peptides termed 3F-2 and 3F14 were chosen for this study. Although they have identical amino acid compositions and many similar biophysical properties, 3F-2 is more potent than 3F14 as an apolipoprotein AI mimetic peptide. The two peptides exhibit similar gross conformational properties, forming structures of high helical content on a membrane surface. However, the thermal denaturation transition of 3F-2 is more cooperative, suggesting a higher degree of oligomerization on the membrane. Both 3F-2 and 3F14 promote the segregation of cholesterol in membranes containing phosphatidylcholine and cholesterol, but 3F-2 exhibits a greater selectivity for partitioning into cholesterol-depleted regions of the membrane. Magic angle spinning/NMR studies indicate that the aromatic residues of 3F-2 are stacked in the presence of lipid. The aromatic side chains of this peptide also penetrate more deeply into membranes of phosphatidylcholine with cholesterol compared with 3F14. Using the fluorescent probe, 1,3-dipyrenylpropane, we monitored the properties of the lipid hydrocarbon environment. 3F-2 had a greater effect in altering the properties of the hydrocarbon region of the membrane. The results are consistent with our proposed model of the effect of peptide shape on the nature of the difference in peptide insertion into the bilayer.
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Affiliation(s)
- Richard M Epand
- Departments of Biochemistry and Biomedical Sciences and Chemistry, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.
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