1
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Hannon Bozorgmehr J. Four classic "de novo" genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences. Mol Genet Genomics 2024; 299:6. [PMID: 38315248 DOI: 10.1007/s00438-023-02090-6] [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: 05/27/2023] [Accepted: 10/15/2023] [Indexed: 02/07/2024]
Abstract
Despite being previously regarded as extremely unlikely, the idea that entirely novel protein-coding genes can emerge from non-coding sequences has gradually become accepted over the past two decades. Examples of "de novo origination", resulting in lineage-specific "orphan" genes, lacking coding orthologs, are now produced every year. However, many are likely cases of duplicates that are difficult to recognize. Here, I re-examine the claims and show that four very well-known examples of genes alleged to have emerged completely "from scratch"- FLJ33706 in humans, Goddard in fruit flies, BSC4 in baker's yeast and AFGP2 in codfish-may have plausible evolutionary ancestors in pre-existing genes. The first two are likely highly diverged retrogenes coding for regulatory proteins that have been misidentified as orphans. The antifreeze glycoprotein, moreover, may not have evolved from repetitive non-genic sequences but, as in several other related cases, from an apolipoprotein that could have become pseudogenized before later being reactivated. These findings detract from various claims made about de novo gene birth and show there has been a tendency not to invest the necessary effort in searching for homologs outside of a very limited syntenic or phylostratigraphic methodology. A robust approach is used for improving detection that draws upon similarities, not just in terms of statistical sequence analysis, but also relating to biochemistry and function, to obviate notable failures to identify homologs.
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2
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Agarwal N, Jaiswal N, Gulati K, Gangele K, Nagar N, Kumar D, Poluri KM. Molecular Insights into Conformational Heterogeneity and Enhanced Structural Integrity of Helicobacter pylori DNA Binding Protein Hup at Low pH. Biochemistry 2021; 60:3236-3252. [PMID: 34665609 DOI: 10.1021/acs.biochem.1c00395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The summarized amalgam of internal relaxation modulations and external forces like pH, temperature, and solvent conditions determine the protein structure, stability, and function. In a free-energy landscape, although conformers are arranged in vertical hierarchy, there exist several adjacent parallel sets with conformers occupying equivalent energy cleft. Such conformational states are pre-requisites for the functioning of proteins that have oscillating environmental conditions. As these conformational changes have utterly small re-arrangements, nuclear magnetic resonance (NMR) spectroscopy is unique in elucidating the structure-dynamics-stability-function relationships for such conformations. Helicobacter pylori survives and causes gastric cancer at extremely low pH also. However, least is known as to how the genome of the pathogen is protected from reactive oxygen species (ROS) scavenging in the gut at low pH under acidic stress. In the current study, biophysical characteristics of H. pylori DNA binding protein (Hup) have been elucidated at pH 2 using a combination of circular dichroism, fluorescence, NMR spectroscopy, and molecular dynamics simulations. Interestingly, the protein was found to have conserved structural features, differential backbone dynamics, enhanced stability, and DNA binding ability at low pH as well. In summary, the study suggests the partaking of Hup protein even at low pH in DNA protection for maintaining the genome integrity.
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Affiliation(s)
- Nipanshu Agarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India
| | - Nancy Jaiswal
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow 226014, India
| | - Khushboo Gulati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India
| | - Krishnakant Gangele
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India
| | - Nupur Nagar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India
| | - Dinesh Kumar
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow 226014, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India.,Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India
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3
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Horie Y, Suzuki T, Inoue J, Iso T, Wells G, Moore TW, Mizushima T, Dinkova-Kostova AT, Kasai T, Kamei T, Koshiba S, Yamamoto M. Molecular basis for the disruption of Keap1-Nrf2 interaction via Hinge & Latch mechanism. Commun Biol 2021; 4:576. [PMID: 33990683 PMCID: PMC8121781 DOI: 10.1038/s42003-021-02100-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/07/2021] [Indexed: 12/30/2022] Open
Abstract
The Keap1-Nrf2 system is central for mammalian cytoprotection against various stresses and a drug target for disease prevention and treatment. One model for the molecular mechanisms leading to Nrf2 activation is the Hinge-Latch model, where the DLGex-binding motif of Nrf2 dissociates from Keap1 as a latch, while the ETGE motif remains attached to Keap1 as a hinge. To overcome the technical difficulties in examining the binding status of the two motifs during protein-protein interaction (PPI) simultaneously, we utilized NMR spectroscopy titration experiments. Our results revealed that latch dissociation is triggered by low-molecular-weight Keap1-Nrf2 PPI inhibitors and occurs during p62-mediated Nrf2 activation, but not by electrophilic Nrf2 inducers. This study demonstrates that Keap1 utilizes a unique Hinge-Latch mechanism for Nrf2 activation upon challenge by non-electrophilic PPI-inhibiting stimuli, and provides critical insight for the pharmacological development of next-generation Nrf2 activators targeting the Keap1-Nrf2 PPI. Using NMR spectroscopy, Horie, Suzuki, Inoue et al. show that the dissociation of Keap1 from Nrf2, or the Hinge-Latch mechanism, is triggered by Keap1-Nrf2 inhibitors and occurs during p62- mediated Nrf2 activation, but not by electrophilic Nrf2 inducers. This study provides insights into the design of Nrf2 activators targeting the Keap1-Nrf2 interaction.
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Affiliation(s)
- Yuta Horie
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takafumi Suzuki
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Jin Inoue
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, Sendai, Japan
| | - Tatsuro Iso
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Geoffrey Wells
- UCL School of Pharmacy, University College London, London, UK
| | - Terry W Moore
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL, United States
| | - Tsunehiro Mizushima
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - Albena T Dinkova-Kostova
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee, United Kingdom.,Department Pharmacology and Molecular Sciences and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Takuma Kasai
- Laboratory for Cellular Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan.,PRESTO, JST, Kawaguchi, Japan
| | - Takashi Kamei
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. .,The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, Sendai, Japan.
| | - Masayuki Yamamoto
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan. .,Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. .,The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, Sendai, Japan.
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4
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Keiffer S, Carneiro MG, Hollander J, Kobayashi M, Pogoryelev D, Ab E, Theisgen S, Müller G, Siegal G. NMR in target driven drug discovery: why not? JOURNAL OF BIOMOLECULAR NMR 2020; 74:521-529. [PMID: 32901320 PMCID: PMC7683447 DOI: 10.1007/s10858-020-00343-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 08/17/2020] [Indexed: 05/09/2023]
Abstract
No matter the source of compounds, drug discovery campaigns focused directly on the target are entirely dependent on a consistent stream of reliable data that reports on how a putative ligand interacts with the protein of interest. The data will derive from many sources including enzyme assays and many types of biophysical binding assays such as TR-FRET, SPR, thermophoresis and many others. Each method has its strengths and weaknesses, but none is as information rich and broadly applicable as NMR. Here we provide a number of examples of the utility of NMR for enabling and providing ongoing support for the early pre-clinical phase of small molecule drug discovery efforts. The examples have been selected for their usefulness in a commercial setting, with full understanding of the need for speed, cost-effectiveness and ease of implementation.
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Affiliation(s)
| | | | | | | | | | - Eiso Ab
- ZoBio, JH Oortweg 19, 2333CH, Leiden, Netherlands
| | | | - Gerhard Müller
- Gotham GmbH, Am Klopferspitz 19a, 82152, Martinsried, Germany
| | - Gregg Siegal
- ZoBio, JH Oortweg 19, 2333CH, Leiden, Netherlands.
- Amsterdam Institute of Molecular and Life Sciences, Free University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
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5
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Gorka M, Cherepanov DA, Semenov AY, Golbeck JH. Control of electron transfer by protein dynamics in photosynthetic reaction centers. Crit Rev Biochem Mol Biol 2020; 55:425-468. [PMID: 32883115 DOI: 10.1080/10409238.2020.1810623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Trehalose and glycerol are low molecular mass sugars/polyols that have found widespread use in the protection of native protein states, in both short- and long-term storage of biological materials, and as a means of understanding protein dynamics. These myriad uses are often attributed to their ability to form an amorphous glassy matrix. In glycerol, the glass is formed only at cryogenic temperatures, while in trehalose, the glass is formed at room temperature, but only upon dehydration of the sample. While much work has been carried out to elucidate a mechanistic view of how each of these matrices interact with proteins to provide stability, rarely have the effects of these two independent systems been directly compared to each other. This review aims to compile decades of research on how different glassy matrices affect two types of photosynthetic proteins: (i) the Type II bacterial reaction center from Rhodobacter sphaeroides and (ii) the Type I Photosystem I reaction center from cyanobacteria. By comparing aggregate data on electron transfer, protein structure, and protein dynamics, it appears that the effects of these two distinct matrices are remarkably similar. Both seem to cause a "tightening" of the solvation shell when in a glassy state, resulting in severely restricted conformational mobility of the protein and associated water molecules. Thus, trehalose appears to be able to mimic, at room temperature, nearly all of the effects on protein dynamics observed in low temperature glycerol glasses.
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Affiliation(s)
- Michael Gorka
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Dmitry A Cherepanov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia.,A.N. Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexey Yu Semenov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia.,A.N. Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - John H Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.,Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
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6
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Bhunia A, Ilyas H, Bhattacharjya S. Salt Dependence Conformational Stability of the Dimeric SAM Domain of MAPKKK Ste11 from Budding Yeast: A Native-State H/D Exchange NMR Study. Biochemistry 2020; 59:2849-2858. [PMID: 32667811 DOI: 10.1021/acs.biochem.0c00522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The sterile α motif, also called the SAM domain, is known to form homo or heterocomplexes that modulate diverse biological functions through the regulation of specific protein-protein interactions. The MAPK pathway of budding yeast Saccharomyces cerevisiae is comprised of a three-tier kinase system akin to mammals. The MAPKKK Ste11 protein of yeast contains a homodimer SAM domain, which is critical for transmitting cues to the downstream kinases. The structural stability of the dimeric Ste11 SAM is maintained by hydrophobic and ionic interactions at the interfacial amino acids. The urea-induced equilibrium-unfolding process of the Ste11 SAM domain is cooperative without evidence of any intermediate states. The native-state H/D exchange under subdenaturing conditions is a useful method for the detection of intermediate states of proteins. In the present study, we investigated the effect of ionic strength on the conformational stability of the dimer using the H/D exchange experiments. The hydrogen exchange behavior of the Ste11 dimer under physiological salt concentrations reveals two partially unfolded metastable intermediate states, which may be generated by a sequential and cooperative unfolding of the five helices present in the domain. These intermediates appear to be significant for the reversible unfolding kinetics via hydrophobic collapse. In contrast, higher ionic concentrations eliminate this cooperative interactions that stabilize the pairs of helices.
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Affiliation(s)
- Anirban Bhunia
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.,Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India
| | - Humaira Ilyas
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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7
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Matviychuk Y, Bostock MJ, Nietlispach D, Holland DJ. Time-domain signal modelling in multidimensional NMR experiments for estimation of relaxation parameters. JOURNAL OF BIOMOLECULAR NMR 2019; 73:93-104. [PMID: 31055682 DOI: 10.1007/s10858-018-00224-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 12/29/2018] [Indexed: 06/09/2023]
Abstract
We present a model-based method for estimation of relaxation parameters from time-domain NMR data specifically suitable for processing data in popular 2D phase-sensitive experiments. Our model is formulated in terms of commutative bicomplex algebra, which allows us to use the complete information available in an NMR signal acquired with principles of quadrature detection without disregarding any of its dimensions. Compared to the traditional intensity-analysis method, our model-based approach offers an important advantage for the analysis of overlapping peaks and is robust over a wide range of signal-to-noise ratios. We assess its performance with simulated experiments and then apply it for determination of [Formula: see text], [Formula: see text], and [Formula: see text] relaxation rates in datasets of a protein with more than 100 cross peaks.
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Affiliation(s)
- Yevgen Matviychuk
- Department of Chemical and Process Engineering, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
| | - Mark J Bostock
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Daniel J Holland
- Department of Chemical and Process Engineering, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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8
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Enhanced dynamics of conformationally heterogeneous T7 bacteriophage lysozyme native state attenuates its stability and activity. Biochem J 2019; 476:613-628. [DOI: 10.1042/bcj20180703] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/17/2019] [Accepted: 01/25/2019] [Indexed: 11/17/2022]
Abstract
Abstract
Proteins are dynamic in nature and exist in a set of equilibrium conformations on various timescale motions. The flexibility of proteins governs various biological functions, and therefore elucidation of such functional dynamics is essential. In this context, we have studied the structure–dynamics–stability–activity relationship of bacteriophage T7 lysozyme/endolysin (T7L) native-state ensemble in the pH range of 6–8. Our studies established that T7L native state is conformationally heterogeneous, as several residues of its C-terminal half are present in two conformations (major and minor) in the slow exchange time scale of nuclear magnetic resonance (NMR). Structural and dynamic studies suggested that the residues belonging to minor conformations do exhibit native-like structural and dynamic features. Furthermore, the NMR relaxation experiments unraveled that the native state is highly dynamic and the dynamic behavior is regulated by the pH, as the pH 6 conformation exhibited enhanced dynamics compared with pH 7 and 8. The stability measurements and cell-based activity studies on T7L indicated that the native protein at pH 6 is ∼2 kcal less stable and is ∼50% less active than those of pH 7 and 8. A comprehensive analysis of the T7L active site, unfolding initiation sites and the residues with altered dynamics outlined that the attenuation of stability and activity is a resultant of its enhanced dynamic properties, which, in turn, can be attributed to the protonation/deprotonation of its partially buried His residues. Our study on T7L structure–dynamics–activity paradigm could assist in engineering novel amidase-based endolysins with enhanced activity and stability over a broad pH range.
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9
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Krylov A, Windus TL, Barnes T, Marin-Rimoldi E, Nash JA, Pritchard B, Smith DGA, Altarawy D, Saxe P, Clementi C, Crawford TD, Harrison RJ, Jha S, Pande VS, Head-Gordon T. Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science. J Chem Phys 2018; 149:180901. [DOI: 10.1063/1.5052551] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Anna Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Theresa L. Windus
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - Taylor Barnes
- Molecular Sciences Software Institute, Blacksburg, Virginia 24061, USA
| | | | - Jessica A. Nash
- Molecular Sciences Software Institute, Blacksburg, Virginia 24061, USA
| | | | | | - Doaa Altarawy
- Molecular Sciences Software Institute, Blacksburg, Virginia 24061, USA
| | - Paul Saxe
- Molecular Sciences Software Institute, Blacksburg, Virginia 24061, USA
| | - Cecilia Clementi
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University, 6100 Main Street, Houston, Texas 77005, USA
- Department of Mathematics and Computer Science, Freie Universitt Berlin, Arnimallee 6, 14195 Berlin, Germany
| | | | - Robert J. Harrison
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794, USA
| | - Shantenu Jha
- Electrical and Computer Engineering, Rutgers The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Vijay S. Pande
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Teresa Head-Gordon
- Department of Chemistry, Department of Bioengineering, Department of Chemical and Biomolecular Engineering, Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, USA
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10
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Varela AE, Lang JF, Wu Y, Dalphin MD, Stangl AJ, Okuno Y, Cavagnero S. Kinetic Trapping of Folded Proteins Relative to Aggregates under Physiologically Relevant Conditions. J Phys Chem B 2018; 122:7682-7698. [DOI: 10.1021/acs.jpcb.8b05360] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Angela E. Varela
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jonathan F. Lang
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Yufan Wu
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Matthew D. Dalphin
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Andrew J. Stangl
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Yusuke Okuno
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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11
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Raznikov VV, Raznikova MO, Pridatchenko ML. Disentangling of Information About the Structure of Biomolecules Based on the Decomposition and Separation of Two-Dimentional Charge Distributions of Ions. JOURNAL OF ANALYTICAL CHEMISTRY 2018. [DOI: 10.1134/s106193481713007x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Abstract
Currently available computational tools, which are many, provide a researcher with the multitude of options for prediction of intrinsic disorder in a protein of interest and for finding at least some of its disorder-based functions. This chapter provides a highly subjective guideline on how not to be lost in the "dark forest" of available tools for the analysis of intrinsic disorder. By no means it gives a unique pathway through this forest, but simply presents some of the tools the author uses in his everyday research.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russian Federation.
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation.
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13
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Lieutaud P, Ferron F, Uversky AV, Kurgan L, Uversky VN, Longhi S. How disordered is my protein and what is its disorder for? A guide through the "dark side" of the protein universe. INTRINSICALLY DISORDERED PROTEINS 2016; 4:e1259708. [PMID: 28232901 DOI: 10.1080/21690707.2016.1259708] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/03/2016] [Accepted: 11/04/2016] [Indexed: 12/18/2022]
Abstract
In the last 2 decades it has become increasingly evident that a large number of proteins are either fully or partially disordered. Intrinsically disordered proteins lack a stable 3D structure, are ubiquitous and fulfill essential biological functions. Their conformational heterogeneity is encoded in their amino acid sequences, thereby allowing intrinsically disordered proteins or regions to be recognized based on properties of these sequences. The identification of disordered regions facilitates the functional annotation of proteins and is instrumental for delineating boundaries of protein domains amenable to structural determination with X-ray crystallization. This article discusses a comprehensive selection of databases and methods currently employed to disseminate experimental and putative annotations of disorder, predict disorder and identify regions involved in induced folding. It also provides a set of detailed instructions that should be followed to perform computational analysis of disorder.
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Affiliation(s)
- Philippe Lieutaud
- Aix-Marseille Université, AFMB UMR, Marseille, France; CNRS, AFMB UMR, Marseille, France
| | - François Ferron
- Aix-Marseille Université, AFMB UMR, Marseille, France; CNRS, AFMB UMR, Marseille, France
| | - Alexey V Uversky
- Center for Data Analytics and Biomedical Informatics, Department of Computer and Information Sciences, College of Science and Technology, Temple University , Philadelphia, PA, USA
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University , Richmond, VA, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Sonia Longhi
- Aix-Marseille Université, AFMB UMR, Marseille, France; CNRS, AFMB UMR, Marseille, France
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14
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Kurland CG, Harish A. The phylogenomics of protein structures: The backstory. Biochimie 2015; 119:284-302. [DOI: 10.1016/j.biochi.2015.07.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 07/28/2015] [Indexed: 12/11/2022]
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15
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Chen SH, Russell DH. How Closely Related Are Conformations of Protein Ions Sampled by IM-MS to Native Solution Structures? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1433-43. [PMID: 26115967 DOI: 10.1007/s13361-015-1191-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 05/07/2015] [Accepted: 05/13/2015] [Indexed: 05/25/2023]
Abstract
Here, we critically evaluate the effects of changes in the ion internal energy (E(int)) on ion-neutral collision cross sections (CCS) of ions of two structurally diverse proteins, specifically the [M + 6H](6+) ion of ubiquitin (ubq(6+)), the [M + 5H](5+) ion of the intrinsically disordered protein (IDP) apo-metallothionein-2A (MT), and its partially- and fully-metalated isoform, the [CdiMT](5+) ion. The ion-neutral CCS for ions formed by "native-state" ESI show a strong dependence on E(int). Collisional activation is used to increase E(int) prior to the ions entering and within the traveling wave (TW) ion mobility analyzer. Comparisons of experimental CCSs with those generated by molecular dynamics (MD) simulation for solution-phase ions and solvent-free ions as a function of temperature provide new insights about conformational preferences and retention of solution conformations. The E(int)-dependent CCSs, which reveal increased conformational diversity of the ion population, are discussed in terms of folding/unfolding of solvent-free ions. For example, ubiquitin ions that have low internal energies retain native-like conformations, whereas ions that are heated by collisional activation possess higher internal energies and yield a broader range of CCS owing to increased conformational diversity due to losses of secondary and tertiary structures. In contrast, the CCS profile for the IDP apoMT is consistent with kinetic trapping of an ion population composed of a wide range of conformers, and as the E(int) is increased, these structurally labile conformers unfold to an elongated conformation.
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Affiliation(s)
- Shu-Hua Chen
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
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16
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Marreiros R, Müller-Schiffmann A, Bader V, Selvarajah S, Dey D, Lingappa VR, Korth C. Viral capsid assembly as a model for protein aggregation diseases: Active processes catalyzed by cellular assembly machines comprising novel drug targets. Virus Res 2014; 207:155-64. [PMID: 25451064 DOI: 10.1016/j.virusres.2014.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/09/2014] [Accepted: 10/01/2014] [Indexed: 11/18/2022]
Abstract
Viruses can be conceptualized as self-replicating multiprotein assemblies, containing coding nucleic acids. Viruses have evolved to exploit host cellular components including enzymes to ensure their replicative life cycle. New findings indicate that also viral capsid proteins recruit host factors to accelerate their assembly. These assembly machines are RNA-containing multiprotein complexes whose composition is governed by allosteric sites. In the event of viral infection, the assembly machines are recruited to support the virus over the host and are modified to achieve that goal. Stress granules and processing bodies may represent collections of such assembly machines, readily visible by microscopy but biochemically labile and difficult to isolate by fractionation. We hypothesize that the assembly of protein multimers such as encountered in neurodegenerative or other protein conformational diseases, is also catalyzed by assembly machines. In the case of viral infection, the assembly machines have been modified by the virus to meet the virus' need for rapid capsid assembly rather than host homeostasis. In the case of the neurodegenerative diseases, it is the monomers and/or low n oligomers of the so-called aggregated proteins that are substrates of assembly machines. Examples for substrates are amyloid β peptide (Aβ) and tau in Alzheimer's disease, α-synuclein in Parkinson's disease, prions in the prion diseases, Disrupted-in-schizophrenia 1 (DISC1) in subsets of chronic mental illnesses, and others. A likely continuum between virus capsid assembly and cell-to-cell transmissibility of aggregated proteins is remarkable. Protein aggregation diseases may represent dysfunction and dysregulation of these assembly machines analogous to the aberrations induced by viral infection in which cellular homeostasis is pathologically reprogrammed. In this view, as for viral infection, reset of assembly machines to normal homeostasis should be the goal of protein aggregation therapeutics. A key basis for the commonality between viral and neurodegenerative disease aggregation is a broader definition of assembly as more than just simple aggregation, particularly suited for the crowded cytoplasm. The assembly machines are collections of proteins that catalytically accelerate an assembly reaction that would occur spontaneously but too slowly to be relevant in vivo. Being an enzyme complex with a functional allosteric site, appropriated for a non-physiological purpose (e.g. viral infection or conformational disease), these assembly machines present a superior pharmacological target because inhibition of their active site will amplify an effect on their substrate reaction. Here, we present this hypothesis based on recent proof-of-principle studies against Aβ assembly relevant in Alzheimer's disease.
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Affiliation(s)
- Rita Marreiros
- Department Neuropathology, Heinrich Heine University Düsseldorf Medical School, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Andreas Müller-Schiffmann
- Department Neuropathology, Heinrich Heine University Düsseldorf Medical School, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Verian Bader
- Department Neuropathology, Heinrich Heine University Düsseldorf Medical School, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | | | | | | | - Carsten Korth
- Department Neuropathology, Heinrich Heine University Düsseldorf Medical School, Moorenstrasse 5, 40225 Düsseldorf, Germany.
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17
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Gupta S, Bhattacharjya S. Characterization of the near native conformational states of the SAM domain of Ste11 protein by NMR spectroscopy. Proteins 2014; 82:2957-69. [PMID: 25066357 DOI: 10.1002/prot.24652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 07/01/2014] [Accepted: 07/15/2014] [Indexed: 12/14/2022]
Abstract
The sterile alpha motif or SAM domain is one of the most frequently present protein interaction modules with diverse functional attributions. SAM domain of the Ste11 protein of budding yeast plays important roles in mitogen-activated protein kinase cascades. In the current study, urea-induced, at subdenaturing concentrations, structural, and dynamical changes in the Ste11 SAM domain have been investigated by nuclear magnetic resonance spectroscopy. Our study revealed that a number of residues from Helix 1 and Helix 5 of the Ste11 SAM domain display plausible alternate conformational states and largest chemical shift perturbations at low urea concentrations. Amide proton (H/D) exchange experiments indicated that Helix 1, loop, and Helix 5 become more susceptible to solvent exchange with increased concentrations of urea. Notably, Helix 1 and Helix 5 are directly involved in binding interactions of the Ste11 SAM domain. Our data further demonstrate that the existence of alternate conformational states around the regions involved in dimeric interactions in native or near native conditions.
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Affiliation(s)
- Sebanti Gupta
- Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
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18
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Sterckx YGJ, Volkov AN. Cofactor-Dependent Structural and Binding Properties of Yeast Cytochrome c Peroxidase. Biochemistry 2014; 53:4526-36. [DOI: 10.1021/bi500603w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yann G. J. Sterckx
- Research
Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Structural
Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Alexander N. Volkov
- Structural
Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Jean
Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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19
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Saio T, Guan X, Rossi P, Economou A, Kalodimos CG. Structural basis for protein antiaggregation activity of the trigger factor chaperone. Science 2014; 344:1250494. [PMID: 24812405 DOI: 10.1126/science.1250494] [Citation(s) in RCA: 213] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Molecular chaperones prevent aggregation and misfolding of proteins, but scarcity of structural data has impeded an understanding of the recognition and antiaggregation mechanisms. We report the solution structure, dynamics, and energetics of three trigger factor (TF) chaperone molecules in complex with alkaline phosphatase (PhoA) captured in the unfolded state. Our data show that TF uses multiple sites to bind to several regions of the PhoA substrate protein primarily through hydrophobic contacts. Nuclear magnetic resonance (NMR) relaxation experiments show that TF interacts with PhoA in a highly dynamic fashion, but as the number and length of the PhoA regions engaged by TF increase, a more stable complex gradually emerges. Multivalent binding keeps the substrate protein in an extended, unfolded conformation. The results show how molecular chaperones recognize unfolded polypeptides and, by acting as unfoldases and holdases, prevent the aggregation and premature (mis)folding of unfolded proteins.
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Affiliation(s)
- Tomohide Saio
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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20
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Jennaro TS, Beaty MR, Kurt-Yilmaz N, Luskin BL, Cavagnero S. Burial of nonpolar surface area and thermodynamic stabilization of globins as a function of chain elongation. Proteins 2014; 82:2318-31. [DOI: 10.1002/prot.24590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/11/2014] [Accepted: 04/12/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Theodore S. Jennaro
- Department of Chemistry; University of Wisconsin-Madison; Madison Wisconsin 53706
| | - Matthew R. Beaty
- Department of Chemistry; University of Wisconsin-Madison; Madison Wisconsin 53706
| | - Neşe Kurt-Yilmaz
- Department of Chemistry; University of Wisconsin-Madison; Madison Wisconsin 53706
| | - Benjamin L. Luskin
- Department of Chemistry; University of Wisconsin-Madison; Madison Wisconsin 53706
| | - Silvia Cavagnero
- Department of Chemistry; University of Wisconsin-Madison; Madison Wisconsin 53706
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21
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Gupta S, Bhattacharjya S. NMR characterization of the near native and unfolded states of the PTB domain of Dok1: alternate conformations and residual clusters. PLoS One 2014; 9:e90557. [PMID: 24587391 PMCID: PMC3938774 DOI: 10.1371/journal.pone.0090557] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 02/03/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Phosphotyrosine binding (PTB) domains are critically involved in cellular signaling and diseases. PTB domains are categorized into three distinct structural classes namely IRS-like, Shc-like and Dab-like. All PTB domains consist of a core pleckstrin homology (PH) domain with additional structural elements in Shc and Dab groups. The core PH fold of the PTB domain contains a seven stranded β-sheet and a long C-terminal helix. PRINCIPAL FINDINGS In this work, the PTB domain of Dok1 protein has been characterized, by use of NMR spectroscopy, in solutions containing sub-denaturing and denaturing concentrations of urea. We find that the Dok1 PTB domain displays, at sub-denaturing concentrations of urea, alternate conformational states for residues located in the C-terminal helix and in the β5 strand of the β-sheet region. The β5 strand of PTB domain has been found to be experiencing significant chemical shift perturbations in the presence of urea. Notably, many of these residues in the helix and in the β5 strand are also involved in ligand binding. Structural and dynamical analyses at 7 M urea showed that the PTB domain is unfolded with islands of motionally restricted regions in the polypeptide chain. Further, the C-terminal helix appears to be persisted in the unfolded state of the PTB domain. By contrast, residues encompassing β-sheets, loops, and the short N-terminal helix lack any preferred secondary structures. Moreover, these residues demonstrated an intimate contact with the denaturant. SIGNIFICANCE This study implicates existence of alternate conformational states around the ligand binding pocket of the PTB domain either in the native or in the near native conditions. Further, the current study demonstrates that the C-terminal helical region of PTB domain may be considered as a potential site for the initiation of folding.
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Affiliation(s)
- Sebanti Gupta
- School of Biological Sciences, Division of Structural and Computational Biology, Nanyang Technological University, Singapore, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Division of Structural and Computational Biology, Nanyang Technological University, Singapore, Singapore
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22
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Odman-Naresh J, Duevel M, Muthukrishnan S, Merzendorfer H. A lepidopteran-specific gene family encoding valine-rich midgut proteins. PLoS One 2013; 8:e82015. [PMID: 24312395 PMCID: PMC3843731 DOI: 10.1371/journal.pone.0082015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/28/2013] [Indexed: 12/27/2022] Open
Abstract
Many lepidopteran larvae are serious agricultural pests due to their feeding activity. Digestion of the plant diet occurs mainly in the midgut and is facilitated by the peritrophic matrix (PM), an extracellular sac-like structure, which lines the midgut epithelium and creates different digestive compartments. The PM is attracting increasing attention to control lepidopteran pests by interfering with this vital function. To identify novel PM components and thus potential targets for insecticides, we performed an immunoscreening with anti-PM antibodies using an expression library representing the larval midgut transcriptome of the tobacco hornworm, Manduca sexta. We identified three cDNAs encoding valine-rich midgut proteins of M. sexta (MsVmps), which appear to be loosely associated with the PM. They are members of a lepidopteran-specific family of nine VMP genes, which are exclusively expressed in larval stages in M. sexta. Most of the MsVMP transcripts are detected in the posterior midgut, with the highest levels observed for MsVMP1. To obtain further insight into Vmp function, we expressed MsVMP1 in insect cells and purified the recombinant protein. Lectin staining and glycosidase treatment indicated that MsVmp1 is highly O-glycosylated. In line with results from qPCR, immunoblots revealed that MsVmp1 amounts are highest in feeding larvae, while MsVmp1 is undetectable in starving and molting larvae. Finally using immunocytochemistry, we demonstrated that MsVmp1 localizes to the cytosol of columnar cells, which secrete MsVmp1 into the ectoperitrophic space in feeding larvae. In starving and molting larvae, MsVmp1 is found in the gut lumen, suggesting that the PM has increased its permeability. The present study demonstrates that lepidopteran species including many agricultural pests have evolved a set of unique proteins that are not found in any other taxon and thus may reflect an important adaptation in the highly specialized lepidopteran digestive tract facing particular immune challenges.
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Affiliation(s)
| | - Margret Duevel
- Department of Biology, Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Subbaratnam Muthukrishnan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
| | - Hans Merzendorfer
- Department of Biology, Chemistry, University of Osnabrück, Osnabrück, Germany
- * E-mail:
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23
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Reduced dimensionality (4,3)D-hnCOCANH experiment: an efficient backbone assignment tool for NMR studies of proteins. ACTA ACUST UNITED AC 2013; 14:109-18. [PMID: 23982149 DOI: 10.1007/s10969-013-9161-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 08/19/2013] [Indexed: 10/26/2022]
Abstract
Sequence specific resonance assignment of proteins forms the basis for variety of structural and functional proteomics studies by NMR. In this context, an efficient standalone method for rapid assignment of backbone ((1)H, (15)N, (13)C(α) and (13)C') resonances of proteins has been presented here. Compared to currently available strategies used for the purpose, the method employs only a single reduced dimensionality experiment--(4,3)D-hnCOCANH and exploits the linear combinations of backbone ((13)C(α) and (13)C') chemical shifts to achieve a dispersion relatively better compared to those of individual chemical shifts (see the text). The resulted increased dispersion of peaks--which is different in sum (CA + CO) and difference (CA - CO) frequency regions--greatly facilitates the analysis of the spectrum by resolving the problems (associated with routine assignment strategies) arising because of degenerate amide (15)N and backbone (13)C chemical shifts. Further, the spectrum provides direct distinction between intra- and inter-residue correlations because of their opposite peak signs. The other beneficial feature of the spectrum is that it provides: (a) multiple unidirectional sequential (i→i + 1) (15)N and (13)C correlations and (b) facile identification of certain specific triplet sequences which serve as check points for mapping the stretches of sequentially connected HSQC cross peaks on to the primary sequence for assigning the resonances sequence specifically. On top of all this, the F₂-F₃ planes of the spectrum corresponding to sum (CA + CO) and difference (CA - CO) chemical shifts enable rapid and unambiguous identification of sequential HSQC peaks through matching their coordinates in these two planes (see the text). Overall, the experiment presented here will serve as an important backbone assignment tool for variety of structural and functional proteomics and drug discovery research programs by NMR involving well behaved small folded proteins (MW < 15 kDa) or a range of intrinsically disordered proteins.
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24
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Williams RW, Xue B, Uversky VN, Dunker AK. Distribution and cluster analysis of predicted intrinsically disordered protein Pfam domains. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e25724. [PMID: 28516017 PMCID: PMC5424788 DOI: 10.4161/idp.25724] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 07/02/2013] [Accepted: 07/11/2013] [Indexed: 11/19/2022]
Abstract
The Pfam database groups regions of proteins by how well hidden Markov models (HMMs) can be trained to recognize similarities among them. Conservation pressure is probably in play here. The Pfam seed training set includes sequence and structure information, being drawn largely from the PDB. A long standing hypothesis among intrinsically disordered protein (IDP) investigators has held that conservation pressures are also at play in the evolution of different kinds of intrinsic disorder, but we find that predicted intrinsic disorder (PID) is not always conserved across Pfam domains. Here we analyze distributions and clusters of PID regions in 193024 members of the version 23.0 Pfam seed database. To include the maximum information available for proteins that remain unfolded in solution, we employ the 10 linearly independent Kidera factors1–3 for the amino acids, combined with PONDR4 predictions of disorder tendency, to transform the sequences of these Pfam members into an 11 column matrix where the number of rows is the length of each Pfam region. Cluster analyses of the set of all regions, including those that are folded, show 6 groupings of domains. Cluster analyses of domains with mean VSL2b scores greater than 0.5 (half predicted disorder or more) show at least 3 separated groups. It is hypothesized that grouping sets into shorter sequences with more uniform length will reveal more information about intrinsic disorder and lead to more finely structured and perhaps more accurate predictions. HMMs could be trained to include this information.
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Affiliation(s)
- Robert W Williams
- Department of Biomedical Informatics; Uniformed Services University; Bethesda, MD USA
| | - Bin Xue
- Center for Computational Biology and Bioinformatics; Indiana School of Medicine; Indianapolis, IN USA.,Department of Molecular Medicine; College of Medicine; University of South Florida; Tampa, FL USA
| | - Vladimir N Uversky
- Center for Computational Biology and Bioinformatics; Indiana School of Medicine; Indianapolis, IN USA.,Department of Molecular Medicine; College of Medicine; University of South Florida; Tampa, FL USA.,Byrd Alzheimer's Research Institute; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Moscow Region, Russia
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics; Indiana School of Medicine; Indianapolis, IN USA
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25
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NMR as a tool to identify and characterize protein folding intermediates. Arch Biochem Biophys 2013; 531:90-9. [DOI: 10.1016/j.abb.2012.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 11/20/2022]
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26
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Abstract
Defining structural features of IDPs (intrinsically disordered proteins) and relating these to biological function requires characterization of their dynamical properties. In the present paper, we review what is known about the IDPs of colicins, protein antibiotics that use their IDPs to enter bacterial cells. The structurally characterized colicin IDPs we consider contain linear binding epitopes for proteins within their target cells that the colicin hijacks during entry. We show that these binding epitopes take part in intramolecular interactions in the absence of protein partners, i.e. self-recognition, and consider the structural origins of this and its functional implications. We suggest that self-recognition is common in other IDPs that contain similar types of binding epitopes.
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27
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Liriano MA, Varney KM, Wright NT, Hoffman CL, Toth EA, Ishima R, Weber DJ. Target binding to S100B reduces dynamic properties and increases Ca(2+)-binding affinity for wild type and EF-hand mutant proteins. J Mol Biol 2012; 423:365-85. [PMID: 22824086 PMCID: PMC3462298 DOI: 10.1016/j.jmb.2012.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 06/06/2012] [Accepted: 07/16/2012] [Indexed: 11/24/2022]
Abstract
Mutations in the second EF-hand (D61N, D63N, D65N, and E72A) of S100B were used to study its Ca(2+) binding and dynamic properties in the absence and presence of a bound target, TRTK-12. With (D63N)S100B as an exception ((D63N)K(D)=50±9 μM), Ca(2+) binding to EF2-hand mutants were reduced by more than 8-fold in the absence of TRTK-12 ((D61N)K(D)=412±67 μM, (D65N)K(D)=968±171 μM, and (E72A)K(D)=471±133 μM), when compared to wild-type protein ((WT)K(D)=56±9 μM). For the TRTK-12 complexes, the Ca(2+)-binding affinity to wild type ((WT+TRTK)K(D)=12±10 μM) and the EF2 mutants was increased by 5- to 14-fold versus in the absence of target ((D61N+TRTK)K(D)=29±1.2 μM, (D63N+TRTK)K(D)=10±2.2 μM, (D65N+TRTK)K(D)=73±4.4 μM, and (E72A+TRTK)K(D)=18±3.7 μM). In addition, R(ex), as measured using relaxation dispersion for side-chain (15)N resonances of Asn63 ((D63N)S100B), was reduced upon TRTK-12 binding when measured by NMR. Likewise, backbone motions on multiple timescales (picoseconds to milliseconds) throughout wild type, (D61N)S100B, (D63N)S100B, and (D65N)S100B were lowered upon binding TRTK-12. However, the X-ray structures of Ca(2+)-bound (2.0Å) and TRTK-bound (1.2Å) (D63N)S100B showed no change in Ca(2+) coordination; thus, these and analogous structural data for the wild-type protein could not be used to explain how target binding increased Ca(2+)-binding affinity in solution. Therefore, a model for how S100B-TRTK-12 complex formation increases Ca(2+) binding is discussed, which considers changes in protein dynamics upon binding the target TRTK-12.
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Affiliation(s)
- Melissa A. Liriano
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St. Baltimore, MD 21201, USA
| | - Kristen M. Varney
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St. Baltimore, MD 21201, USA
| | - Nathan T. Wright
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St. Baltimore, MD 21201, USA
| | - Cassandra L. Hoffman
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St. Baltimore, MD 21201, USA
| | - Eric A. Toth
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St. Baltimore, MD 21201, USA
| | - Rieko Ishima
- Department of Structural Biology, The University of Pittsburgh School of Medicine, 3501 5 Avenue N. Pittsburgh, PA 15260, USA
| | - David J. Weber
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St. Baltimore, MD 21201, USA
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28
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Abstract
Proteins are a remarkable class of molecules that exhibit wide diversity of shapes or topological features that underpin protein interactions and give rise to biological function. In addition to quantitation of abundance levels of proteins in biological systems under a variety of conditions, the field of proteome research has as a primary mission the assignment of function for proteins and if possible, illumination of factors that enable function. For many years, chemical cross-linking methods have been used to provide structural data on single purified proteins and purified protein complexes. However, these methods also offer the alluring possibility to extend capabilities to complex biological samples such as cell lysates or intact living cells where proteins may exhibit native topological features that do not exist in purified form. Recent efforts are beginning to provide glimpses of protein complexes and topologies in cells that suggest continued development will yield novel capabilities to view functional topological features of many proteins and complexes as they exist in cells, tissues, or other complex samples. This review will describe rationale, challenges, and a few success stories along the path of development of cross-linking technologies for measurement of in vivo protein interaction topologies.
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Affiliation(s)
- James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA.
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29
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Roy S, Lessing J, Meisl G, Ganim Z, Tokmakoff A, Knoester J, Jansen TLC. Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline. J Chem Phys 2012; 135:234507. [PMID: 22191886 DOI: 10.1063/1.3665417] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a mixed quantum-classical model for studying the amide I vibrational dynamics (predominantly CO stretching) in peptides and proteins containing proline. There are existing models developed for determining frequencies of and couplings between the secondary amide units. However, these are not applicable to proline because this amino acid has a tertiary amide unit. Therefore, a new parametrization is required for infrared-spectroscopic studies of proteins that contain proline, such as collagen, the most abundant protein in humans and animals. Here, we construct the electrostatic and dihedral maps accounting for solvent and conformation effects on frequency and coupling for the proline unit. We examine the quality and the applicability of these maps by carrying out spectral simulations of a number of peptides with proline in D(2)O and compare with experimental observations.
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Affiliation(s)
- Santanu Roy
- Center for Theoretical Physics and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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30
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Abstract
The lengths of orthologous protein families in Eukarya are almost double the lengths found in Bacteria and Archaea. Here we examine protein structures in 745 genomes and show that protein length differences between superkingdoms arise as much shorter prokaryotic nondomain linker sequences. Eukaryotic, bacterial, and archaeal linkers are 250, 86, and 73 aa residues in length, respectively, whereas folded domain sequences are 281, 280, and 256 residues, respectively. Cryptic domains match linkers (P < 0.0001) with probabilities ranging between 0.022 and 0.042; accordingly, they do not affect length estimates significantly. Linker sequences support intermolecular binding within proteomes and they are probably enriched in intrinsically disordered regions as well. Reductively evolved linker sequence lengths in growth rate maximized cells should be proportional to proteome diversity. By using total in-frame coding capacity of a genome [i.e., coding sequence (CDS)] as a reliable measure of proteome diversity, we find linker lengths of prokaryotes clearly evolve in proportion to CDS values, whereas those of eukaryotes are more randomly larger than expected. Domain lengths scarcely change over the entire range of CDS values. Thus, the protein linkers of prokaryotes evolve reductively whereas those of eukaryotes do not.
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31
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Giammaria V, Grandellis C, Bachmann S, Gargantini PR, Feingold SE, Bryan G, Ulloa RM. StCDPK2 expression and activity reveal a highly responsive potato calcium-dependent protein kinase involved in light signalling. PLANTA 2011; 233:593-609. [PMID: 21132327 DOI: 10.1007/s00425-010-1319-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 11/12/2010] [Indexed: 05/11/2023]
Abstract
Calcium-dependent protein kinases (CDPKs) are essential calcium sensors. In this work, we have studied StCDPK2 isoform from potato both at gene and protein level. StCdpk2 genomic sequence contains eight exons and seven introns, as was observed for StCdpk1. There is one copy of the gene per genome located in chromosome 7. StCDPK2 encodes an active CDPK of 515 aminoacids, with an apparent MW of 57 kDa, which presents myristoylation and palmitoylation consensus in its N-terminus. StCDPK2 is highly expressed in leaves and green sprouts; enhanced expression was detected under light treatment, which corresponds well with light responsive cis-acting elements found in its promoter sequence. Antibodies against the recombinant StCDPK2::6xHis protein detected this isoform in soluble and particulate fractions from leaves. StCDPK2 autophosphorylation and kinase activity are both calcium dependent reaching half maximal activation at 0.6 μM calcium. The active kinase is autophosphorylated on serine and tyrosine residues and its activity is negatively modulated by phosphatidic acid (PA). Our results reveal StCDPK2 as a signalling element involved in plant growth and development and show that its activity is tightly regulated.
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Affiliation(s)
- Verónica Giammaria
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), CONICET and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Vuelta de Obligado 2490 2do piso, 1428, Buenos Aires, Argentina
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32
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Uversky VN. Flexible Nets of Malleable Guardians: Intrinsically Disordered Chaperones in Neurodegenerative Diseases. Chem Rev 2010; 111:1134-66. [DOI: 10.1021/cr100186d] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, Florida 33612, United States, Institute for Intrinsically Disordered Protein Research, Center for Computational Biology and Bioinformatics, University of Indiana School of Medicine, Indianapolis, Indiana 46202, United States, and Institute for Biological Instrumentation, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia
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Kleckner IR, Foster MP. An introduction to NMR-based approaches for measuring protein dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:942-68. [PMID: 21059410 DOI: 10.1016/j.bbapap.2010.10.012] [Citation(s) in RCA: 339] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 10/27/2010] [Accepted: 10/29/2010] [Indexed: 01/15/2023]
Abstract
Proteins are inherently flexible at ambient temperature. At equilibrium, they are characterized by a set of conformations that undergo continuous exchange within a hierarchy of spatial and temporal scales ranging from nanometers to micrometers and femtoseconds to hours. Dynamic properties of proteins are essential for describing the structural bases of their biological functions including catalysis, binding, regulation and cellular structure. Nuclear magnetic resonance (NMR) spectroscopy represents a powerful technique for measuring these essential features of proteins. Here we provide an introduction to NMR-based approaches for studying protein dynamics, highlighting eight distinct methods with recent examples, contextualized within a common experimental and analytical framework. The selected methods are (1) Real-time NMR, (2) Exchange spectroscopy, (3) Lineshape analysis, (4) CPMG relaxation dispersion, (5) Rotating frame relaxation dispersion, (6) Nuclear spin relaxation, (7) Residual dipolar coupling, (8) Paramagnetic relaxation enhancement. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Ian R Kleckner
- The Ohio State University Biophysics Program, 484 West 12th Ave Room 776, Columbus, OH 43210, USA
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34
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Roy S, Jansen TLC, Knoester J. Structural classification of the amide I sites of a beta-hairpin with isotope label 2DIR spectroscopy. Phys Chem Chem Phys 2010; 12:9347-57. [PMID: 20596553 DOI: 10.1039/b925645h] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a theoretical study of the possibility to use isotope label two-dimensional infrared (2DIR) spectroscopy to obtain site specific structural information in trpzip2. This small beta-hairpin peptide was designed as a model system for studying protein folding in beta-sheet structures. In order to unravel the folding mechanism, the surroundings of local sites should be characterized, which in principle is possible by using 2DIR in combination with isotope labeling. This requires a classification that correlates local structures to two-dimensional spectra. To this end, we provide the first spectral simulation of the isotope label spectra of all the amide I sites in trpzip2. We find that the anti-diagonal width of the 2DIR peak associated with a labelled site is a good measure of solvent exposure and the key parameter to distinguish between solvent exposed and internal sites. The diagonal widths are not particularly sensitive to this, but they do reveal the presence of slowly interconverting turn structures.
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Affiliation(s)
- Santanu Roy
- Center for Theoretical Physics and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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35
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Abstract
Most transcription factors including nuclear receptors (NRs) act as sensors of the extracellular and intracellular compartments. As such, NRs serve as integrating platforms for a variety of stimuli and are targets for Post-translational modifications such as phosphorylations. During the last decade, knowledge of NRs phosphorylation advanced considerably because of the emergence of new technologies. Indeed, the development of a wide range of phosphorylation site databases, high accuracy mass spectrometry, and phospho-specific antibodies allowed the identification of multiple novel phosphorylation sites in NRs. New and improved methods also emerge to connect these data with the downstream consequences of phosphorylation on NRs structure (computational prediction, NMR), intracellular localization (FRAP), interaction with coregulators (proteomics, FRET, FLIM), and affinity for DNA (ChIP, ChIP-seq, FRAP). In the future, such integrated strategies should provide data with a treasure-trove of information about the integration of numerous signaling events by NRs.
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Non-native hydrophobic interactions detected in unfolded apoflavodoxin by paramagnetic relaxation enhancement. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:689-98. [PMID: 19894043 PMCID: PMC2841281 DOI: 10.1007/s00249-009-0556-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Revised: 09/30/2009] [Accepted: 10/09/2009] [Indexed: 11/15/2022]
Abstract
Transient structures in unfolded proteins are important in elucidating the molecular details of initiation of protein folding. Recently, native and non-native secondary structure have been discovered in unfolded A. vinelandii flavodoxin. These structured elements transiently interact and subsequently form the ordered core of an off-pathway folding intermediate, which is extensively formed during folding of this α–β parallel protein. Here, site-directed spin-labelling and paramagnetic relaxation enhancement are used to investigate long-range interactions in unfolded apoflavodoxin. For this purpose, glutamine-48, which resides in a non-native α-helix of unfolded apoflavodoxin, is replaced by cysteine. This replacement enables covalent attachment of nitroxide spin-labels MTSL and CMTSL. Substitution of Gln-48 by Cys-48 destabilises native apoflavodoxin and reduces flexibility of the ordered regions in unfolded apoflavodoxin in 3.4 M GuHCl, because of increased hydrophobic interactions in the unfolded protein. Here, we report that in the study of the conformational and dynamic properties of unfolded proteins interpretation of spin-label data can be complicated. The covalently attached spin-label to Cys-48 (or Cys-69 of wild-type apoflavodoxin) perturbs the unfolded protein, because hydrophobic interactions occur between the label and hydrophobic patches of unfolded apoflavodoxin. Concomitant hydrophobic free energy changes of the unfolded protein (and possibly of the off-pathway intermediate) reduce the stability of native spin-labelled protein against unfolding. In addition, attachment of MTSL or CMTSL to Cys-48 induces the presence of distinct states in unfolded apoflavodoxin. Despite these difficulties, the spin-label data obtained here show that non-native contacts exist between transiently ordered structured elements in unfolded apoflavodoxin.
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37
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Livernois AM, Hnatchuk DJ, Findlater EE, Graether SP. Obtaining highly purified intrinsically disordered protein by boiling lysis and single step ion exchange. Anal Biochem 2009; 392:70-6. [DOI: 10.1016/j.ab.2009.05.023] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2009] [Revised: 05/09/2009] [Accepted: 05/13/2009] [Indexed: 11/27/2022]
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38
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Krishna Mohan PM, Hosur RV. Structure-function-folding relationships and native energy landscape of dynein light chain protein: nuclear magnetic resonance insights. J Biosci 2009; 34:465-79. [DOI: 10.1007/s12038-009-0052-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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39
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Kang TS, Kini RM. Structural determinants of protein folding. Cell Mol Life Sci 2009; 66:2341-61. [PMID: 19367367 PMCID: PMC11115868 DOI: 10.1007/s00018-009-0023-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Revised: 03/07/2009] [Accepted: 03/20/2009] [Indexed: 12/11/2022]
Abstract
The last several decades have seen an explosion of knowledge in the field of structural biology. With critical advances in spectroscopic techniques in examining structures of biomacromolecules, in maturation of molecular biology techniques, as well as vast improvements in computation prowess, protein structures are now being elucidated at an unprecedented rate. In spite of all the recent advances, the protein folding puzzle remains as one of the fundamental biochemical challenges. A facet to this empiric problem is the structural determinants of protein folding. What are the driving forces that pivot a polypeptide chain to a specific conformation amongst the vast conformation space? In this review, we shall discuss some of the structural determinants to protein folding that have been identified in the recent decades.
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Affiliation(s)
- Tse Siang Kang
- The Scripps Research Institute, 10550 North Torrey Pines Road GAC 1200, La Jolla, CA 92037 USA
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Block S4, Singapore, 117543 Singapore
| | - R. Manjunatha Kini
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Block S3 #03-17, Singapore, 117543 Singapore
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40
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Bagchi S, Charnley AK, Smith AB, Hochstrasser RM. Equilibrium exchange processes of the aqueous tryptophan dipeptide. J Phys Chem B 2009; 113:8412-7. [PMID: 19459617 PMCID: PMC2929808 DOI: 10.1021/jp811168x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The tryptophan dipeptide (NATMA) in D2O shows two conformers having distinctive acetyl end amide-I' transition frequencies. In 2D echo spectroscopy, cross peaks between these conformer transitions are used to show that they are undergoing exchange on the 1.5 ps time scale. Simulations suggest that the accessibility of the amide group to water is restricted in one of the conformations.
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Affiliation(s)
- Sayan Bagchi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, U. S. A
| | - Adam K. Charnley
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, U. S. A
| | - Amos B. Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, U. S. A
| | - Robin M. Hochstrasser
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, U. S. A
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41
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An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms. Nat Struct Mol Biol 2009; 16:582-8. [DOI: 10.1038/nsmb.1592] [Citation(s) in RCA: 205] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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42
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Libich DS, Schwalbe M, Kate S, Venugopal H, Claridge JK, Edwards PJB, Dutta K, Pascal SM. Intrinsic disorder and coiled-coil formation in prostate apoptosis response factor 4. FEBS J 2009; 276:3710-28. [PMID: 19490121 DOI: 10.1111/j.1742-4658.2009.07087.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Prostate apoptosis response factor-4 (Par-4) is an ubiquitously expressed pro-apoptotic and tumour suppressive protein that can both activate cell-death mechanisms and inhibit pro-survival factors. Par-4 contains a highly conserved coiled-coil region that serves as the primary recognition domain for a large number of binding partners. Par-4 is also tightly regulated by the aforementioned binding partners and by post-translational modifications. Biophysical data obtained in the present study indicate that Par-4 primarily comprises an intrinsically disordered protein. Bioinformatic analysis of the highly conserved Par-4 reveals low sequence complexity and enrichment in polar and charged amino acids. The high proteolytic susceptibility and an increased hydrodynamic radius are consistent with a largely extended structure in solution. Spectroscopic measurements using CD and NMR also reveal characteristic features of intrinsic disorder. Under physiological conditions, the data obtained show that Par-4 self-associates via the C-terminal domain, forming a coiled-coil. Interruption of self-association by urea also resulted in loss of secondary structure. These results are consistent with the stabilization of the coiled-coil motif through an intramolecular association.
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Affiliation(s)
- David S Libich
- Centre for Structural Biology, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
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43
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Nabuurs SM, Westphal AH, van Mierlo CPM. Noncooperative Formation of the off-pathway molten globule during folding of the alpha-beta parallel protein apoflavodoxin. J Am Chem Soc 2009; 131:2739-46. [PMID: 19170491 DOI: 10.1021/ja8089476] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
During folding of many proteins, molten globules are formed. These partially folded forms of proteins have a substantial amount of secondary structure but lack virtually all tertiary side-chain packing characteristic of native structures. Molten globules are ensembles of interconverting conformers and are prone to aggregation, which can have detrimental effects on organisms. Consequently, molten globules attract considerable attention. The molten globule that is observed during folding of flavodoxin from Azotobacter vinelandii is a kinetically off-pathway species, as it has to unfold before the native state of the protein can be formed. This intermediate contains helices and can be populated at equilibrium using guanidinium hydrochloride as denaturant, allowing the use of NMR spectroscopy to follow molten globule formation at the residue level. Here, we track changes in chemical shifts of backbone amides, as well as disappearance of resonances of unfolded apoflavodoxin, upon decreasing denaturant concentration. Analysis of the data shows that structure formation within virtually all parts of the unfolded protein precedes folding to the molten globule state. This folding transition is noncooperative and involves a series of distinct transitions. Four structured elements in unfolded apoflavodoxin transiently interact and subsequently form the ordered core of the molten globule. Although hydrophobic, tryptophan side chains are not involved in the latter process. This ordered core is gradually extended upon decreasing denaturant concentration, but part of apoflavodoxin's molten globule remains random coil in the denaturant range investigated. The results presented here, together with those reported on the molten globule of alpha-lactalbumin, show that helical molten globules apparently fold in a noncooperative manner.
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Affiliation(s)
- Sanne M Nabuurs
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
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44
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Abstract
NMR is a powerful tool for quantitative measurement of the thermodynamic properties of biological systems. In this review, we discuss the role NMR has played in understanding the various coupled equilibria in dimerization of dynein light chain LC8 and in its interactions with its ligands. LC8, a very highly conserved 89-residue homodimer also known as DYNLL, is an essential component of the dynein and Myosin V molecular motors and is also found in various other complexes. LC8 binds to disordered segments of its partners, promoting them to dimerize and form more ordered structures, often coiled coils. The monomer-dimer equilibrium is controlled by electrostatic interactions at the dimer interface, such as by phosphorylation of residue Ser88, which is a regulatory mechanism for LC8 in vivo. NMR experiments have uncovered several subtle interactions--weak dimerization of a phosphomimetic mutant, and allosteric interaction between the LC8 binding sites--that have been overlooked by other methods. NMR has also provided a residue-specific view of the titration of histidine residues at the LC8 dimer interface, and of a nascent helix in one of the binding partners, the primarily disordered dynein intermediate chain IC74. We give special attention to methods for quantitative interpretation of NMR spectra, an important consideration when using NMR to measure equilibria.
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45
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Wright PE, Dyson HJ. Linking folding and binding. Curr Opin Struct Biol 2009; 19:31-8. [PMID: 19157855 DOI: 10.1016/j.sbi.2008.12.003] [Citation(s) in RCA: 803] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Accepted: 12/04/2008] [Indexed: 01/17/2023]
Abstract
Many cellular proteins are intrinsically disordered and undergo folding, in whole or in part, upon binding to their physiological targets. The past few years have seen an exponential increase in papers describing characterization of intrinsically disordered proteins, both free and bound to targets. Although NMR spectroscopy remains the favored tool, a number of new biophysical techniques are proving exceptionally useful in defining the limits of the conformational ensembles. Advances have been made in prediction of the recognition elements in disordered proteins, in elucidating the kinetics and mechanism of the coupled folding and binding process, and in understanding the role of post-translational modifications in tuning the biological response. Here we review these and other recent advances that are providing new insights into the conformational propensities and interactions of intrinsically disordered proteins and are beginning to reveal general principles underlying their biological functions.
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Affiliation(s)
- Peter E Wright
- Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States.
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46
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Intrinsic Disorder in Proteins Associated with Neurodegenerative Diseases. PROTEIN FOLDING AND MISFOLDING: NEURODEGENERATIVE DISEASES 2008. [DOI: 10.1007/978-1-4020-9434-7_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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47
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United we stand: combining structural methods. Curr Opin Struct Biol 2008; 18:617-22. [DOI: 10.1016/j.sbi.2008.07.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Accepted: 07/29/2008] [Indexed: 01/20/2023]
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48
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Mohan PMK, Chakraborty S, Hosur RV. Residue-wise conformational stability of DLC8 dimer from native-state hydrogen exchange. Proteins 2008; 75:40-52. [PMID: 18767155 DOI: 10.1002/prot.22219] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Dynein light chain (DLC8) is the smallest subunit of the dynein motor complex, which is known to act as a cargo adaptor in intracellular trafficking. The protein exists as a pure dimer at physiological pH and a completely folded monomer below pH 4. Here, we have determined the energy landscape of the dimeric protein using a combination of optical techniques and native-state hydrogen exchange of amide groups, the former giving the global features and the latter yielding the residue level details. The data indicated the presence of intermediates along the equilibrium unfolding transition. The hydrogen exchange data suggested that the molecule has differential stability in its various segments. We deduce from the free energy data that the antiparallel beta-sheets (beta4 and beta5) that form the hydrophobic core of the protein and the alpha2 helix, all of which are highly protected with regard to hydrogen exchange, contribute significantly to the initial step of the protein folding mechanism. Denaturant-dependent hydrogen exchange indicated further that some amides exchange via local fluctuations, whereas there are others which exchange via global unfolding events. Implications of these to cargo adaptability of the dimer are discussed.
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Affiliation(s)
- P M Krishna Mohan
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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49
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Lakomek NA, Walter KFA, Farès C, Lange OF, de Groot BL, Grubmüller H, Brüschweiler R, Munk A, Becker S, Meiler J, Griesinger C. Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics. JOURNAL OF BIOMOLECULAR NMR 2008; 41:139-55. [PMID: 18523727 PMCID: PMC2480484 DOI: 10.1007/s10858-008-9244-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Revised: 04/21/2008] [Accepted: 04/22/2008] [Indexed: 05/19/2023]
Abstract
Residual dipolar couplings (RDCs) provide information about the dynamic average orientation of inter-nuclear vectors and amplitudes of motion up to milliseconds. They complement relaxation methods, especially on a time-scale window that we have called supra-tau(c) (tau(c) < supra-tau(c) < 50 micros). Here we present a robust approach called Self-Consistent RDC-based Model-free analysis (SCRM) that delivers RDC-based order parameters-independent of the details of the structure used for alignment tensor calculation-as well as the dynamic average orientation of the inter-nuclear vectors in the protein structure in a self-consistent manner. For ubiquitin, the SCRM analysis yields an average RDC-derived order parameter of the NH vectors <S2(rdc)>0.72 +/- 0.02 compared to <S2(LS)> = 0.778 +/- 0.003 for the Lipari-Szabo order parameters, indicating that the inclusion of the supra-tau(c) window increases the averaged amplitude of mobility observed in the sub-supra-tau(c) window by about 34%. For the beta-strand spanned by residues Lys48 to Leu50, an alternating pattern of backbone NH RDC order parameter S2(rdc)(NH) = (0.59, 0.72, 0.59) was extracted. The backbone of Lys48, whose side chain is known to be involved in the poly-ubiquitylation process that leads to protein degradation, is very mobile on the supra-tau(c) time scale (S2(rdc)(NH) = 0.59 +/- 0.03), while it is inconspicuous (S2(LS)(NH)= 0.82) on the sub-tau(c) as well as on micros-ms relaxation dispersion time scales. The results of this work differ from previous RDC dynamics studies of ubiquitin in the sense that the results are essentially independent of structural noise providing a much more robust assessment of dynamic effects that underlie the RDC data.
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Affiliation(s)
- Nils-Alexander Lakomek
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen, 37077 Germany
| | - Korvin F. A. Walter
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen, 37077 Germany
| | - Christophe Farès
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen, 37077 Germany
| | - Oliver F. Lange
- Department for Theoretical and Computational Biophysics, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Bert L. de Groot
- Department for Theoretical and Computational Biophysics, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Helmut Grubmüller
- Department for Theoretical and Computational Biophysics, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | | | - Axel Munk
- Institut for Mathematical Stochastics, University of Goettingen, Goettingen, Germany
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen, 37077 Germany
| | - Jens Meiler
- Department of Chemistry, Center of Structural Biology, Vanderbilt University, Nashville, TN USA
| | - Christian Griesinger
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen, 37077 Germany
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50
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Chugh J, Sharma S, Kumar D, Misra JR, Hosur RV. Effect of a single point mutation on the stability, residual structure and dynamics in the denatured state of GED: relevance to self-assembly. Biophys Chem 2008; 137:13-8. [PMID: 18586378 DOI: 10.1016/j.bpc.2008.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Revised: 06/05/2008] [Accepted: 06/05/2008] [Indexed: 10/21/2022]
Abstract
The GTPase effector domain (GED) of dynamin forms large soluble oligomers in vitro, while its mutant--I697A--lacks this property at low concentrations. With a view to understand the intrinsic structural characteristics of the polypeptide chain, the global unfolding characteristics of GED wild type (WT) and I697A were compared using biophysical techniques. Quantitative analysis of the CD and fluorescence denaturation profiles revealed that unfolding occurred by a two-state process and the mutant was less stable than the WT. Even in the denatured state, the mutation caused chemical shift perturbations and significant differences were observed in the 15N transverse relaxation rates (R2), not only at the mutation site but all around. These results demonstrate that the hydrophobic change associated with the mutation perturbs the structural and motional preferences locally, which are then relayed via different folding pathways along the chain and the property of oligomerization in the native state is affected.
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Affiliation(s)
- Jeetender Chugh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai-400005, India
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