1
|
Molecular and thermodynamic mechanisms for protein adaptation. EUROPEAN BIOPHYSICS JOURNAL 2022; 51:519-534. [DOI: 10.1007/s00249-022-01618-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 08/01/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022]
|
2
|
Ullah I, Khan MS, Khan SS, Ahmad W, Zheng L, Shah SUA, Ullah M, Iqbal A. Identification and characterization of thermophilic amylase producing bacterial isolates from the brick kiln soil. Saudi J Biol Sci 2021; 28:970-979. [PMID: 33424389 PMCID: PMC7783820 DOI: 10.1016/j.sjbs.2020.11.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 12/01/2022] Open
Abstract
The present experiment was designed to isolate bacterial strains from the brick kiln soil and to check the activity and enzyme kinetics of amylase from these isolates. The bacterial colonies were isolated from soil samples through the serial dilution method. The bacterial isolates were identified through morphological, electron microscopic and molecular analysis. The 16S ribosomal RNA sequences of the isolates IR-1, IR-2, IR-3, IR-8, and IR-9 showed high similarities with Bacillus tequilensis, Bacillus paramycoides, Proteus alimentorum, Bacillus wiedmannii, and Pseudomonas aeruginosa, respectively. All of the bacterial isolates showed a positive catalase activity except IR-9. Furthermore, the isolates showed variable antagonistic effects against different bacterial pathogens. All of the strains produced indole acetic acid (IAA), and the concentrations increased in the presence of tryptophan application. The isolates showed the amylase enzyme activity and maximum activity of isolates was achieved in 4% starch concentration. The IR-9 isolate showed the highest amylase activity of 5.9 U/ml. The V max values of the extracellular amylase from different bacterial isolates ranged between 12.90 and 50.00 IU ml-1. The lowest K m value of 6.33 mg starch was recorded for IR-8 and the maximum K cat value of 2.50 min-1 was observed for IR-3. The amylase activity of the isolates was significantly affected by a range of different incubation time, temperature, and pH values. Further tests are required before the potential utilization of these isolates for amylase production, and in the biopesticide and biofertilizer applications.
Collapse
Affiliation(s)
- Irfan Ullah
- Institute of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar 25000, Khyber Pakhtunkhwa, Pakistan
| | - Mohammad Sayyar Khan
- Institute of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar 25000, Khyber Pakhtunkhwa, Pakistan
| | - Shahin Shah Khan
- Institute of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar 25000, Khyber Pakhtunkhwa, Pakistan
| | - Waqar Ahmad
- Institute of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar 25000, Khyber Pakhtunkhwa, Pakistan
| | - Lingjie Zheng
- College of Life Science and Technology, Beijing University of Chemical Technology, National Energy Bio-Refining R&D Center, Beijing Key Laboratory of Bio-Processing, China
| | - Syed Usman Ali Shah
- Institute of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar 25000, Khyber Pakhtunkhwa, Pakistan
| | - Mazhar Ullah
- Institute of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar 25000, Khyber Pakhtunkhwa, Pakistan
| | - Aqib Iqbal
- Institute of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar 25000, Khyber Pakhtunkhwa, Pakistan
| |
Collapse
|
3
|
Moosa MM, Ferreon JC, Ferreon ACM. Ligand interactions and the protein order-disorder energetic continuum. Semin Cell Dev Biol 2018; 99:78-85. [PMID: 29753880 DOI: 10.1016/j.semcdb.2018.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 04/05/2018] [Accepted: 05/04/2018] [Indexed: 12/11/2022]
Abstract
Intrinsically disordered proteins as computationally predicted account for ∼1/3 of eukaryotic proteomes, are involved in a plethora of biological functions, and have been linked to several human diseases as a result of their dysfunctions. Here, we present a picture wherein an energetic continuum describes protein structural and conformational propensities, ranging from the hyperstable folded proteins on one end to the hyperdestabilized and sometimes functionally disordered proteins on the other. We distinguish between proteins that are folding-competent but disordered because of marginal stability and those that are disordered due mainly to the absence of folding code-completing structure-determining interactions, and postulate that disordered proteins that are unstructured by way of partial population of protein denatured states represent a sizable proportion of the proteome.
Collapse
Affiliation(s)
- Mahdi Muhammad Moosa
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Josephine C Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA.
| | - Allan Chris M Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA.
| |
Collapse
|
4
|
Sala D, Giachetti A, Rosato A. Molecular dynamics simulations of metalloproteins: A folding study of rubredoxin from <em>Pyrococcus furiosus</em>. AIMS BIOPHYSICS 2018. [DOI: 10.3934/biophy.2018.1.77] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
5
|
Tych KM, Batchelor M, Hoffmann T, Wilson MC, Hughes ML, Paci E, Brockwell DJ, Dougan L. Differential Effects of Hydrophobic Core Packing Residues for Thermodynamic and Mechanical Stability of a Hyperthermophilic Protein. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:7392-7402. [PMID: 27338140 DOI: 10.1021/acs.langmuir.6b01550] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Proteins from organisms that have adapted to environmental extremes provide attractive systems to explore and determine the origins of protein stability. Improved hydrophobic core packing and decreased loop-length flexibility can increase the thermodynamic stability of proteins from hyperthermophilic organisms. However, their impact on protein mechanical stability is not known. Here, we use protein engineering, biophysical characterization, single-molecule force spectroscopy (SMFS), and molecular dynamics (MD) simulations to measure the effect of altering hydrophobic core packing on the stability of the cold shock protein TmCSP from the hyperthermophilic bacterium Thermotoga maritima. We make two variants of TmCSP in which a mutation is made to reduce the size of aliphatic groups from buried hydrophobic side chains. In the first, a mutation is introduced in a long loop (TmCSP L40A); in the other, the mutation is introduced on the C-terminal β-strand (TmCSP V62A). We use MD simulations to confirm that the mutant TmCSP L40A shows the most significant increase in loop flexibility, and mutant TmCSP V62A shows greater disruption to the core packing. We measure the thermodynamic stability (ΔGD-N) of the mutated proteins and show that there is a more significant reduction for TmCSP L40A (ΔΔG = 63%) than TmCSP V62A (ΔΔG = 47%), as might be expected on the basis of the relative reduction in the size of the side chain. By contrast, SMFS measures the mechanical stability (ΔG*) and shows a greater reduction for TmCSP V62A (ΔΔG* = 8.4%) than TmCSP L40A (ΔΔG* = 2.5%). While the impact on the mechanical stability is subtle, the results demonstrate the power of tuning noncovalent interactions to modulate both the thermodynamic and mechanical stability of a protein. Such understanding and control provide the opportunity to design proteins with optimized thermodynamic and mechanical properties.
Collapse
Affiliation(s)
- Katarzyna M Tych
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Matthew Batchelor
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Toni Hoffmann
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Michael C Wilson
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Megan L Hughes
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Emanuele Paci
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - David J Brockwell
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Lorna Dougan
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| |
Collapse
|
6
|
Some like it hot, some like it cold: Temperature dependent biotechnological applications and improvements in extremophilic enzymes. Biotechnol Adv 2015; 33:1912-22. [DOI: 10.1016/j.biotechadv.2015.11.001] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 11/12/2015] [Accepted: 11/12/2015] [Indexed: 11/23/2022]
|
7
|
Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 549] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
8
|
Prakash S, Sundd M, Guptasarma P. The key to the extraordinary thermal stability of P. furiosus holo-rubredoxin: iron binding-guided packing of a core aromatic cluster responsible for high kinetic stability of the native structure. PLoS One 2014; 9:e89703. [PMID: 24603898 PMCID: PMC3945938 DOI: 10.1371/journal.pone.0089703] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 01/22/2014] [Indexed: 11/30/2022] Open
Abstract
Pyrococcus furiosus rubredoxin (PfRd), a small, monomeric, 53 residues-long, iron-containing, electron-transfer protein of known structure is sometimes referred to as being the most structurally-stable protein known to man. Here, using a combination of mutational and spectroscopic (CD, fluorescence, and NMR) studies of differently made holo- and apo-forms of PfRd, we demonstrate that it is not the presence of iron, or even the folding of the PfRd chain into a compact well-folded structure that causes holo-PfRd to display its extraordinary thermal stability, but rather the correct iron binding-guided packing of certain residues (specifically, Trp3, Phe29, Trp36, and also Tyr10) within a tight aromatic cluster of six residues in PfRd's hydrophobic core. Binding of the iron atom appears to play a remarkable role in determining subtle details of residue packing, forcing the chain to form a hyper-thermally stable native structure which is kinetically stable enough to survive (subsequent) removal of iron. On the other hand, failure to bind iron causes the same chain to adopt an equally well-folded native-like structure which, however, has a differently-packed aromatic cluster in its core, causing it to be only as stable as any other ordinary mesophile-derived rubredoxin. Our studies demonstrate, perhaps for the very first time ever that hyperthermal stability in proteins can owe to subtle differences in residue packing vis a vis mesostable proteins, without there being any underlying differences in either amino acid sequence, or bound ligand status.
Collapse
Affiliation(s)
- Satya Prakash
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, SAS Nagar, Punjab, India
- Protein Engineering Division, Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Monica Sundd
- NMR Laboratory, National Institute of Immunology (NII), New Delhi, India
| | - Purnananda Guptasarma
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, SAS Nagar, Punjab, India
- Protein Engineering Division, Institute of Microbial Technology (IMTECH), Chandigarh, India
- * E-mail:
| |
Collapse
|
9
|
Kinetic study of the thermal denaturation of a hyperthermostable extracellular α-amylase from Pyrococcus furiosus. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2600-5. [DOI: 10.1016/j.bbapap.2013.09.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 09/13/2013] [Accepted: 09/14/2013] [Indexed: 11/17/2022]
|
10
|
Dhaunta N, Arora K, Chandrayan SK, Guptasarma P. Introduction of a thermophile-sourced ion pair network in the fourth beta/alpha unit of a psychophile-derived triosephosphate isomerase from Methanococcoides burtonii significantly increases its kinetic thermal stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1023-33. [DOI: 10.1016/j.bbapap.2013.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 12/07/2012] [Accepted: 01/03/2013] [Indexed: 10/27/2022]
|
11
|
Cuypers MG, Mason SA, Blakeley MP, Mitchell EP, Haertlein M, Forsyth VT. Near-atomic resolution neutron crystallography on perdeuterated Pyrococcus furiosus rubredoxin: implication of hydronium ions and protonation state equilibria in redox changes. Angew Chem Int Ed Engl 2012; 52:1022-5. [PMID: 23225503 DOI: 10.1002/anie.201207071] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Indexed: 11/09/2022]
Affiliation(s)
- M G Cuypers
- EPSAM/ISTM, Keele University, Staffordshire, ST5 5BG, UK
| | | | | | | | | | | |
Collapse
|
12
|
Cuypers MG, Mason SA, Blakeley MP, Mitchell EP, Haertlein M, Forsyth VT. Near-Atomic Resolution Neutron Crystallography on PerdeuteratedPyrococcus furiosusRubredoxin: Implication of Hydronium Ions and Protonation State Equilibria in Redox Changes. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207071] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
13
|
Chung JK, Thielges MC, Fayer MD. Conformational dynamics and stability of HP35 studied with 2D IR vibrational echoes. J Am Chem Soc 2012; 134:12118-24. [PMID: 22764745 DOI: 10.1021/ja303017d] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Two-dimensional infrared (2D IR) vibrational echo spectroscopy was used to measure the fast dynamics of two variants of chicken villin headpiece 35 (HP35). The CN of cyanophenylalanine residues inserted in the hydrophobic core were used as a vibrational probe. Experiments were performed on both singly (HP35-P) and doubly CN-labeled peptide (HP35-P(2)) within the wild-type sequence, as well as on HP-35 containing a singly labeled cyanophenylalanine and two norleucine mutations (HP35-P NleNle). There is a remarkable similarity between the dynamics measured in singly and doubly CN-labeled HP35, demonstrating that the presence of an additional CN vibrational probe does not significantly alter the dynamics of the small peptide. The substitution of two lysine residues by norleucines markedly improves the stability of HP35 by replacing charged with nonpolar residues, stabilizing the hydrophobic core. The results of the 2D IR experiments reveal that the dynamics of HP35-P are significantly faster than those of HP35-P NleNle. These observations suggest that the slower structural fluctuations in the hydrophobic core, indicating a more tightly structured core, may be an important contributing factor to HP35-P NleNle's increased stability.
Collapse
Affiliation(s)
- Jean K Chung
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | | |
Collapse
|
14
|
Hernández G, Anderson JS, Lemaster DM. Electrostatics of hydrogen exchange for analyzing protein flexibility. Methods Mol Biol 2012; 831:369-405. [PMID: 22167684 DOI: 10.1007/978-1-61779-480-3_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Electrostatic interactions at the protein-aqueous interface modulate the reactivity of solvent-exposed backbone amides by a factor of at least a billion fold. The brief (∼10 ps) lifetime of the peptide anion formed during the hydroxide-catalyzed exchange reaction helps enable the experimental rates to be robustly predictable by continuum dielectric methods. Since this ability to predict the structural dependence of exchange reactivity also applies to the protein amide hydrogens that are only rarely exposed to the bulk solvent phase, electrostatic analysis of the experimental exchange rates provides an effective assessment of whether a given model ensemble is consistent with the properly weighted Boltzmann conformational distribution of the protein native state.
Collapse
Affiliation(s)
- Griselda Hernández
- Department of Health and Department of Biomedical Sciences, Wadsworth Center, School of Public Health, University at Albany - SUNY, Albany, NY, USA
| | | | | |
Collapse
|
15
|
Penzkofer A, Stierl M, Hegemann P, Kateriya S. Thermal protein unfolding in photo-activated adenylate cyclase nano-clusters from the amoeboflagellate Naegleria gruberi NEG-M strain. J Photochem Photobiol A Chem 2011. [DOI: 10.1016/j.jphotochem.2011.09.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
16
|
Girdhar K, Scott G, Chemla YR, Gruebele M. Better biomolecule thermodynamics from kinetics. J Chem Phys 2011; 135:015102. [DOI: 10.1063/1.3607605] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
17
|
Feller G. Protein stability and enzyme activity at extreme biological temperatures. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:323101. [PMID: 21386475 DOI: 10.1088/0953-8984/22/32/323101] [Citation(s) in RCA: 163] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Psychrophilic microorganisms thrive in permanently cold environments, even at subzero temperatures. To maintain metabolic rates compatible with sustained life, they have improved the dynamics of their protein structures, thereby enabling appropriate molecular motions required for biological activity at low temperatures. As a consequence of this structural flexibility, psychrophilic proteins are unstable and heat-labile. In the upper range of biological temperatures, thermophiles and hyperthermophiles grow at temperatures > 100 °C and synthesize ultra-stable proteins. However, thermophilic enzymes are nearly inactive at room temperature as a result of their compactness and rigidity. At the molecular level, both types of extremophilic proteins have adapted the same structural factors, but in opposite directions, to address either activity at low temperatures or stability in hot environments. A model based on folding funnels is proposed accounting for the stability-activity relationships in extremophilic proteins.
Collapse
Affiliation(s)
- Georges Feller
- Laboratory of Biochemistry, Centre for Protein Engineering, Institute of Chemistry B6a, University of Liège, B-4000 Liège, Belgium.
| |
Collapse
|
18
|
Kawamura K, Nagayoshi H, Yao T. In situ analysis of proteins at high temperatures mediated by capillary-flow hydrothermal UV–vis spectrophotometer with a water-soluble chromogenic reagent. Anal Chim Acta 2010; 667:88-95. [DOI: 10.1016/j.aca.2010.04.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 04/01/2010] [Accepted: 04/03/2010] [Indexed: 11/30/2022]
|
19
|
Rubredoxin mutant A51C unfolding dynamics: A Förster Resonance Energy Transfer study. Biophys Chem 2010; 148:131-7. [DOI: 10.1016/j.bpc.2010.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 03/03/2010] [Accepted: 03/05/2010] [Indexed: 11/18/2022]
|
20
|
Abstract
The source of increased stability in proteins from organisms that thrive in extreme thermal environments is not well understood. Previous experimental and theoretical studies have suggested many different features possibly responsible for such thermostability. Many of these thermostabilizing mechanisms can be accounted for in terms of structural rigidity. Thus a plausible hypothesis accounting for this remarkable stability in thermophilic enzymes states that these enzymes have enhanced conformational rigidity at temperatures below their native, functioning temperature. Experimental evidence exists to both support and contradict this supposition. We computationally investigate the relationship between thermostability and rigidity using rubredoxin as a case study. The mechanical rigidity is calculated using atomic models of homologous rubredoxin structures from the hyperthermophile Pyrococcus furiosus and mesophile Clostridium pasteurianum using the FIRST software. A global increase in structural rigidity (equivalently a decrease in flexibility) corresponds to an increase in thermostability. Locally, rigidity differences (between mesophilic and thermophilic structures) agree with differences in protection factors.
Collapse
Affiliation(s)
- A J Rader
- Department of Physics and Center for Mathematical Biosciences, Indiana University-Purdue University at Indianapolis, Indianapolis, IN, USA.
| |
Collapse
|
21
|
Krishnamurthy H, Munro K, Yan H, Vieille C. Dynamics in Thermotoga neapolitana adenylate kinase: 15N relaxation and hydrogen-deuterium exchange studies of a hyperthermophilic enzyme highly active at 30 degrees C. Biochemistry 2009; 48:2723-39. [PMID: 19220019 DOI: 10.1021/bi802001w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Backbone conformational dynamics of Thermotoga neapolitana adenylate kinase in the free form (TNAK) and inhibitor-bound form (TNAK*Ap5A) were investigated at 30 degrees C using (15)N NMR relaxation measurements and NMR monitored hydrogen-deuterium exchange. With kinetic parameters identical to those of Escherichia coli AK (ECAK) at 30 degrees C, TNAK is a unique hyperthermophilic enzyme. These catalytic properties make TNAK an interesting and novel model to study the interplay between protein rigidity, stability, and activity. Comparison of fast time scale dynamics (picosecond to nanosecond) in the open and closed states of TNAK and ECAK at 30 degrees C reveals a uniformly higher rigidity across all domains of TNAK. Within this framework of a rigid TNAK structure, several residues located in the AMP-binding domain and in the core-lid hinge regions display high picosecond to nanosecond time scale flexibility. Together with the recent comparison of ECAK dynamics with those of hyperthermophilic Aquifex aeolicus AK (AAAK), our results provide strong evidence for the role of picosecond to nanosecond time scale fluctuations in both stability and activity. In the slow time scales, TNAK's increased rigidity is not uniform but localized in the AMP-binding and lid domains. The core domain amides of ECAK and TNAK in the open and closed states show comparable protection against exchange. Significantly, the hinges framing the lid domain show similar exchange data in ECAK and TNAK open and closed forms. Our NMR relaxation and hydrogen-deuterium exchange studies therefore suggest that TNAK maintains high activity at 30 degrees C by localizing flexibility to the hinge regions that are key to facilitating conformational changes.
Collapse
Affiliation(s)
- Harini Krishnamurthy
- Program in Cell and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | | | | | | |
Collapse
|
22
|
NMR analysis of native-state protein conformational flexibility by hydrogen exchange. Methods Mol Biol 2009; 490:285-310. [PMID: 19157088 DOI: 10.1007/978-1-59745-367-7_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
The rate of hydrogen exchange for the most protected amides of a protein is widely used to provide an estimate of global conformational stability by analyzing the exchange kinetics in the unfolded state in terms of model peptide exchange rates. The exchange behavior of the other amides of the protein which do not exchange via a global unfolding mechanism can provide insight into the smaller-scale conformational transitions that facilitate access to solvent as required for the exchange reaction. However, since the residual tertiary structure in the exchange-competent conformation can modulate the chemistry of the exchange reaction, equilibrium values estimated from normalization with model peptide rates are open to question. To overcome this limitation, the most robust approaches utilize differential analyses as a function of experimental variables such as denaturant concentration, temperature, pH, and mutational variation. Practical aspects of these various differential analysis techniques are considered with illustrations drawn from the literature.
Collapse
|
23
|
Weiss KL, Meilleur F, Blakeley MP, Myles DAA. Preliminary neutron crystallographic analysis of selectively CH3-protonated deuterated rubredoxin from Pyrococcus furiosus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:537-40. [PMID: 18540070 PMCID: PMC2496865 DOI: 10.1107/s1744309108013997] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Accepted: 05/09/2008] [Indexed: 11/10/2022]
Abstract
Neutron crystallography is used to locate H atoms in biological materials and can distinguish between negatively scattering hydrogen-substituted and positively scattering deuterium-substituted positions in isomorphous neutron structures. Recently, Hauptman & Langs (2003; Acta Cryst. A59, 250-254) have shown that neutron diffraction data can be used to solve macromolecular structures by direct methods and that solution is aided by the presence of negatively scattering H atoms in the structure. Selective-labeling protocols allow the design and production of H/D-labeled macromolecular structures in which the ratio of H to D atoms can be precisely controlled. Methyl selective-labeling protocols were applied to introduce (1H-delta methyl)-leucine and (1H-gamma methyl)-valine into deuterated rubredoxin from Pyrococcus furiosus (PfRd). Here, the production, crystallization and preliminary neutron analysis of a selectively CH3-protonated deuterated PfRd sample, which provided a high-quality neutron data set that extended to 1.75 A resolution using the new LADI-III instrument at the Institut Laue-Langevin, are reported. Preliminary analysis of neutron density maps allows unambiguous assignment of the positions of H atoms at the methyl groups of the valine and leucine residues in the otherwise deuterated rubredoxin structure.
Collapse
Affiliation(s)
- K. L. Weiss
- Oak Ridge National Laboratory, Chemical Sciences Division, Center for Structural Molecular Biology, PO Box 2008, Oak Ridge, TN 37831, USA
| | - F. Meilleur
- North Carolina State University, Department of Molecular and Structural Biochemistry, Raleigh, NC 27695, USA
- Oak Ridge National Laboratory, Neutron Scattering Sciences Division, PO Box 2008, Oak Ridge, TN 37831, USA
| | - M. P. Blakeley
- Institut Laue-Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - D. A. A. Myles
- Oak Ridge National Laboratory, Chemical Sciences Division, Center for Structural Molecular Biology, PO Box 2008, Oak Ridge, TN 37831, USA
| |
Collapse
|
24
|
Anderson JS, Hernández G, Lemaster DM. A billion-fold range in acidity for the solvent-exposed amides of Pyrococcus furiosus rubredoxin. Biochemistry 2008; 47:6178-88. [PMID: 18479148 DOI: 10.1021/bi800284y] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The exchange rates of the static solvent-accessible amide hydrogens of Pyrococcus furiosus rubredoxin range from near the diffusion-limited rate to a billion-fold slower for the non-hydrogen-bonded Val 38 (eubacterial numbering). Hydrogen exchange directly monitors the kinetic acidity of the peptide nitrogen. Electrostatic solvation free energies were calculated by Poisson-Boltzmann methods for the individual peptide anions that form during the hydroxide-catalyzed exchange reaction to examine how well the predicted thermodynamic acidities match the experimentally determined kinetic acidities. With the exception of the Ile 12 amide, the differential exchange rate constant for each solvent-exposed amide proton that is not hydrogen bonded to a backbone carbonyl can be predicted within a factor of 6 (10 (0.78)) root-mean-square deviation (rmsd) using the CHARMM22 electrostatic parameter set and an internal dielectric value of 3. Under equivalent conditions, the PARSE parameter set yields a larger rmsd value of 1.28 pH units, while the AMBER parm99 parameter set resulted in a considerably poorer correlation. Either increasing the internal dielectric value to 4 or reducing it to a value of 2 significantly degrades the quality of the prediction. Assigning the excess charge of the peptide anion equally between the peptide nitrogen and the carbonyl oxygen also reduces the correlation to the experimental data. These continuum electrostatic calculations were further analyzed to characterize the specific structural elements that appear to be responsible for the wide range of peptide acidities observed for these solvent-exposed amides. The striking heterogeneity in the potential at sites along the protein-solvent interface should prove germane to the ongoing challenge of quantifying the contribution that electrostatic interactions make to the catalytic acceleration achieved by enzymes.
Collapse
Affiliation(s)
- Janet S Anderson
- Department of Chemistry, Union College, Schenectady, New York 12308, USA.
| | | | | |
Collapse
|
25
|
Chandrayan SK, Guptasarma P. Partial destabilization of native structure by a combination of heat and denaturant facilitates cold denaturation in a hyperthermophile protein. Proteins 2008; 72:539-46. [DOI: 10.1002/prot.22077] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
26
|
Luke KA, Higgins CL, Wittung-Stafshede P. Thermodynamic stability and folding of proteins from hyperthermophilic organisms. FEBS J 2007; 274:4023-33. [PMID: 17683332 DOI: 10.1111/j.1742-4658.2007.05955.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Life grows almost everywhere on earth, including in extreme environments and under harsh conditions. Organisms adapted to high temperatures are called thermophiles (growth temperature 45-75 degrees C) and hyperthermophiles (growth temperature >or= 80 degrees C). Proteins from such organisms usually show extreme thermal stability, despite having folded structures very similar to their mesostable counterparts. Here, we summarize the current data on thermodynamic and kinetic folding/unfolding behaviors of proteins from hyperthermophilic microorganisms. In contrast to thermostable proteins, rather few (i.e. less than 20) hyperthermostable proteins have been thoroughly characterized in terms of their in vitro folding processes and their thermodynamic stability profiles. Examples that will be discussed include co-chaperonin proteins, iron-sulfur-cluster proteins, and DNA-binding proteins from hyperthermophilic bacteria (i.e. Aquifex and Theromotoga) and archea (e.g. Pyrococcus, Thermococcus, Methanothermus and Sulfolobus). Despite the small set of studied systems, it is clear that super-slow protein unfolding is a dominant strategy to allow these proteins to function at extreme temperatures.
Collapse
Affiliation(s)
- Kathryn A Luke
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251, USA
| | | | | |
Collapse
|
27
|
LeMaster DM, Anderson JS, Hernández G. Spatial distribution of dielectric shielding in the interior of Pyrococcus furiosus rubredoxin as sampled in the subnanosecond timeframe by hydrogen exchange. Biophys Chem 2007; 129:43-8. [PMID: 17544203 PMCID: PMC2063458 DOI: 10.1016/j.bpc.2007.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Revised: 05/08/2007] [Accepted: 05/10/2007] [Indexed: 11/23/2022]
Abstract
Experimental pK values of ionizable sidechains provide the most direct test for models representing dielectric shielding within the interior of a protein. However, only the strongly shifted pK values are particularly useful for discriminating among models. NMR titration studies have usually found only one or two such shifted pK values in each protein, so that the fitting of the experimental data to a uniform internal dielectric (epsilon(int)) model is not well constrained. The observed variation among proteins for such epsilon(int) estimates may reflect nonuniformity of dielectric shielding within each protein interior or qualitative differences between individual proteins. The differential amide kinetic acidities for a series of metal-substituted rubredoxins are shown to be consistent with Poisson-Boltzmann predictions of dielectric shielding that is relatively uniform for all of the amides that are sensitive to the metal charge, a region which corresponds to roughly 1/3 of the internal volume. The effective epsilon(int) values near 6 that are found in this study are significantly lower than many such estimates derived from sidechain pK measurements. The differing timeframes in which dielectric relaxation can respond to the highly transient peptide anion as compared to the longer lived states of the charged sidechains offers an explanation for the lower apparent dielectric constant deduced from these measurements.
Collapse
Affiliation(s)
- David M. LeMaster
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, School of Public Health, University at Albany - SUNY, Empire State Plaza, Albany, New York, 12201 USA
| | - Janet S. Anderson
- Department of Chemistry, Union College, Schenectady, New York, 12308 USA
| | - Griselda Hernández
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, School of Public Health, University at Albany - SUNY, Empire State Plaza, Albany, New York, 12201 USA
- * Corresponding author Tel: (+1)518-474-4673, Fax: (+1)518-473-2900, E-mail:
| |
Collapse
|
28
|
LeMaster DM, Hernández G. Additivity of Differential Conformational Dynamics in Hyperthermophile/Mesophile Rubredoxin Chimeras as Monitored by Hydrogen Exchange. Chembiochem 2006; 7:1886-9. [PMID: 17068837 DOI: 10.1002/cbic.200600276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David M LeMaster
- Wadsworth Center, New York State Department of Health, University at Albany-SUNY, Empire State Plaza, Albany, NY 12201-0509, USA
| | | |
Collapse
|
29
|
Abstract
Studies that compare proteins from thermophilic and mesophilic organisms can provide insights into ability of thermophiles to function at their high habitat temperatures and may provide clues that enable us to better define the forces that stabilize all proteins. Most of the comparative studies have focused on thermal stability and show, as expected, that thermophilic proteins have higher Tm values than their mesophilic counterparts. Although these comparisons are useful, more detailed thermodynamic analyses are required to reach a more complete understanding of the mechanisms thermophilic protein employ to remain folded over a wider range of temperatures. This complete thermodynamic description allows one to generate a stability curve for a protein that defines how the conformational stability (DeltaG) varies with temperature. Here we compare stability curves for many pairs of homologous proteins from thermophilic and mesophilc organisms. Of the basic methods that can be employed to achieve enhanced thermostability, we find that most thermophilic proteins use the simple method that raises the DeltaG at all temperatures as the principal way to increase their Tm. We discuss and compare this thermodynamic method with the possible alternatives. In addition we propose ways that structural alterations and changes to the amino acid sequences might give rise to varied methods used to obtain thermostability.
Collapse
Affiliation(s)
- Abbas Razvi
- Department of Biochemistry and Biophysics, Texas A&M University, College Station 77843-1114, USA
| | | |
Collapse
|
30
|
Castano E, Rodrigez-Zapata L, Patricia Rodrigez H, Mobius N. Conformational dynamics of the tetrameric hemoglobin molecule as revealed by hydrogen exchange: I. Effects of pH, temperature, and ligand binding. Mol Biol 2006; 40:284-8. [PMID: 16637269 DOI: 10.1134/s0026893306020154] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Transcriptional regulation depends on the appropriate set of positive and negative signals that provide correct gene expression. Studies in eukaryotic gene expression have shown NC2 to be a general repressor of transcription which blocks the interaction between TFIIB and TBP. However, during the last few years NC2 has been found to bind the transcriptionally active promoters and interact with several positive transcription factors. These data suggested a controversial role of NC2 in transcription. Using in vitro transcription on minimal LTR promoter of HIV-1, we show that removal of NC2 from HeLa nuclear extract increases the yield of transcripts as well as unspecific transcription initiation in a template amount dependent manner. Fractions of HeLa nuclear extract containing NC2 can restore basal transcription repression and precise selection of transcription initiation point. This points to a new role for NC2 as a repressor of inaccurate transcription initiation that allows specific transcription to take place.
Collapse
|
31
|
Mukherjee S, Sharma S, Kumar S, Guptasarma P. Slow irreversible unfolding of Pyrococcus furiosus triosephosphate isomerase: Separation and quantitation of conformers through a novel electrophoretic approach. Anal Biochem 2005; 347:49-59. [PMID: 16236239 DOI: 10.1016/j.ab.2005.08.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2005] [Revised: 08/21/2005] [Accepted: 08/24/2005] [Indexed: 11/20/2022]
Abstract
The thermostability of hyperthermophile proteins is not easily studied because such proteins tend to be extremely recalcitrant to unfolding. Weeks of exposure to structurally destabilizing conditions are generally required to elicit any evidence of conformational change(s). The main reason for this extreme kinetic stability would appear to be the dominance of local unfolding transitions that occur within different parts of the structures of these molecules; put differently, local sub structural unfolding transitions that occur autonomously and reversibly are thought to fail to cooperate to bring about global unfolding in a facile manner, leading to a low overall observed rate of unfolding. For reasons that are not yet fully understood, unfolding is also reported to occur irreversibly in hyperthermophile proteins. Therefore, conventional experimental approaches are often unsuited to the study of their unfolding. Here, we describe a novel electrophoretic approach that facilitates separation, direct visualization, and quantitation of the folded, partially folded, and unfolded forms of the hyperthermophile protein triosephosphate isomerase from Pyrococcus furiosus, produced in the course of its irreversible structural destabilization by the combined action of heat and chemical agents. Our approach exploits (i) the irreversibility of global unfolding effected by heat and denaturants such as urea or guanidine hydrochloride, (ii) the stability of the native form of the protein to unfolding by the anionic detergent sodium dodecyl sulfate, (iii) the differential susceptibilities of various protein conformations to being bound by SDS, and (iv) the differential electrophoretic migration behavior displayed as a consequence of differential SDS binding.
Collapse
|
32
|
Stirpe A, Guzzi R, Wijma H, Verbeet MP, Canters GW, Sportelli L. Calorimetric and spectroscopic investigations of the thermal denaturation of wild type nitrite reductase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1752:47-55. [PMID: 16085470 DOI: 10.1016/j.bbapap.2005.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2005] [Revised: 07/12/2005] [Accepted: 07/12/2005] [Indexed: 11/25/2022]
Abstract
Nitrite reductase (NiR) is a multicopper protein, with a trimeric structure containing two types of copper site: type 1 is present in each subunit whereas type 2 is localized at the subunits interface. The paper reports on the thermal behaviour of wild type NiR from Alcaligenes faecalis S-6. The temperature-induced changes of the copper centres are characterized by optical spectroscopy and electron paramagnetic resonance spectroscopy, and by establishing the thermal stability by differential scanning calorimetry. The calorimetric profile of the enzyme shows a single endothermic peak with maximum heat absorption at T(m) approximately 100 degrees C, revealing an exceptional thermal stability. The thermal transition is irreversible and the scan rate dependence of the calorimetric trace indicates that the denaturation of NiR is kinetically controlled. The divergence of the activation energy values determined by different methods is used as a criterion for the inapplicability of the one-step irreversible model. The best fit of the DSC profiles is obtained when the classical Lumry-Eyring model, N<-->U-->F, is considered. The simulation results indicate that the irreversible step prevails on the reversible one. Moreover, it is found that the conformational changes within the type-1 copper environments precede the denaturation of the whole protein. No evidence of protein dissociation within the temperature range investigated was observed.
Collapse
Affiliation(s)
- Andrea Stirpe
- Dipartimento di Fisica e Unità INFM, Laboratorio di Biofisica Molecolare, Università della Calabria, Ponte P. Bucci-Cubo 31C, I-87036, Arcavacata di Rende (CS), Italy
| | | | | | | | | | | |
Collapse
|
33
|
LeMaster DM, Tang J, Paredes DI, Hernández G. Enhanced thermal stability achieved without increased conformational rigidity at physiological temperatures: Spatial propagation of differential flexibility in rubredoxin hybrids. Proteins 2005; 61:608-16. [PMID: 16130131 DOI: 10.1002/prot.20594] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The extreme thermal stability of proteins from hyperthermophilic organisms is widely believed to arise from an increased conformational rigidity in the native state. In apparent contrast to this paradigm, both Pyrococcus furiosus (Pf) rubredoxin, the most thermostable protein characterized to date, and its Clostridium pasteurianum (Cp) mesophile homolog undergo a transient conformational opening of their multi-turn segments, which is more favorable in hyperthermophile proteins below room temperature. Substitution of the hyperthermophile multi-turn sequence into the mesophile protein sequence yields a hybrid, (14-33(Pf)) Cp, that exhibits a 12 degrees increase in its reversible thermal unfolding transition midpoint. Nuclear magnetic resonance (NMR) magnetization transfer-based hydrogen exchange was used to monitor backbone conformational dynamics in the subsecond time regime. Despite the substantially increased thermostability, flexibility throughout the entire main chain of the more thermostable hybrid is equal to or greater than that of the wild type mesophile rubredoxin near its normal growth temperature. In comparison to the identical core residues of the (14-33(Pf)) Cp rubredoxin hybrid, six spatially clustered residues in the parental mesophile protein exhibit a substantially larger temperature dependence of exchange. The exchange behavior of these six residues closely matches that observed in the multi-turn segment, consistent with a more extensive conformational process. These six core residues exhibit a much weaker temperature dependence of exchange in the (14-33(Pf)) Cp hybrid, similar to that observed for the multi-turn segment in its parental Pf rubredoxin. These results suggest that differential temperature dependence of flexibility can underlie variations in thermostability observed for mesophile versus hyperthermophile homologs.
Collapse
Affiliation(s)
- David M LeMaster
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, University at Albany- SUNY, 12201-0509, USA
| | | | | | | |
Collapse
|
34
|
LeMaster DM, Tang J, Paredes DI, Hernández G. Contribution of the multi-turn segment in the reversible thermal stability of hyperthermophile rubredoxin: NMR thermal chemical exchange analysis of sequence hybrids. Biophys Chem 2005; 116:57-65. [PMID: 15911082 DOI: 10.1016/j.bpc.2005.01.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2004] [Revised: 01/27/2005] [Accepted: 01/31/2005] [Indexed: 11/21/2022]
Abstract
Pyrococcus furiosus (Pf) rubredoxin is the most thermostable protein characterized to date. Reflecting the complications arising from irreversible denaturation of this protein, predictions of which structural regions confer differential thermal stability have utilized kinetic stability measurements, hydrogen exchange protection factors, long range hydrogen bond NMR spin couplings, and molecular dynamics simulations, and have primarily implicated the three-stranded beta-sheet and the adjacent metal binding site. Herein, NMR chemical exchange experiments demonstrate reversible two-state unfolding at the thermal transition temperature (T(m)) for hybrids of Pf and the mesophile Clostridium pasteurianum (Cp) rubredoxins which interchange residues 14-33, the so-called multi-turn segment. This complementary pair of hybrid rubredoxins exhibits largely additive incremental thermal stabilizations vs. the parental proteins. Both stabilization free energy measurements as well as incremental T(m) values indicate that a minimum of 37% of the total differential thermal stability resides in this multi-turn segment. Such a proportionality between DeltaDeltaG and incremental T(m) values is predicted for hybrid pairs exhibiting thermodynamic additivity in which the differential stability is predominantly enthalpic.
Collapse
Affiliation(s)
- David M LeMaster
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, University at Albany-SUNY, Empire State Plaza, Albany, NY 12201-0509, USA
| | | | | | | |
Collapse
|
35
|
Tang J, Hernández G, LeMaster DM. Increased peptide deformylase activity for N-formylmethionine processing of proteins overexpressed in Escherichia coli: application to homogeneous rubredoxin production. Protein Expr Purif 2005; 36:100-5. [PMID: 15177290 DOI: 10.1016/j.pep.2004.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2004] [Revised: 03/08/2004] [Indexed: 11/17/2022]
Abstract
Deformylation of the initiator N-formylmethionine does not always proceed to completion for proteins overexpressed in Escherichia coli. To overcome this limitation, the def gene encoding the Escherichia coli peptide deformylase was cloned into the plysS plasmid under the tetracycline (Tc) promoter control. The efficiency of this constitutive level of peptide deformylase expression was demonstrated for the case of the rubredoxins from both mesophilic and hyperthermophilic organisms which normally retain a majority of their N-formyl terminal form. Indicating the potential structural/functional significance of residual formylation, the presence of a highly solvent exposed N-formyl group in rubredoxin is discernable in the amide NMR chemical shifts for the active site metal-coordinating cysteines more than 21A away.
Collapse
Affiliation(s)
- Jianzhong Tang
- Wadsworth Center, New York State Department of Health, University at Albany-SUNY, Empire State Plaza, P.O. Box 509, 12201-0509, USA
| | | | | |
Collapse
|
36
|
Kurihara K, Tanaka I, Chatake T, Adams MWW, Jenney FE, Moiseeva N, Bau R, Niimura N. Neutron crystallographic study on rubredoxin from Pyrococcus furiosus by BIX-3, a single-crystal diffractometer for biomacromolecules. Proc Natl Acad Sci U S A 2004; 101:11215-20. [PMID: 15272083 PMCID: PMC509186 DOI: 10.1073/pnas.0403807101] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2003] [Indexed: 11/18/2022] Open
Abstract
The structure of a partially deuterated rubredoxin from the hyperthermophilic archaeon Pyrococcus furiosus, an organism that grows optimally at 100 degrees C, was determined by using the neutron single-crystal diffractometer dedicated for biological macromolecules (BIX-3) at the JRR-3M reactor of the Japan Atomic Energy Research Institute. Data were collected at room temperature up to a resolution of 1.5 A, and the completeness factor of the data set was 81.9%. The model contains 306 H and 50 D atoms. A total of 37 hydration water molecules were identified, with 15 having all three atoms fully located and the remaining D2O molecules partially defined. The model has been refined to final agreement factors of R = 18.6% and Rfree = 21.7%. Several orientations of the O-D bonds of side chains, whose assignments from x-ray data were previously ambiguous, were clearly visible in the neutron structure. Although most backbone N-H bonds had undergone some degree of H/D exchange throughout the rubredoxin molecule, 5 H atom positions still had distinctly negative (H) peaks. The neutron Fourier maps clearly showed the details of an extensive set of H bonds involving the ND3+ terminus that may contribute to the unusual thermostability of this molecule.
Collapse
Affiliation(s)
- Kazuo Kurihara
- Neutron Science Research Center, Japan Atomic Energy Research Institute, Tokai, Ibaraki 319-1195, Japan
| | | | | | | | | | | | | | | |
Collapse
|
37
|
LeMaster DM, Tang J, Hernández G. Absence of kinetic thermal stabilization in a hyperthermophile rubredoxin indicated by 40 microsecond folding in the presence of irreversible denaturation. Proteins 2004; 57:118-27. [PMID: 15326598 DOI: 10.1002/prot.20181] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The striking kinetic stability of many proteins derived from hyperthermophilic organisms has led to the proposal that such stability may result from a heightened activation barrier for unfolding independent of a corresponding increase in the thermodynamic stability. This in turn implies a corresponding retardation of the folding reaction. A commonly cited model for kinetic thermal stabilization is the rubredoxin from Pyrococcus furiosus (Pf), which exhibits an irreversible denaturation lifetime at 100 degrees C of nearly a week. Utilizing protein resonances shifted well outside of the random coil chemical shift envelope, nuclear magnetic resonance (NMR) chemical exchange measurements on Pf rubredoxin as well as on the mesophile Clostridium pasteurianum (Cp) rubredoxin demonstrate reversible thermal transition temperatures of 144 degrees C (137 degrees C for the N-terminal modified A2K variant) and 104 degrees C, respectively, with similar (un)folding rates of approximately 25,000 s(-1), only modestly slower than the diffusion controlled rate. The absence of a substantial activation barrier to rubredoxin folding as well as the similar folding kinetics of the mesophile protein indicate that kinetic stabilization has not been utilized by the hyperthermophile rubredoxin in achieving its extreme thermal stability. The two-state folding kinetics observed for Pf rubredoxin contradict a previous assertion of multiphasic folding based on hydrogen exchange data extrapolated to an estimated midpoint of transition temperature (T(m)) of nearly 200 degrees C. This discrepancy is resolved by the observation that the base-catalyzed hydrogen exchange of the model dipeptide (N-acetyl-L-cysteine-N-methylamide)4-Cd2+ is 23-fold slower than that of the free cysteine model dipeptide used to normalize the Pf rubredoxin hydrogen exchange data.
Collapse
Affiliation(s)
- David M LeMaster
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, University at Albany-SUNY, Empire State Plaza, Albany, New York 12201-0509, USA
| | | | | |
Collapse
|
38
|
Bonomi F, Eidsness MK, Iametti S, Kurtz DM, Mazzini S, Morleo A. Contribution of the [FeII(SCys)4] site to the thermostability of rubredoxins. J Biol Inorg Chem 2004; 9:297-306. [PMID: 14770302 DOI: 10.1007/s00775-004-0525-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2003] [Accepted: 01/12/2004] [Indexed: 10/26/2022]
Abstract
The thermostabilities of Fe(2+) ligation in rubredoxins (Rds) from the hyperthermophile Pyrococcus furiosus (Pf) and the mesophiles Clostridium pasteurianum (Cp) and Desulfovibrio vulgaris (Dv) were compared. Residue 44 forms an NH.S(Cys) hydrogen bond to one of the cysteine ligands to the [Fe(SCys)(4)] site, and substitutions at this location affect the redox properties of the [Fe(SCys)(4)] site. Both Pf Rd and Dv Rd have an alanine residue at position 44, whereas Cp Fd has a valine residue. Wild-type proteins were examined along with V44A and A44V "exchange" mutants of Cp and Pf Rds, respectively, in order to assess the effects of the residue at position 44 on the stability of the [Fe(SCys)(4)] site. Stability of iron ligation was measured by temperature-ramp and fixed-temperature time course experiments, monitoring iron release in both the absence and presence of more thiophilic metals (Zn(2+), Cd(2+)) and over a range of pH values. The thermostability of the polypeptide fold was concomitantly measured by fluorescence, circular dichroism, and (1)H NMR spectroscopies. The A44V mutation strongly lowered the stability of the [Fe(II)(SCys)(4)] site in Pf Rd, whereas the converse V44A mutation of Cp Rd significantly raised the stability of the [Fe(II)(SCys)(4)] site, but not to the levels measured for wild-type Dv Rd. The region around residue 44 is thus a significant contributor to stability of iron coordination in reduced Rds. This region, however, made only a minor contribution to the thermostability of the protein folding, which was found to be higher for hyperthermophilic versus mesophilic Rds, and largely independent of the residue at position 44. These results, together with our previous studies, show that localized charge density, solvent accessibility, and iron site/backbone interactions control the thermostability of the [Fe(SCys)(4)] site. The iron site thermostability does make a minor contribution to the overall Rd thermostability. From a mechanistic standpoint, we also found that attack of displacing ions (H(+), Cd(2+)) on the Cys42 sulfur ligand at the [Fe(SCys)(4)] site occurs through the V8 side and not the V44 side of the iron site.
Collapse
|
39
|
Lamosa P, Turner DL, Ventura R, Maycock C, Santos H. Protein stabilization by compatible solutes. ACTA ACUST UNITED AC 2003; 270:4606-14. [PMID: 14622247 DOI: 10.1046/j.1432-1033.2003.03861.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Heteronuclear NMR relaxation measurements and hydrogen exchange data have been used to characterize protein dynamics in the presence or absence of stabilizing solutes from hyperthermophiles. Rubredoxin from Desulfovibrio gigas was selected as a model protein and the effect of diglycerol phosphate on its dynamic behaviour was studied. The presence of 100 mM diglycerol phosphate induces a fourfold increase in the half-life for thermal denaturation of D. gigas rubredoxin. A model-free analysis of the protein backbone relaxation parameters shows an average increase of generalized order parameters of 0.015 reflecting a small overall reduction in mobility of fast-scale motions. Hydrogen exchange data acquired over a temperature span of 20 degrees C yielded thermodynamic parameters for the structural opening reactions that allow for the exchange. This shows that the closed form of the protein is stabilized by an additional 1.6 kJ x mol(-1) in the presence of the solute. The results seem to indicate that the stabilizing effect is due mainly to a reduction in mobility of the slower, larger-scale motions within the protein structure with an associated increase in the enthalpy of interactions.
Collapse
Affiliation(s)
- Pedro Lamosa
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | | | | | | | | |
Collapse
|
40
|
Maity H, Lim WK, Rumbley JN, Englander SW. Protein hydrogen exchange mechanism: local fluctuations. Protein Sci 2003; 12:153-60. [PMID: 12493838 PMCID: PMC2312409 DOI: 10.1110/ps.0225803] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2002] [Revised: 10/01/2002] [Accepted: 10/03/2002] [Indexed: 10/27/2022]
Abstract
Experiments were done to study the dynamic structural motions that determine protein hydrogen exchange (HX) behavior. The replacement of a solvent-exposed lysine residue with glycine (Lys8Gly) in a helix of recombinant cytochrome c does not perturb the native structure, but it entropically potentiates main-chain flexibility and thus can promote local distortional motions and large-scale unfolding. The mutation accelerates amide hydrogen exchange of the mutated residue by about 50-fold, neighboring residues in the same helix by less, and residues elsewhere in the protein not at all, except for Leu98, which registers the change in global stability. The pattern of HX changes shows that the coupled structural distortions that dominate exchange can be several residues in extent, but they expose to exchange only one amide NH at a time. This "local fluctuation" mode of hydrogen exchange may be generally recognized by disparate near-neighbor rates and a low dependence on destabilants (denaturant, temperature, pressure). In contrast, concerted unfolding reactions expose multiple neighboring amide NHs with very similar computed protection factors, and they show marked destabilant sensitivity. In both modes, ionic hydrogen exchange catalysts attack from the bulk solvent without diffusing through the protein matrix.
Collapse
Affiliation(s)
- Haripada Maity
- The Johnson Research Foundation, Department of Biochemistry & Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
| | | | | | | |
Collapse
|
41
|
Englander SW, Mayne L, Rumbley JN. Submolecular cooperativity produces multi-state protein unfolding and refolding. Biophys Chem 2002; 101-102:57-65. [PMID: 12487989 DOI: 10.1016/s0301-4622(02)00190-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Hydrogen exchange experiments show that cytochrome c and other proteins under native conditions reversibly unfold in a multi-step manner. The step from one intermediate to the next is determined by the intrinsically cooperative nature of secondary structural elements, which is retained in the native protein. Folding uses the same pathway in the reverse direction, moving from the unfolded to the native state through relatively discrete intermediate forms by the sequential addition of native-like secondary structural units.
Collapse
Affiliation(s)
- S Walter Englander
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6059, USA.
| | | | | |
Collapse
|
42
|
Blond A, Cheminant M, Destoumieux-Garzón D, Ségalas-Milazzo I, Peduzzi J, Goulard C, Rebuffat S. Thermolysin-linearized microcin J25 retains the structured core of the native macrocyclic peptide and displays antimicrobial activity. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:6212-22. [PMID: 12473117 DOI: 10.1046/j.1432-1033.2002.03340.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Microcin J25 (MccJ25) is the single macrocyclic antimicrobial peptide belonging to the ribosomally synthesized class of microcins that are secreted by Enterobacteriaceae. It showed potent antibacterial activity against several Salmonella and Escherichia strains and exhibited a compact three-dimensional structure [Blond et al. (2001) Eur. J. Biochem., 268, 2124-2133]. The molecular mechanisms involved in the biosynthesis, folding and mode of action of MccJ25 are still unknown. We have investigated the structure and the antimicrobial activity of thermolysin-linearized MccJ25 (MccJ25-L1-21: VGIGTPISFY10GGGAGHVPEY20F), as well as two synthetic analogs, sMccJ25-L1-21 (sequence of the thermolysin-cleaved MccJ25) and sMccJ25-L12-11 (C-terminal sequence of the MccJ25 precursor: G12GAGHVPEYF21V1GIGTPISFYG11). The three-dimensional solution structure of MccJ25-L1-21, determined by two-dimensional NMR, consists of a boot-shaped hairpin-like well-defined 8-19 region flanked by disordered N and C termini. This structure is remarkably similar to that of cyclic MccJ25, and includes a short double-stranded antiparallel beta-sheet (8-10/17-19) perpendicular to a loop (Gly11-His16). The thermolysin-linearized MccJ25-L1-21 had antibacterial activity against E. coli and S. enteritidis strains, while both synthetic analogues lacked activity and organized structure. We show that the 8-10/17-19 beta-sheet, as well as the Gly11-His16 loop are required for moderate antibacterial activity and that the Phe21-Pro6 loop and the MccJ25 macrocyclic backbone are necessary for complete antibacterial activity. We also reveal a highly stable 8-19 structured core present in both the native MccJ25 and the thermolysin-linearized peptide, which is maintained under thermolysin treatment and resists highly denaturing conditions.
Collapse
Affiliation(s)
- Alain Blond
- Laboratory of Chemistry and Biochemistry of Natural Substances, Department of Regulation, Development and Molecular Diversity, National Museum of Natural History, Paris, France
| | | | | | | | | | | | | |
Collapse
|
43
|
Higgins CL, Meyer J, Wittung-Stafshede P. Exceptional stability of a [2Fe-2S] ferredoxin from hyperthermophilic bacterium Aquifex aeolicus. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1599:82-9. [PMID: 12479408 DOI: 10.1016/s1570-9639(02)00405-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aquifex aeolicus is the only hyperthermophile that is known to contain a plant- and mammalian-type [2Fe-2S] ferredoxin (Aae Fd1). This unique protein contains two cysteines, in addition to the four that act as ligands of the [2Fe-2S] cluster, which form a disulfide bridge. We have investigated the stability of Aae Fd1 with (wild-type) and without (C87A variant) the disulfide bond, with respect to pH, thermal and chemical perturbation, and compared the results to those for the mesophilic [2Fe-2S] ferredoxin from spinach. Unfolding reactions of all three proteins are irreversible due to cluster decomposition in the unfolded state. Wild-type and C87A Aae Fd1 proteins are extremely stable: unfolding at 20 degrees C requires high concentrations of the chemical denaturant and long incubation times. Moreover, their thermal-unfolding midpoints are 40-50 degrees higher than that for spinach ferredoxin (pH 7). The stability of the Aae Fd1 protein is significantly lower at pH 2.5 than pH 7 and 10, suggesting that ionic interactions play a role in structural integrity. Interestingly, the iron-sulfur cluster in C87A Aae Fd1 rearranges into a transient species with absorption bands at 520 and 610 nm, presumably a linear three-iron cluster, in the high-pH unfolded state.
Collapse
Affiliation(s)
- Catherine L Higgins
- Department of Chemistry, Tulane University, 6823 St. Charles Avenue, New Orleans, LA 70118-5698, USA
| | | | | |
Collapse
|
44
|
Hoang L, Bedard S, Krishna MMG, Lin Y, Englander SW. Cytochrome c folding pathway: kinetic native-state hydrogen exchange. Proc Natl Acad Sci U S A 2002; 99:12173-8. [PMID: 12196629 PMCID: PMC129417 DOI: 10.1073/pnas.152439199] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Native-state hydrogen exchange experiments under EX1 conditions can distinguish partially unfolded intermediates by their formation rates and identify the amide hydrogens exposed and protected in each. Results obtained define a cytochrome c intermediate seen only poorly before and place it early on the major unfolding pathway. Four distinct unfolding steps are found to be kinetically ordered in the same pathway sequence inferred before.
Collapse
Affiliation(s)
- Linh Hoang
- The Johnson Research Foundation, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6059, USA.
| | | | | | | | | |
Collapse
|
45
|
Sadqi M, Casares S, López-Mayorga O, Conejero-Lara F. The temperature dependence of the hydrogen exchange in the SH3 domain of alpha-spectrin. FEBS Lett 2002; 527:86-90. [PMID: 12220639 DOI: 10.1016/s0014-5793(02)03172-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The amide hydrogen-deuterium exchange (HX) in the Src homology region 3 (SH3) domain of alpha-spectrin has been measured by nuclear magnetic resonance as a function of temperature between 8 and 46 degrees C. The analysis of the temperature dependence of HX from a statistical thermodynamic point of view has allowed us to estimate the enthalpies and entropies of the conformational processes leading to HX. The results indicate that under native conditions the domain undergoes a wide variety of conformational fluctuations, ranging from local motions, mainly located in loops, turns and chain ends and involving only low enthalpy and entropy, to extensive structural disruptions affecting its core and involving enthalpies and entropies that come fairly close to those observed during global unfolding.
Collapse
Affiliation(s)
- M Sadqi
- Departamento de Qui;mica Fi;sica e Instituto de Biotecnologi;a, Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain.
| | | | | | | |
Collapse
|
46
|
Hernández G, Teng CL, Bryant RG, LeMaster DM. O2 penetration and proton burial depth in proteins: applicability to fold family recognition. J Am Chem Soc 2002; 124:4463-72. [PMID: 11960476 DOI: 10.1021/ja017340k] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Paramagnetically induced relaxation effects of O2 and the nitroxide 4-hydroxy TEMPO were measured for the amide protons of perdeuterated rubredoxin from the hyperthermophilic archaeon Pyrococcus furiosus and the mesophilic bacterium Clostridium pasteurianum. For both O2 and the impermeant nitroxide, the induced relaxation at the static solvent inaccessible amide sites is dominated by long-range interactions with the paramagnetic species in the bulk aqueous phase. The upper bound of O2 solubility in the internal matrix of the rubredoxins is one-tenth that of the bulk aqueous phase. Furthermore, the difference between the oxygen solubilities inside the two rubredoxins is at most 1% that of bulk water O2 solubility, suggesting that there are only modest differences in this measure of fluidity for the mesophile vs hyperthermophile protein interiors. Calculations based on the assumption of a paramagnet uniformly distributed on the protein exterior yield accurate predictions at nearly all amide sites for the minimum relaxation value observed from either the O2 or nitroxide data. Model calculations indicate that the readily obtained paramagnetically induced relaxation effects should prove effective in recognition of structural homology for proteins that are too widely diverged for sequence-based recognition.
Collapse
Affiliation(s)
- Griselda Hernández
- Wadsworth Center and Department of Biomedical Sciences, University at Albany-SUNY, Empire State Plaza, Albany, New York 12201-0509, USA
| | | | | | | |
Collapse
|
47
|
Sadqi M, Casares S, López-Mayorga O, Martínez JC, Conejero-Lara F. pH dependence of the hydrogen exchange in the SH3 domain of alpha-spectrin. FEBS Lett 2002; 514:295-9. [PMID: 11943169 DOI: 10.1016/s0014-5793(02)02385-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Using nuclear magnetic resonance we have measured the hydrogen exchange (HX) in the Src homology region 3 (SH3) domain of alpha-spectrin as a function of pH*. At very acidic pH* values the exchange of most residues appears to occur via global unfolding, although several residues show abnormally large Gibbs energies of exchange, suggesting the presence of some residual structure in the unfolded state. At higher pH* HX occurs mainly via local or partial unfoldings. We have been able to characterize the coupling between the electrostatic interactions in this domain and the conformational fluctuations occurring under native conditions by analyzing the dependence upon pH* of the Gibbs energy of exchange. The SH3 domain seems to be composed of a central core, which requires large structural disruptions to become exposed to the solvent, surrounded by smaller subdomains, which fluctuate independently.
Collapse
Affiliation(s)
- M Sadqi
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | | | | | | | | |
Collapse
|
48
|
Zhong D, Pal SK, Zhang D, Chan SI, Zewail AH. Femtosecond dynamics of rubredoxin: tryptophan solvation and resonance energy transfer in the protein. Proc Natl Acad Sci U S A 2002; 99:13-8. [PMID: 11752400 PMCID: PMC117505 DOI: 10.1073/pnas.012582399] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2001] [Indexed: 11/18/2022] Open
Abstract
We report here studies of tryptophan (Trp) solvation dynamics in water and in the Pyrococcus furiosus rubredoxin protein, including the native and its apo and denatured forms. We also report results on energy transfer from Trp to the iron-sulfur [Fe-S] cluster. Trp fluorescence decay with the onset of solvation dynamics of the chromophore in water was observed with femtosecond resolution ( approximately 160 fs; 65% component), but the emission extended to the picosecond range (1.1 ps; 35% component). In contrast, the decay is much slower in the native rubredoxin; the Trp fluorescence decay extends to 10 ps and longer, reflecting the local rigidity imposed by residues and by the surface water layer. The dynamics of resonance energy transfer from the two Trps to the [Fe-S] cluster in the protein was observed to follow a temporal behavior characterized by a single exponential (15-20 ps) decay. This unusual observation in a protein indicates that the resonance transfer is to an acceptor of a well-defined orientation and separation. From studies of the mutant protein, we show that the two Trp residues have similar energy-transfer rates. The critical distance for transfer (R(0)) was determined, by using the known x-ray data, to be 19.5 A for Trp-36 and 25.2 A for Trp-3, respectively. The orientation factor (kappa(2)) was deduced to be 0.13 for Trp-36, clearly indicating that molecular orientation of chromophores in the protein cannot be isotropic with kappa(2) value of 2/3. These studies of solvation and energy-transfer dynamics, and of the rotational anisotropy, of the wild-type protein, the (W3Y, I23V, L32I) mutant, and the fmetPfRd variant at various pH values reveal a dynamically rigid protein structure, which is probably related to the hyperthermophilicity of the protein.
Collapse
Affiliation(s)
- Dongping Zhong
- Laboratory for Molecular Sciences, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | | | | | | | | |
Collapse
|
49
|
Motono C, Oshima T, Yamagishi A. High thermal stability of 3-isopropylmalate dehydrogenase from Thermus thermophilus resulting from low DeltaC(p) of unfolding. Protein Eng Des Sel 2001; 14:961-6. [PMID: 11809926 DOI: 10.1093/protein/14.12.961] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To characterize the thermal stability of 3-isopropylmalate dehydrogenase (IPMDH) from an extreme thermophile, Thermus thermophilus, urea-induced unfolding of the enzyme and of its mesophilic counterpart from Escherichia coli was investigated at various temperatures. The unfolding curves were analyzed with a three-state model for E.coli IPMDH and with a two-state model for T.thermophilus IPMDH, to obtain the free energy change DeltaG degrees of each unfolding process. Other thermodynamic parameters, enthalpy change DeltaH, entropy change DeltaS and heat capacity change DeltaC(p), were derived from the temperature dependence of DeltaG degrees. The main feature of the thermophilic enzyme was its lower dependence of DeltaG degrees on temperature resulting from a low DeltaC(p). The thermophilic IPMDH had a significantly lower DeltaC(p), 1.73 kcal/mol.K, than that of E.coli IPMDH (20.7 kcal/mol.K). The low DeltaC(p) of T.thermophilus IPMDH could not be predicted from its change in solvent-accessible surface area DeltaASA. The results suggested that there is a large structural difference between the unfolded state of T.thermophilus and that of E.coli IPMDH. Another responsible factor for the higher thermal stability of T.thermophilus IPMDH was the increase in the most stable temperature T(s). The DeltaG degrees maximum of T.thermophilus IPMDH was much smaller than that of E.coli IPMDH. The present results clearly demonstrated that a higher melting temperature T(m) is not necessarily accompanied by a higher DeltaG degrees maximum.
Collapse
Affiliation(s)
- C Motono
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | | | | |
Collapse
|
50
|
Feng Z, Butler MC, Alam SL, Loh SN. On the nature of conformational openings: native and unfolded-state hydrogen and thiol-disulfide exchange studies of ferric aquomyoglobin. J Mol Biol 2001; 314:153-66. [PMID: 11724540 DOI: 10.1006/jmbi.2001.5117] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Native-state amide hydrogen exchange (HX) of proteins in the presence of denaturant has provided valuable details on the structures of equilibrium folding intermediates. Here, we extend HX theory to model thiol group exchange (SX) in single cysteine-containing variants of sperm whale ferric aquomyoglobin. SX is complementary to HX in that it monitors conformational opening events that expose side-chains, rather than the main chain, to solvent. A simple two-process model, consisting of EX2-limited local structural fluctuations and EX1-limited global unfolding, adequately accounts for all HX data. SX is described by the same model except at very low denaturant concentrations and when the bulky labeling reagent 5,5'-dithiobis (2-nitrobenzoic acid) (DTNB) is used. Under these conditions SX can occur by a novel denaturant-dependent process. This anomalous behavior is not observed when the smaller labeling reagent methyl methanethiosulfonate is employed, suggesting that it reflects a denaturant-induced increase in the amplitudes of local structural fluctuations. It also is not seen in heme-free apomyoglobin, which may indicate that local openings are sufficiently large in the absence of denaturant to allow DTNB unhindered access. Differences in SX kinetics obtained using the two labeling reagents provide estimates of the sizes of local opening reactions at different sites in the protein. At all sequence positions examined except for position 73, the same opening event appears to facilitate exchange of both backbone amide and side-chain thiol groups. The C73 thiol group is exposed by a low-energy fluctuation that does not expose its amide group to exchange.
Collapse
Affiliation(s)
- Z Feng
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 E. Adams Street, Syracuse, NY 13210, USA
| | | | | | | |
Collapse
|