1
|
Chakravorty D, Khan MF, Patra S. Multifactorial level of extremostability of proteins: can they be exploited for protein engineering? Extremophiles 2017; 21:419-444. [PMID: 28283770 DOI: 10.1007/s00792-016-0908-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 12/19/2016] [Indexed: 12/20/2022]
Abstract
Research on extremostable proteins has seen immense growth in the past decade owing to their industrial importance. Basic research of attributes related to extreme-stability requires further exploration. Modern mechanistic approaches to engineer such proteins in vitro will have more impact in industrial biotechnology economy. Developing a priori knowledge about the mechanism behind extreme-stability will nurture better understanding of pathways leading to protein molecular evolution and folding. This review is a vivid compilation about all classes of extremostable proteins and the attributes that lead to myriad of adaptations divulged after an extensive study of 6495 articles belonging to extremostable proteins. Along with detailing on the rationale behind extreme-stability of proteins, emphasis has been put on modern approaches that have been utilized to render proteins extremostable by protein engineering. It was understood that each protein shows different approaches to extreme-stability governed by minute differences in their biophysical properties and the milieu in which they exist. Any general rule has not yet been drawn regarding adaptive mechanisms in extreme environments. This review was further instrumental to understand the drawback of the available 14 stabilizing mutation prediction algorithms. Thus, this review lays the foundation to further explore the biophysical pleiotropy of extreme-stable proteins to deduce a global prediction model for predicting the effect of mutations on protein stability.
Collapse
Affiliation(s)
- Debamitra Chakravorty
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Mohd Faheem Khan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Sanjukta Patra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
| |
Collapse
|
2
|
Alemasov NA, Ivanisenko NV, Medvedev SP, Zakian SM, Kolchanov NA, Ivanisenko VA. Dynamic properties of SOD1 mutants can predict survival time of patients carrying familial amyotrophic lateral sclerosis. J Biomol Struct Dyn 2016; 35:645-656. [DOI: 10.1080/07391102.2016.1158666] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nikolay A. Alemasov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nikita V. Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Laboratory of Molecular Epidemiology and Bioinformatics, Novosibirsk State University, Novosibirsk, Russia
| | - Sergey P. Medvedev
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Suren M. Zakian
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nikolay A. Kolchanov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Vladimir A. Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| |
Collapse
|
3
|
Miao Y, Baudry J, Smith JC, McCammon JA. General trends of dihedral conformational transitions in a globular protein. Proteins 2016; 84:501-14. [PMID: 26799251 DOI: 10.1002/prot.24996] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/28/2015] [Accepted: 01/08/2016] [Indexed: 11/06/2022]
Abstract
Dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and adaptive biasing force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions approximately two times faster on average using dihedral boost, and ∼ 3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the bend, coil, and turn flexible regions, followed by the β bridge and β sheet, and then the helices. Moreover, protein side chains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Side chains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. These general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins.
Collapse
Affiliation(s)
- Yinglong Miao
- Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California, 92093.,Department of Pharmacology, University of California at San Diego, La Jolla, California, 92093
| | - Jerome Baudry
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Jeremy C Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - J Andrew McCammon
- Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California, 92093.,Department of Pharmacology, University of California at San Diego, La Jolla, California, 92093.,Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, 92093
| |
Collapse
|
4
|
Kondratyev MS, Kabanov AV, Kholyavka MG, Sharapov MG, Khechinashvili NN. Computational grounding of point mutagenesis to enhance the thermostability of human peroxiredoxin 6. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916010115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
5
|
Murakami S, Oshima H, Hayashi T, Kinoshita M. On the physics of thermal-stability changes upon mutations of a protein. J Chem Phys 2015; 143:125102. [DOI: 10.1063/1.4931814] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Shota Murakami
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hiraku Oshima
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| |
Collapse
|
6
|
Khechinashvili NN, Capital Ka Cyrillicabanov AV, Kondratyev MS, Polozov RV. The entropic nature of protein thermal stabilization. J Biomol Struct Dyn 2013; 32:1396-405. [PMID: 23879480 DOI: 10.1080/07391102.2013.819788] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We performed thermodynamic analysis of temperature-induced unfolding of mesophilic and thermophilic proteins. It was shown that the variability in protein thermostability associated with pH-dependent unfolding or linked to the substitution of amino acid residues on the protein surface is evidence of the governing role of the entropy factor. Numerical values of conformational components in enthalpy, entropy and free energy which characterize protein unfolding in the "gas phase" were obtained. Based on the calculated absolute values of entropy and free energy, a model of protein unfolding is proposed in which the driving force is the conformational entropy of native protein, as an energy of the heat motion (T·S(NC)) increasing with temperature and acting as an factor devaluating the energy of intramolecular weak bonds in the transition state.
Collapse
Affiliation(s)
- Nikolay N Khechinashvili
- a Institute of Cell Biophysics, Russian Academy of Sciences , Pushchino, Moscow Region 142290 , Russia
| | | | | | | |
Collapse
|
7
|
Ruvinsky AM, Kirys T, Tuzikov AV, Vakser IA. Structure fluctuations and conformational changes in protein binding. J Bioinform Comput Biol 2012; 10:1241002. [PMID: 22809338 DOI: 10.1142/s0219720012410028] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Structure fluctuations and conformational changes accompany all biological processes involving macromolecules. The paper presents a classification of protein residues based on the normalized equilibrium fluctuations of the residue centers of mass in proteins and a statistical analysis of conformation changes in the side-chains upon binding. Normal mode analysis and an elastic network model were applied to a set of protein complexes to calculate the residue fluctuations and develop the residue classification. Comparison with a classification based on normalized B-factors suggests that the B-factors may underestimate protein flexibility in solvent. Our classification shows that protein loops and disordered fragments are enriched with highly fluctuating residues and depleted with weakly fluctuating residues. Strategies for engineering thermostable proteins are discussed. To calculate the dihedral angles distribution functions, the configuration space was divided into cells by a cubic grid. The effect of protein association on the distribution functions depends on the amino acid type and a grid step in the dihedral angles space. The changes in the dihedral angles increase from the near-backbone dihedral angle to the most distant one, for most residues. On average, one fifth of the interface residues change the rotamer state upon binding, whereas the rest of the interface residues undergo local readjustments within the same rotamer.
Collapse
Affiliation(s)
- Anatoly M Ruvinsky
- Center for Bioinformatics, University of Kansas, Lawrence, KS 66047, USA.
| | | | | | | |
Collapse
|
8
|
Permyakov SE, Vologzhannikova AA, Emelyanenko VI, Knyazeva EL, Kazakov AS, Lapteva YS, Permyakova ME, Zhadan AP, Permyakov EA. The impact of alpha-N-acetylation on structural and functional status of parvalbumin. Cell Calcium 2012; 52:366-76. [DOI: 10.1016/j.ceca.2012.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 05/30/2012] [Accepted: 06/01/2012] [Indexed: 01/09/2023]
|
9
|
Durdenko EV, Saburova EA. A special role of phosphate in the stability of lactate dehydrogenase against destruction by a polyelectrolyte. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2012. [DOI: 10.1134/s1068162012040061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
10
|
Kondrat’ev MS, Kabanov AV, Komarov VM, Khechinashvili NN, Samchenko AA. Experience in simulating the structural and dynamic features of small proteins using table supercomputers. Biophysics (Nagoya-shi) 2011. [DOI: 10.1134/s0006350911060108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
11
|
Kolombet VA. Calculation of the hydration energy of polyvalent metal ions by the RISM method. RUSS J INORG CHEM+ 2011. [DOI: 10.1134/s0036023611080110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
12
|
Kolombet VA, Frolov AI. Na+/K+ selectivity in the formation of ion pairs in aqueous solutions. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2011. [DOI: 10.1134/s1990793110060011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
13
|
Fedorov MV, Goodman JM, Nerukh D, Schumm S. Self-assembly of trehalose molecules on a lysozyme surface: the broken glass hypothesis. Phys Chem Chem Phys 2010; 13:2294-9. [PMID: 21116551 DOI: 10.1039/c0cp01705a] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To help understand how sugar interactions with proteins stabilise biomolecular structures, we compare the three main hypotheses for the phenomenon with the results of long molecular dynamics simulations on lysozyme in aqueous trehalose solution (0.75 M). We show that the water replacement and water entrapment hypotheses need not be mutually exclusive, because the trehalose molecules assemble in distinctive clusters on the surface of the protein. The flexibility of the protein backbone is reduced under the sugar patches supporting earlier findings that link reduced flexibility of the protein with its higher stability. The results explain the apparent contradiction between different experimental and theoretical results for trehalose effects on proteins.
Collapse
Affiliation(s)
- Maxim V Fedorov
- Max Planck Institute for Mathematics in the Sciences, Inselstr. 22-26, 04103 Leipzig, Germany
| | | | | | | |
Collapse
|
14
|
Kolombet VA. A study by RISM method of the features of the environment dielectric response on the hydration of monatomic ions. RUSS J GEN CHEM+ 2010. [DOI: 10.1134/s1070363210080062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
15
|
Kolombet VA, Sergievskii VP. The special features of the thermodynamic characteristics of hydration of univalent ions according to the reference interaction site model. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2010. [DOI: 10.1134/s0036024410090025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
16
|
Thermal stability of proteins does not correlate with the energy of intramolecular interactions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1830-4. [DOI: 10.1016/j.bbapap.2008.07.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Revised: 07/07/2008] [Accepted: 07/09/2008] [Indexed: 11/20/2022]
|