1
|
Synergistic effects between the additions of a disulphide bridge and an N-terminal hydrophobic sidechain on the binding pocket tilting and enhanced Xyn11A activity. Arch Biochem Biophys 2019; 672:108068. [DOI: 10.1016/j.abb.2019.108068] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/20/2019] [Accepted: 08/07/2019] [Indexed: 11/22/2022]
|
2
|
Paloni JM, Miller EA, Sikes HD, Olsen BD. Improved Ordering in Low Molecular Weight Protein-Polymer Conjugates Through Oligomerization of the Protein Block. Biomacromolecules 2018; 19:3814-3824. [PMID: 30132651 DOI: 10.1021/acs.biomac.8b00928] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The self-assembly of protein-polymer conjugates incorporating oligomers of a small, engineered high-affinity binding protein, rcSso7d.SA, is studied to determine the effect of protein oligomerization on nanoscale ordering. Oligomerization enables a systematic increase in the protein molar mass without changing its overall folded structure, leading to a higher driving force for self-assembly into well-ordered structures. Though conjugates of monomeric rcSso7d.SA are found to only exist in disordered states, oligomers of this protein linked to a poly( N-isopropylacrylamide) (PNIPAM) block self-assemble into lamellar nanostructures. Conjugates of trimeric and tetrameric rcSso7d.SA are observed to produce the strongest ordering in concentrated solution, displaying birefringent lamellae at concentrations as low as 40 wt %. In highly concentrated solution, the oligomeric rcSso7d.SA-PNIPAM block copolymers exhibit ordering and domain spacing trends atypical from that of most block copolymers. Fluorescent binding assays indicate that oligomerized protein blocks retain binding functionality and exhibit limits of detection up to three times lower than that of surface-immobilized protein sensors. Therefore, oligomerization of the protein block in these block copolymers serves as an effective method to improve both nanoscale ordering and biosensing capabilities.
Collapse
Affiliation(s)
- Justin M Paloni
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Eric A Miller
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Hadley D Sikes
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Bradley D Olsen
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| |
Collapse
|
3
|
pH driven fibrillar aggregation of the super-sweet protein Y65R-MNEI: A step-by-step structural analysis. Biochim Biophys Acta Gen Subj 2018; 1862:808-815. [DOI: 10.1016/j.bbagen.2017.12.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 12/14/2017] [Accepted: 12/22/2017] [Indexed: 11/22/2022]
|
4
|
Sutthibutpong T, Rattanarojpong T, Khunrae P. Effects of helix and fingertip mutations on the thermostability of xyn11A investigated by molecular dynamics simulations and enzyme activity assays. J Biomol Struct Dyn 2017; 36:3978-3992. [DOI: 10.1080/07391102.2017.1404934] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Thana Sutthibutpong
- Theoretical and Computational Physics Group, Department of Physics, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand
- Theoretical and Computational Science Center (TaCS), Science Laboratory Building, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand
| | - Triwit Rattanarojpong
- Department of Microbiology, Science Laboratory Building, Faculty of Science, King Mongkut’s University of Technology Thonburi, 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand
| | - Pongsak Khunrae
- Department of Microbiology, Science Laboratory Building, Faculty of Science, King Mongkut’s University of Technology Thonburi, 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand
| |
Collapse
|
5
|
Kalichuk V, Renodon-Cornière A, Béhar G, Carrión F, Obal G, Maillasson M, Mouratou B, Préat V, Pecorari F. A novel, smaller scaffold for Affitins: Showcase with binders specific for EpCAM. Biotechnol Bioeng 2017; 115:290-299. [DOI: 10.1002/bit.26463] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 09/17/2017] [Accepted: 09/25/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Valentina Kalichuk
- CRCINA, Inserm, CNRS, Université d'Angers; Université de Nantes; Nantes France
- Université Catholique de Louvain; Louvain Drug Research Institute; Advanced Drug Delivery and Biomaterials; Brussels Belgium
| | | | - Ghislaine Béhar
- CRCINA, Inserm, CNRS, Université d'Angers; Université de Nantes; Nantes France
| | - Federico Carrión
- Institut Pasteur de Montevideo; Protein Biophysics Unit; Montevideo Uruguay
| | - Gonzalo Obal
- Institut Pasteur de Montevideo; Protein Biophysics Unit; Montevideo Uruguay
| | - Mike Maillasson
- CRCINA, Inserm, CNRS, Université d'Angers; Université de Nantes; Nantes France
- Impact, CRCINA, Inserm, CNRS; Université d'Angers; Université de Nantes; Nantes France
| | - Barbara Mouratou
- CRCINA, Inserm, CNRS, Université d'Angers; Université de Nantes; Nantes France
| | - Véronique Préat
- Université Catholique de Louvain; Louvain Drug Research Institute; Advanced Drug Delivery and Biomaterials; Brussels Belgium
| | - Frédéric Pecorari
- CRCINA, Inserm, CNRS, Université d'Angers; Université de Nantes; Nantes France
| |
Collapse
|
6
|
Vashist A, Prithvi Raj D, Gupta UD, Bhat R, Tyagi JS. The α10 helix of DevR, the Mycobacterium tuberculosis dormancy response regulator, regulates its DNA binding and activity. FEBS J 2016; 283:1286-99. [PMID: 26799615 DOI: 10.1111/febs.13664] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 01/05/2016] [Accepted: 01/18/2016] [Indexed: 11/26/2022]
Abstract
The crystal structures of several bacterial response regulators provide insight into the various interdomain molecular interactions potentially involved in maintaining their 'active' or 'inactive' states. However, the requirement of high concentrations of protein, an optimal pH and ionic strength buffers during crystallization may result in a structure somewhat different from that observed in solution. Therefore, functional assessment of the physiological relevance of the crystal structure data is imperative. DevR/DosR dormancy regulator of Mycobacterium tuberculosis (Mtb) belongs to the NarL subfamily of response regulators. The crystal structure of unphosphorylated DevR revealed that it forms a dimer through the α5/α6 interface. It was proposed that phosphorylation may trigger extensive structural rearrangements in DevR that culminate in the formation of a DNA-binding competent dimeric species via α10-α10 helix interactions. The α10 helix-deleted DevR protein (DevR∆α10 ) was hyperphosphorylated but defective with respect to in vitro DNA binding. Biophysical characterization reveals that DevR∆α10 has an open but less stable conformation. The combined cross-linking and DNA-binding data demonstrate that the α10 helix is essential for the formation and stabilization of the DNA-binding proficient DevR structure in both the phosphorylated and unphosphorylated states. Genetic studies establish that Mtb strains expressing DevR∆α10 are defective with respect to dormancy regulon expression under hypoxia. The present study highlights the indispensable role of the α10 helix in DevR activation and function under hypoxia and establishes the α10-α10 helix interface as a novel target for developing inhibitors against DevR, a key regulator of hypoxia-triggered dormancy.
Collapse
Affiliation(s)
- Atul Vashist
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India.,Experimental Animal Facility, National JALMA Institute of Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, India
| | - D Prithvi Raj
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Umesh Datta Gupta
- Experimental Animal Facility, National JALMA Institute of Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, India
| | - Rajiv Bhat
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Jaya Sivaswami Tyagi
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
7
|
Kumar K, Patel K, Agrawal DC, Khire JM. Insights into the unfolding pathway and identification of thermally sensitive regions of phytase from Aspergillus niger by molecular dynamics simulations. J Mol Model 2015; 21:163. [PMID: 26037148 DOI: 10.1007/s00894-015-2696-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 05/04/2015] [Indexed: 11/29/2022]
Abstract
Thermal stability is of great importance in the application of commercial phytases. Phytase A (PhyA) is a monomeric protein comprising twelve α-helices and ten β-sheets. Comparative molecular dynamics (MD) simulations (at 310, 350, 400, and 500 K) revealed that the thermal stability of PhyA from Aspergillus niger (A. niger) is associated with its conformational rigidity. The most thermally sensitive regions were identified as loops 8 (residues 83-106), 10 (161-174), 14 (224-230), 17 (306-331), and 24 (442-444), which are present on the surface of the protein. It was observed that solvent-exposed loops denature before or show higher flexibility than buried residues. We observed that PhyA begins to unfold at loops 8 and 14, which further extends to loop 24 at the C-terminus. The intense movement of loop 8 causes the helix H2 and beta-sheet B3 to fluctuate at high temperature. The high flexibility of the H2, H10, and H12 helices at high temperature resulted in complete denaturation. The high mobility of loop 14 easily transfers to the adjacent helices H7, H8, and H9, which fluctuate and partially unfold at high temperature (500 K). It was also observed that the salt bridges Asp110-Lys149, Asp205-Lys277, Asp335-Arg136, Asp416-Arg420, and Glu387-Arg400 are important influences on the structural stability but not the thermostability, as the lengths of these salt bridges did not increase with rising temperature. The salt bridges Glu125-Arg163, Asp299-Arg136, Asp266-Arg219, Asp339-Lys278, Asp335-Arg136, and Asp424-Arg428 are all important for thermostability, as the lengths of these bridges increased dramatically with increasing temperature. Here, for the first time, we have computationally identified the thermolabile regions of PhyA, and this information could be used to engineer novel thermostable phytases. Numerous homologous phytases of fungal as well as bacterial origin are known, and these homologs show high sequence similarity. Our findings could prove useful in attempts to increase the thermostability of homologous phytases via protein engineering.
Collapse
Affiliation(s)
- Kapil Kumar
- NCIM, Biochemical Sciences Division, Dr. Homi Bhabha Road, Pune, 411 008, India
| | | | | | | |
Collapse
|
8
|
Chu WT, Zheng QC. Conformational changes of enzymes and DNA in molecular dynamics: influenced by pH, temperature, and ligand. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 92:179-217. [PMID: 23954102 DOI: 10.1016/b978-0-12-411636-8.00005-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Protein conformation, which has been a research hotspot for human diseases, is an important factor of protein properties. Recently, a series of approaches have been utilized to investigate the conformational changes under different conditions. Some of them have gained promising achievements, but it is still deficient in the detail researches at the atomic level. In this chapter, a series of computational examples of protein conformational changes under different pH environment, temperature, and ligand binding are described. We further show some useful methods, such as constant pH molecular dynamics simulations, molecular docking, and molecular mechanics Poisson-Boltzmann surface area/generalized Born surface area calculations. In comparison with the experimental results, the methods mentioned above are reasonable to detect and predict the interaction between residue and residue, residue and DNA, and residue and ligand. Additionally, some crucial interactions that cause protein conformational changes are discovered and discussed in this chapter. In summary, our work can give penetrating information to understand the pH-, temperature-, and ligand-induced conformational change mechanisms.
Collapse
Affiliation(s)
- Wen-Ting Chu
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, PR China
| | | |
Collapse
|
9
|
Ding Y, Cai Y. Conformational dynamics of xylanase a fromStreptomyces lividans: Implications for TIM-barrel enzyme thermostability. Biopolymers 2013; 99:594-604. [DOI: 10.1002/bip.22220] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 02/05/2013] [Indexed: 11/11/2022]
|
10
|
Chen L, Zhang JL, Zheng QC, Chu WT, Xue Q, Zhang HX, Sun CC. Influence of C-terminal tail deletion on structure and stability of hyperthermophile Sulfolobus tokodaii RNase HI. J Mol Model 2013; 19:2647-56. [DOI: 10.1007/s00894-013-1816-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 03/04/2013] [Indexed: 01/07/2023]
|
11
|
Béhar G, Bellinzoni M, Maillasson M, Paillard-Laurance L, Alzari PM, He X, Mouratou B, Pecorari F. Tolerance of the archaeal Sac7d scaffold protein to alternative library designs: characterization of anti-immunoglobulin G Affitins. Protein Eng Des Sel 2013; 26:267-75. [PMID: 23315487 DOI: 10.1093/protein/gzs106] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Engineered protein scaffolds have received considerable attention as alternatives to antibodies in both basic and applied research, as they can offer superior biophysical properties often associated with a simpler molecular organization. Sac7d has been demonstrated as an effective scaffold for molecular recognition. Here, we used the initial L1 'flat surface' library constructed by randomization of 14 residues, to identify ligands specific for human immunoglobulin G. To challenge the plasticity of the Sac7d protein scaffold, we designed the alternative L2 'flat surface & loops' library whereof only 10 residues are randomized. Representative binders (Affitins) of the two libraries exhibited affinities in the low nanomolar range and were able to recognize different epitopes within human immunoglobulin G. These Affitins were stable up to pH 12 while largely conserving other favorable properties of Sac7d protein, such as high expression yields in Escherichia coli, solubility, thermal stability up to 80.7°C, and acidic stability (pH 0). In agreement with our library designs, mutagenesis study revealed two distinct binding areas, one including loops. Together, our results indicate that the Sac7d scaffold tolerates alternative library designs, which further expands the diversity of Affitins and may provide a general way to create tailored affinity tools for demanding applications.
Collapse
Affiliation(s)
- Ghislaine Béhar
- Université de Nantes, UMR CNRS 6204, Ingénierie de la reconnaissance, F-44322 Nantes, France
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Chen L, Zheng QC, Yu LY, Chu WT, Zhang JL, Xue Q, Zhang HX, Sun CC. Insights into the thermal stabilization and conformational transitions of DNA by hyperthermophile protein Sso7d: molecular dynamics simulations and MM-PBSA analysis. J Biomol Struct Dyn 2012; 30:716-27. [PMID: 22731116 DOI: 10.1080/07391102.2012.689702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the assembly of DNA-protein complex, the DNA kinking plays an important role in nucleoprotein structures and gene regulation. Molecular dynamics (MD) simulations were performed on specific protein-DNA complexes in this study to investigate the stability and structural transitions of DNA depending on temperature. Furthermore, we introduced the molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) approach to analyze the interactions between DNA and protein in hyperthermophile. Focused on two specific Sso7d-DNA complexes (PDB codes: 1BNZ and 1BF4), we performed MD simulations at four temperatures (300, 360, 420, and 480 K) and MM-PBSA at 300 and 360 K to illustrate detailed information on the changes of DNA. Our results show that Sso7d stabilizes DNA duplex over a certain temperature range and DNA molecules undergo B-like to A-like form transitions in the binary complex with the temperature increasing, which are consistent with the experimental data. Our work will contribute to a better understanding of protein-DNA interaction.
Collapse
Affiliation(s)
- Lin Chen
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, P.R. China
| | | | | | | | | | | | | | | |
Collapse
|
13
|
Priyakumar UD. Role of Hydrophobic Core on the Thermal Stability of Proteins—Molecular Dynamics Simulations on a Single Point Mutant of Sso7d. J Biomol Struct Dyn 2012; 29:961-71. [DOI: 10.1080/07391102.2012.10507415] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
14
|
Pagano B, Del Vecchio P, Mattia CA, Graziano G. Molecular dynamics study of the conformational stability of esterase 2 from Alicyclobacillus acidocaldarius. Int J Biol Macromol 2011; 49:1072-7. [DOI: 10.1016/j.ijbiomac.2011.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 08/30/2011] [Accepted: 09/01/2011] [Indexed: 11/16/2022]
|
15
|
Xu X, Su J, Chen W, Wang C. Thermal stability and unfolding pathways of Sso7d and its mutant F31A: insight from molecular dynamics simulation. J Biomol Struct Dyn 2011; 28:717-27. [PMID: 21294584 DOI: 10.1080/07391102.2011.10508601] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The thermo-stability and unfolding behaviors of a small hyperthermophilic protein Sso7d as well as its single-point mutation F31A are studied by molecular dynamics simulation at temperatures of 300 K, 371 K and 500 K. Simulations at 300 K show that the F31A mutant displays a much larger flexibility than the wild type, which implies that the mutation obviously decreases the protein's stability. In the simulations at 371 K, although larger fluctuations were observed, both of these two maintain their stable conformations. High temperature simulations at 500 K suggest that the unfolding of these two proteins evolves along different pathways. For the wild-type protein, the C-terminal alpha-helix is melted at the early unfolding stage, whereas it is destroyed much later in the unfolding process of the F31A mutant. The results also show that the mutant unfolds much faster than its parent protein. The deeply buried aromatic cluster in the F31A mutant dissociates quickly relative to the wild-type protein at high temperature. Besides, it is found that the triple-stranded antiparallel β-sheet in the wild-type protein plays an important role in maintaining the stability of the entire structure.
Collapse
Affiliation(s)
- Xianjin Xu
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | | | | | | |
Collapse
|
16
|
Abstract
Recently, extracellular RNases of the RNase A superfamily, with the characteristic CKxxNTF sequence signature, have been identified in fish. This has led to the recognition that these RNases are present in the whole vertebrate subphylum. In fact, they comprise the only enzyme family unique to vertebrates. Four RNases from zebrafish (Danio rerio) have been previously reported and have a very low RNase activity; some of these are endowed, like human angiogenin, with powerful angiogenic and bactericidal activities. In the present paper, we report the three-dimensional structure, the thermodynamic behaviour and the biological properties of a novel zebrafish RNase, ZF-RNase-5. The investigation of its structural and functional properties, extended to all other subfamily members, provides an inclusive description of the whole zebrafish RNase subfamily.
Collapse
|
17
|
Kim SJ, Lee JA, Joo JC, Yoo YJ, Kim YH, Song BK. The development of a thermostable CiP (Coprinus cinereus peroxidase) through in silico design. Biotechnol Prog 2010; 26:1038-46. [PMID: 20730760 DOI: 10.1002/btpr.408] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Protein thermostability is a crucial issue in the practical application of enzymes, such as inorganic synthesis and enzymatic polymerization of phenol derivatives. Much attention has been focused on the enhancement and numerous successes have been achieved through protein engineering methods. Despite fruitful results based on random mutagenesis, it was still necessary to develop a novel strategy that can reduce the time and effort involved in this process. In this study, a rapid and effective strategy is described for increasing the thermal stability of a protein. Instead of random mutagenesis, a rational strategy was adopted to theoretically stabilize the thermo labile residues of a protein using computational methods. Protein residues with high flexibility can be thermo labile due to their large range of movement. Here, residue B factor values were used to identify putatively thermo labile residues and the RosettaDesign program was applied to search for stable sequences. Coprinus cinereus (CiP) heme peroxidase was selected as a model protein for its importance in commercial applications, such as the polymerization of phenolic compounds. Eleven CiP residues with the highest B factor values were chosen as target mutation sites for thermostabilization, and then redesigned using RosettaDesign to identify sequences. Eight mutants based on the redesigns, were produced as functional enzymes and two of these (S323Y and E328D) showed increased thermal stability over the wild-type in addition to conserved catalytic activity. Thus, this strategy can be used as a rapid and effective in silico design tool for obtaining thermostable proteins.
Collapse
Affiliation(s)
- Su Jin Kim
- Chemical Biotechnology Research Center, Korea Research Institute of Chemical Technology, Yuseong-gu, Daejeon, Korea
| | | | | | | | | | | |
Collapse
|
18
|
Priyakumar UD, Ramakrishna S, Nagarjuna KR, Reddy SK. Structural and Energetic Determinants of Thermal Stability and Hierarchical Unfolding Pathways of Hyperthermophilic Proteins, Sac7d and Sso7d. J Phys Chem B 2010; 114:1707-18. [DOI: 10.1021/jp909122x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- U. Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - S. Ramakrishna
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - K. R. Nagarjuna
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - S. Karunakar Reddy
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| |
Collapse
|
19
|
Alone PV, Malik G, Krishnan A, Garg LC. Deletion mutations in N-terminal alpha1 helix render heat labile enterotoxin B subunit susceptible to degradation. Proc Natl Acad Sci U S A 2007; 104:16056-61. [PMID: 17911243 PMCID: PMC2042161 DOI: 10.1073/pnas.0707897104] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2007] [Indexed: 11/18/2022] Open
Abstract
Heat-labile enterotoxin (LT) from enterotoxigenic Escherichia coli is a heterohexameric protein consisting of an enzymatically active A subunit, LTA, and a carrier pentameric B subunit, LTB. It is clear from the crystal structure of LTB that the N-terminal alpha1 helix lies outside the core structure. However, the function of the N-terminal alpha1 helix of LTB is unknown. The present work was carried out to investigate the effect of site-directed mutagenesis of the alpha1 helix on LTB synthesis. Six amino acids (PQSITE) located at positions 2-7 from the N terminus, including 4 aa from the alpha1 helix, were deleted by site-directed mutagenesis. The deletion resulted in complete inhibition of LTB expression in E. coli when expressed along with its signal sequence. A single amino acid deletion within the alpha1 helix also resulted in loss of expression. However, a single amino acid deletion outside the alpha1 helix did not affect LTB synthesis. Mutant proteins, whose synthesis was not detected in vivo, could be successfully translated in vitro by using the coupled transcription-translation system. Immunoblot analysis, Northern blot analysis, and in vitro transcription-translation data collectively indicate that the lack of synthesis of the mutant proteins is caused by the immediate degradation of the expressed product by cellular proteases rather than by faulty translation of mutant LTB mRNA. Coexpression of the LTA could not rescue the degradation of LTB mutants.
Collapse
MESH Headings
- Amino Acid Sequence
- Bacterial Toxins/chemistry
- Bacterial Toxins/genetics
- Bacterial Toxins/metabolism
- Base Sequence
- DNA Primers/genetics
- Enterotoxigenic Escherichia coli/genetics
- Enterotoxigenic Escherichia coli/metabolism
- Enterotoxins/chemistry
- Enterotoxins/genetics
- Enterotoxins/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Genes, Bacterial
- Magnesium/metabolism
- Models, Molecular
- Mutagenesis, Site-Directed
- Protein Structure, Quaternary
- Protein Structure, Secondary
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Deletion
- Transcription, Genetic
Collapse
Affiliation(s)
- Pankaj V. Alone
- Gene Regulation Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Gunjan Malik
- Gene Regulation Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anuja Krishnan
- Gene Regulation Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Lalit C. Garg
- Gene Regulation Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| |
Collapse
|
20
|
Consonni R, Arosio I, Recca T, Fusi P, Zetta L. Structural determinants responsible for the thermostability of Sso7d and its single point mutants. Proteins 2007; 67:766-75. [PMID: 17340638 DOI: 10.1002/prot.21256] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Roberto Consonni
- Istituto per lo Studio delle Macromolecole, lab. NMR, C.N.R., v. Bassini 15, I-20133 Milan, Italy.
| | | | | | | | | |
Collapse
|
21
|
Reich L, Weikl TR. Substructural cooperativity and parallel versus sequential events during protein unfolding. Proteins 2006; 63:1052-8. [PMID: 16544293 DOI: 10.1002/prot.20966] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
According to the "old view," proteins fold along well-defined sequential pathways, whereas the "new view" sees protein folding as a highly parallel stochastic process on funnel-shaped energy landscapes. We have analyzed parallel and sequential processes on a large number of molecular dynamics unfolding trajectories of the protein CI2 at high temperatures. Using rigorous statistical measures, we quantify the degree of sequentiality on two structural levels. The unfolding process is highly parallel on the microstructural level of individual contacts. On a coarser, macrostructural level of contact clusters, characteristic parallel and sequential events emerge. These characteristic events can be understood from loop-closure dependencies between the contact clusters. A correlation analysis of the unfolding times of the contacts reveals a high degree of substructural cooperativity within the contact clusters.
Collapse
Affiliation(s)
- Lothar Reich
- Theory Department, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | | |
Collapse
|
22
|
Chapter 13 Principal Components Analysis: A Review of its Application on Molecular Dynamics Data. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2006. [DOI: 10.1016/s1574-1400(06)02013-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
23
|
Merlino A, Mazzarella L, Carannante A, Di Fiore A, Di Donato A, Notomista E, Sica F. The Importance of Dynamic Effects on the Enzyme Activity. J Biol Chem 2005; 280:17953-60. [PMID: 15728177 DOI: 10.1074/jbc.m501339200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Onconase (ONC), a member of the RNase A superfamily extracted from oocytes of Rana pipiens, is an effective cancer killer. It is currently used in treatment of various forms of cancer. ONC antitumor properties depend on its ribonucleolytic activity that is low in comparison with other members of the superfamily. The most damaging side effect from Onconase treatment is renal toxicity, which seems to be caused by the unusual stability of the enzyme. Therefore, mutants with reduced thermal stability and/or increased catalytic activity may have significant implications for human cancer chemotherapy. In this context, we have determined the crystal structures of two Onconase mutants (M23L-ONC and C87S,des103-104-ONC) and performed molecular dynamic simulations of ONC and C87S,des103-104-ONC with the aim of explaining on structural grounds the modifications of the activity and thermal stability of the mutants. The results also provide the molecular bases to explain the lower catalytic activity of Onconase compared with RNase A and the unusually high thermal stability of the amphibian enzyme.
Collapse
Affiliation(s)
- Antonello Merlino
- Dipartimento di Chimica, Università degli Studi di Napoli "Federico II," Via Cynthia, 80126 Napoli, Italy
| | | | | | | | | | | | | |
Collapse
|
24
|
Merlino A, Ceruso MA, Vitagliano L, Mazzarella L. Open interface and large quaternary structure movements in 3D domain swapped proteins: insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A. Biophys J 2004; 88:2003-12. [PMID: 15596505 PMCID: PMC1305252 DOI: 10.1529/biophysj.104.048611] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bovine pancreatic ribonuclease (RNase A) forms two three-dimensional (3D) domain swapped dimers. Crystallographic investigations have revealed that these dimers display completely different quaternary structures: one dimer (N-dimer), which presents the swapping of the N-terminal helix, is characterized by a compact structure, whereas the other (C-dimer), which is stabilized by the exchange of the C-terminal end, shows a rather loose assembly of the two subunits. The dynamic properties of monomeric RNase A and of the N-dimer have been extensively characterized. Here, we report a molecular dynamics investigation carried out on the C-dimer. This computational experiment indicates that the quaternary structure of the C-dimer undergoes large fluctuations. These motions do not perturb the proper folding of the two subunits, which retain the dynamic properties of RNase A and the N-dimer. Indeed, the individual subunits of the C-dimer display the breathing motion of the beta-sheet structure, which is important for the enzymatic activity of pancreatic-like ribonucleases. In contrast to what has been observed for the N-dimer, the breathing motion of the two subunits of the C-dimer is not coupled. This finding suggests that the intersubunit communications in a 3D domain swapped dimer strongly rely on the extent of the interchain interface. Furthermore, the observation that the C-dimer is endowed with a high intrinsic flexibility holds interesting implications for the specific properties of 3D domain swapped dimers. Indeed, a survey of the quaternary structures of the other 3D domain swapped dimers shows that large variations are often observed when the structural determinations are conducted in different experimental conditions. The 3D domain swapping phenomenon coupled with the high flexibility of the quaternary structure may be relevant for protein-protein recognition, and in particular for the pathological aggregations.
Collapse
Affiliation(s)
- Antonello Merlino
- Centro Interdipartimentale Ricerca e Management, Complesso Ristrutturato S. Andrea delle Dame, 80138, Naples, Italy
| | | | | | | |
Collapse
|