1
|
Gangele K, Gulati K, Joshi N, Kumar D, Poluri KM. Molecular insights into the differential structure-dynamics-stability features of interleukin-8 orthologs: Implications to functional specificity. Int J Biol Macromol 2020; 164:3221-3234. [PMID: 32853623 DOI: 10.1016/j.ijbiomac.2020.08.176] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 11/17/2022]
Abstract
Chemokines are a sub-group of chemotactic cytokines that regulate the leukocyte migration by binding to G-protein coupled receptors (GPCRs) and cell surface glycosaminoglycans (GAGs). Interleukin-8 (CXCL8/IL8) is one of the most essential CXC chemokine that has been reported to be involved in various pathophysiological conditions. Structure-function relationships of human IL8 have been studied extensively. However, no such detailed information is available on IL8 orthologs, although they exhibit significant functional divergence. In order to unravel the differential structure-dynamics-stability-function relationship of IL8 orthologs, comparative molecular analysis was performed on canine (laurasians) and human (primates) IL8 proteins using in-silico molecular evolutionary analysis and solution NMR spectroscopy methods. The residue level NMR studies suggested that, although the overall structural architecture of canine IL8 is similar to that of human IL8, systematic differences were observed in their backbone dynamics and low-energy excited states due to amino acid substitutions. Further, these substitutions also resulted in attenuation of stability and heparin binding affinity in the canine IL8 as compared to its human counterpart. Indeed, structural and sequence analysis evidenced for specificity of molecular interactions with cognate receptor (CXCR1) and glycosaminoglycan (heparin), thus providing evidence for a noticeable functional specificity and divergence between the two IL8 orthologs.
Collapse
Affiliation(s)
- Krishnakant Gangele
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Khushboo Gulati
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Nidhi Joshi
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Dinesh Kumar
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow 226014, Uttar Pradesh, India
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India; Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India.
| |
Collapse
|
2
|
Enhanced dynamics of conformationally heterogeneous T7 bacteriophage lysozyme native state attenuates its stability and activity. Biochem J 2019; 476:613-628. [DOI: 10.1042/bcj20180703] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/17/2019] [Accepted: 01/25/2019] [Indexed: 11/17/2022]
Abstract
Abstract
Proteins are dynamic in nature and exist in a set of equilibrium conformations on various timescale motions. The flexibility of proteins governs various biological functions, and therefore elucidation of such functional dynamics is essential. In this context, we have studied the structure–dynamics–stability–activity relationship of bacteriophage T7 lysozyme/endolysin (T7L) native-state ensemble in the pH range of 6–8. Our studies established that T7L native state is conformationally heterogeneous, as several residues of its C-terminal half are present in two conformations (major and minor) in the slow exchange time scale of nuclear magnetic resonance (NMR). Structural and dynamic studies suggested that the residues belonging to minor conformations do exhibit native-like structural and dynamic features. Furthermore, the NMR relaxation experiments unraveled that the native state is highly dynamic and the dynamic behavior is regulated by the pH, as the pH 6 conformation exhibited enhanced dynamics compared with pH 7 and 8. The stability measurements and cell-based activity studies on T7L indicated that the native protein at pH 6 is ∼2 kcal less stable and is ∼50% less active than those of pH 7 and 8. A comprehensive analysis of the T7L active site, unfolding initiation sites and the residues with altered dynamics outlined that the attenuation of stability and activity is a resultant of its enhanced dynamic properties, which, in turn, can be attributed to the protonation/deprotonation of its partially buried His residues. Our study on T7L structure–dynamics–activity paradigm could assist in engineering novel amidase-based endolysins with enhanced activity and stability over a broad pH range.
Collapse
|
3
|
Accelerating NMR-Based Structural Studies of Proteins by Combining Amino Acid Selective Unlabeling and Fast NMR Methods. MAGNETOCHEMISTRY 2017. [DOI: 10.3390/magnetochemistry4010002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
4
|
Sharma M, Kumar D, Poluri KM. Elucidating the pH-Dependent Structural Transition of T7 Bacteriophage Endolysin. Biochemistry 2016; 55:4614-25. [PMID: 27513288 DOI: 10.1021/acs.biochem.6b00240] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Bacteriophages are the most abundant and diverse biological entities on earth. Bacteriophage endolysins are unique peptidoglycan hydrolases and have huge potential as effective enzybiotics in various infectious models. T7 bacteriophage endolysin (T7L), also known as N-acetylmuramoyl-l-alanine amidase or T7 lysozyme, is a 17 kDa protein that lyses a range of Gram-negative bacteria by hydrolyzing the amide bond between N-acetylmuramoyl residues and the l-alanine of the peptidoglycan layer. Although the activity profiles of several of the T7 family members have been known for many years, the molecular basis for their pH-dependent differential activity is not clear. In this study, we explored the pH-induced structural, stability, and activity characteristics of T7L by applying a variety of biophysical techniques and protein nuclear magnetic resonance (NMR) spectroscopy. Our studies established a reversible structural transition of T7L below pH 6 and the formation of a partially denatured conformation at pH 3. This low-pH conformation is thermally stable and exposed its hydrophobic pockets. Further, NMR relaxation measurements and structural analysis unraveled that T7L is highly dynamic in its native state and a network of His residues are responsible for the observed pH-dependent conformational dynamics and transitions. As bacteriophage chimeric and engineered endolysins are being developed as novel therapeutics against multiple drug resistance pathogens, we believe that our results are of great help in designing these entities as broadband antimicrobial and/or antibacterial agents.
Collapse
Affiliation(s)
| | - Dinesh Kumar
- Centre of Biomedical Research, SGPGIMS , Lucknow 226014, Uttar Pradesh, India
| | | |
Collapse
|
5
|
Dubey A, Kadumuri RV, Jaipuria G, Vadrevu R, Atreya HS. Rapid NMR Assignments of Proteins by Using Optimized Combinatorial Selective Unlabeling. Chembiochem 2016; 17:334-40. [DOI: 10.1002/cbic.201500513] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Abhinav Dubey
- NMR Research Center; Indian Institute of Science, Malleswaram; Bangalore 560012 India
- IISc Mathematics Initiative; Indian Institute of Science, Malleswaram; Bangalore 560012 India
| | - Rajashekar Varma Kadumuri
- Department of Biological Sciences; Birla Institute of Technology and Science-Pilani; Hyderabad Campus Hyderabad 500078 India
| | - Garima Jaipuria
- NMR Research Center; Indian Institute of Science, Malleswaram; Bangalore 560012 India
| | - Ramakrishna Vadrevu
- Department of Biological Sciences; Birla Institute of Technology and Science-Pilani; Hyderabad Campus Hyderabad 500078 India
| | - Hanudatta S. Atreya
- NMR Research Center; Indian Institute of Science, Malleswaram; Bangalore 560012 India
| |
Collapse
|
6
|
Prasanna C, Dubey A, Atreya HS. Amino Acid Selective Unlabeling in Protein NMR Spectroscopy. Methods Enzymol 2015; 565:167-89. [DOI: 10.1016/bs.mie.2015.05.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
7
|
Jaipuria G, Krishnarjuna B, Mondal S, Dubey A, Atreya HS. Amino acid selective labeling and unlabeling for protein resonance assignments. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 992:95-118. [PMID: 23076581 DOI: 10.1007/978-94-007-4954-2_6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Structural characterization of proteins by NMR spectroscopy begins with the process of sequence specific resonance assignments in which the (1)H, (13)C and (15)N chemical shifts of all backbone and side-chain nuclei in the polypeptide are assigned. This process requires different isotope labeled forms of the protein together with specific experiments for establishing the sequential connectivity between the neighboring amino acid residues. In the case of spectral overlap, it is useful to identify spin systems corresponding to the different amino acid types selectively. With isotope labeling this can be achieved in two ways: (i) amino acid selective labeling or (ii) amino acid selective 'unlabeling'. This chapter describes both these methods with more emphasis on selective unlabeling describing the various practical aspects. The recent developments involving combinatorial selective labeling and unlabeling are also discussed.
Collapse
Affiliation(s)
- Garima Jaipuria
- NMR Research Centre, Indian Institute of Science, Bangalore, India
| | | | | | | | | |
Collapse
|
8
|
Chakraborty S, Krishna Mohan P, Hosur RV. Residual structure and dynamics in DMSO-d6 denatured Dynein Light Chain protein. Biochimie 2012; 94:231-41. [DOI: 10.1016/j.biochi.2011.10.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 10/25/2011] [Indexed: 10/15/2022]
|
9
|
Krishnarjuna B, Jaipuria G, Thakur A, D’Silva P, Atreya HS. Amino acid selective unlabeling for sequence specific resonance assignments in proteins. JOURNAL OF BIOMOLECULAR NMR 2011; 49:39-51. [PMID: 21153044 PMCID: PMC3020294 DOI: 10.1007/s10858-010-9459-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 11/16/2010] [Indexed: 05/14/2023]
Abstract
Sequence specific resonance assignment constitutes an important step towards high-resolution structure determination of proteins by NMR and is aided by selective identification and assignment of amino acid types. The traditional approach to selective labeling yields only the chemical shifts of the particular amino acid being selected and does not help in establishing a link between adjacent residues along the polypeptide chain, which is important for sequential assignments. An alternative approach is the method of amino acid selective 'unlabeling' or reverse labeling, which involves selective unlabeling of specific amino acid types against a uniformly (13)C/(15)N labeled background. Based on this method, we present a novel approach for sequential assignments in proteins. The method involves a new NMR experiment named, {(12)CO( i )-(15)N( i+1)}-filtered HSQC, which aids in linking the (1)H(N)/(15)N resonances of the selectively unlabeled residue, i, and its C-terminal neighbor, i + 1, in HN-detected double and triple resonance spectra. This leads to the assignment of a tri-peptide segment from the knowledge of the amino acid types of residues: i - 1, i and i + 1, thereby speeding up the sequential assignment process. The method has the advantage of being relatively inexpensive, applicable to (2)H labeled protein and can be coupled with cell-free synthesis and/or automated assignment approaches. A detailed survey involving unlabeling of different amino acid types individually or in pairs reveals that the proposed approach is also robust to misincorporation of (14)N at undesired sites. Taken together, this study represents the first application of selective unlabeling for sequence specific resonance assignments and opens up new avenues to using this methodology in protein structural studies.
Collapse
Affiliation(s)
- B. Krishnarjuna
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012 India
| | - Garima Jaipuria
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012 India
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560012 India
| | - Anushikha Thakur
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012 India
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560012 India
- Chemical Biology Programme, Indian Institute of Science, Bangalore, 560012 India
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012 India
| | - Patrick D’Silva
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012 India
| | | |
Collapse
|
10
|
Mohan PK, Chakraborty S, Hosur RV. Hierarchy of local structural and dynamics perturbations due to subdenaturing urea in the native state ensemble of DLC8 dimer. Biophys Chem 2010; 153:17-26. [DOI: 10.1016/j.bpc.2010.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/28/2010] [Accepted: 09/29/2010] [Indexed: 11/28/2022]
|
11
|
Krishna Mohan PM, Hosur RV. Structure-function-folding relationships and native energy landscape of dynein light chain protein: nuclear magnetic resonance insights. J Biosci 2009; 34:465-79. [DOI: 10.1007/s12038-009-0052-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
12
|
Mohan PMK, Chakraborty S, Hosur RV. NMR investigations on residue level unfolding thermodynamics in DLC8 dimer by temperature dependent native state hydrogen exchange. JOURNAL OF BIOMOLECULAR NMR 2009; 44:1-11. [PMID: 19308329 DOI: 10.1007/s10858-009-9311-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Revised: 01/21/2009] [Accepted: 02/26/2009] [Indexed: 05/27/2023]
Abstract
Understanding protein stability at residue level detail in the native state ensemble of a protein is crucial to understanding its biological function. At the same time, deriving thermodynamic parameters using conventional spectroscopic and calorimetric techniques remains a major challenge for some proteins due to protein aggregation and irreversibility of denaturation at higher temperature values. In this regard, we describe here the NMR investigations on the conformational stabilities and related thermodynamic parameters such as local unfolding enthalpies, heat capacities and transition midpoints in DLC8 dimer, by using temperature dependent native state hydrogen exchange; this protein aggregates at high (>65 degrees C) temperatures. The stability (free energy) of the native state was found to vary substantially with temperature at every residue. Significant differences were found in the thermodynamic parameters at individual residue sites indicating that the local environments in the protein structure would respond differently to external perturbations; this reflects on plasticity differences in different regions of the protein. Further, comparison of this data with similar data obtained from GdnHCl dependent native state hydrogen exchange indicated many similarities at residue level, suggesting that local unfolding transitions may be similar in both the cases. This has implications for the folding/unfolding mechanisms of the protein.
Collapse
Affiliation(s)
- P M Krishna Mohan
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400 005, India
| | | | | |
Collapse
|
13
|
Mohan PK, Joshi MV, Hosur RV. Hierarchy in guanidine unfolding of DLC8 dimer: Regulatory functional implications. Biochimie 2009; 91:401-7. [DOI: 10.1016/j.biochi.2008.10.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Accepted: 10/28/2008] [Indexed: 10/21/2022]
|
14
|
Mohan PK, Hosur RV. pH dependent unfolding characteristics of DLC8 dimer: Residue level details from NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1795-803. [DOI: 10.1016/j.bbapap.2008.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 06/30/2008] [Accepted: 07/04/2008] [Indexed: 10/21/2022]
|
15
|
Hall J, Hall A, Pursifull N, Barbar E. Differences in Dynamic Structure of LC8 Monomer, Dimer, and Dimer−Peptide Complexes. Biochemistry 2008; 47:11940-52. [DOI: 10.1021/bi801093k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Justin Hall
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Andrea Hall
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Nathan Pursifull
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| |
Collapse
|
16
|
Mohan PMK, Chakraborty S, Hosur RV. Residue-wise conformational stability of DLC8 dimer from native-state hydrogen exchange. Proteins 2008; 75:40-52. [PMID: 18767155 DOI: 10.1002/prot.22219] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Dynein light chain (DLC8) is the smallest subunit of the dynein motor complex, which is known to act as a cargo adaptor in intracellular trafficking. The protein exists as a pure dimer at physiological pH and a completely folded monomer below pH 4. Here, we have determined the energy landscape of the dimeric protein using a combination of optical techniques and native-state hydrogen exchange of amide groups, the former giving the global features and the latter yielding the residue level details. The data indicated the presence of intermediates along the equilibrium unfolding transition. The hydrogen exchange data suggested that the molecule has differential stability in its various segments. We deduce from the free energy data that the antiparallel beta-sheets (beta4 and beta5) that form the hydrophobic core of the protein and the alpha2 helix, all of which are highly protected with regard to hydrogen exchange, contribute significantly to the initial step of the protein folding mechanism. Denaturant-dependent hydrogen exchange indicated further that some amides exchange via local fluctuations, whereas there are others which exchange via global unfolding events. Implications of these to cargo adaptability of the dimer are discussed.
Collapse
Affiliation(s)
- P M Krishna Mohan
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | | | | |
Collapse
|
17
|
Mohan PMK, Hosur RV. NMR Characterization of Structural and Dynamics Perturbations Due to a Single Point Mutation in Drosophila DLC8 Dimer: Functional Implications. Biochemistry 2008; 47:6251-9. [DOI: 10.1021/bi800531g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- P. M. Krishna Mohan
- Department of Chemical Sciences, Tata Institute of Fundamental Research Homi Bhabha Road, Mumbai 400 005, India
| | - Ramakrishna V. Hosur
- Department of Chemical Sciences, Tata Institute of Fundamental Research Homi Bhabha Road, Mumbai 400 005, India
| |
Collapse
|