1
|
Sen S, Dey A, Bandhyopadhyay S, Uversky VN, Maulik U. Understanding structural malleability of the SARS-CoV-2 proteins and relation to the comorbidities. Brief Bioinform 2021; 22:6304388. [PMID: 34143202 DOI: 10.1093/bib/bbab232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/13/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a causative agent of the coronavirus disease (COVID-19), is a part of the $\beta $-Coronaviridae family. The virus contains five major protein classes viz., four structural proteins [nucleocapsid (N), membrane (M), envelop (E) and spike glycoprotein (S)] and replicase polyproteins (R), synthesized as two polyproteins (ORF1a and ORF1ab). Due to the severity of the pandemic, most of the SARS-CoV-2-related research are focused on finding therapeutic solutions. However, studies on the sequences and structure space throughout the evolutionary time frame of viral proteins are limited. Besides, the structural malleability of viral proteins can be directly or indirectly associated with the dysfunctionality of the host cell proteins. This dysfunctionality may lead to comorbidities during the infection and may continue at the post-infection stage. In this regard, we conduct the evolutionary sequence-structure analysis of the viral proteins to evaluate their malleability. Subsequently, intrinsic disorder propensities of these viral proteins have been studied to confirm that the short intrinsically disordered regions play an important role in enhancing the likelihood of the host proteins interacting with the viral proteins. These interactions may result in molecular dysfunctionality, finally leading to different diseases. Based on the host cell proteins, the diseases are divided in two distinct classes: (i) proteins, directly associated with the set of diseases while showing similar activities, and (ii) cytokine storm-mediated pro-inflammation (e.g. acute respiratory distress syndrome, malignancies) and neuroinflammation (e.g. neurodegenerative and neuropsychiatric diseases). Finally, the study unveils that males and postmenopausal females can be more vulnerable to SARS-CoV-2 infection due to the androgen-mediated protein transmembrane serine protease 2.
Collapse
Affiliation(s)
- Sagnik Sen
- Department of Computer Science and Engineering, Jadavpur University, Kolkata-32, West Bengal, India
| | - Ashmita Dey
- Department of Computer Science and Engineering, Jadavpur University, Kolkata-32, West Bengal, India
| | | | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America.,Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region, 142290 Russia
| | - Ujjwal Maulik
- Department of Computer Science and Engineering, Jadavpur University, Kolkata-32, West Bengal, India
| |
Collapse
|
2
|
Kutyshenko VP, Mikoulinskaia GV, Molochkov NV, Prokhorov DA, Taran SA, Uversky VN. Structure and dynamics of the retro-form of the bacteriophage T5 endolysin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1281-91. [PMID: 27376687 DOI: 10.1016/j.bbapap.2016.06.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/29/2016] [Accepted: 06/30/2016] [Indexed: 10/21/2022]
Abstract
Using high-resolution NMR spectroscopy we conducted a comparative analysis of the structural and dynamic properties of the bacteriophage T5 endolysin (EndoT5) and its retro-form; i.e., a protein with the reversed direction of the polypeptide chain (R-EndoT5). We show that structurally, retro-form can be described as the molten globule-like polypeptide that is easily able to form large oligomers and aggregates. To avoid complications associated with this high aggregation propensity of the retro protein, we compared EndoT5 and R-EndoT5 in the presence of strong denaturants. This analysis revealed that these two proteins possess different internal dynamics in solutions containing 8M urea, with the retro-form being characterized by larger dimensions and slower internal dynamics. We also show that in the absence of denaturant, both forms of the bacteriophage T5 endolysin are able to interact with micelles formed by the zwitterionic detergent dodecylphosphocholine (DPC), and that the formation of the protein-micelle complexes leads to the significant structural rearrangement of polypeptide chain and to the formation of stable hydrophobic core in the R-Endo T5.
Collapse
Affiliation(s)
- Victor P Kutyshenko
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.
| | - Galina V Mikoulinskaia
- Branch of Shemyakin & Ovchinnikov's Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Nikolai V Molochkov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Dmitry A Prokhorov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Sergei A Taran
- Branch of Shemyakin & Ovchinnikov's Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg 194064, Russia.
| |
Collapse
|
3
|
Prokhorov DA, Mikoulinskaia GV, Molochkov NV, Uversky VN, Kutyshenko VP. High-resolution NMR structure of a Zn2+-containing form of the bacteriophage T5l-alanyl-d-glutamate peptidase. RSC Adv 2015. [DOI: 10.1039/c5ra05993c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The 3D-structure solution structure of the Zn2+-containing form of the bacteriophage T5 EndoT5-Zn2+is determined by the high-resolution NMR spectroscopy. The structural integrity of the entire molecule is controlled by the Zn2+binding.
Collapse
Affiliation(s)
- Dmitry A. Prokhorov
- Institute of Theoretical and Experimental Biophysics
- Russian Academy of Sciences
- Pushchino
- Russia
| | - Galina V. Mikoulinskaia
- Branch of Shemyakin & Ovchinnikov's Institute of Bioorganic Chemistry
- Russian Academy of Sciences
- Pushchino
- Russia
| | - Nikolai V. Molochkov
- Institute of Theoretical and Experimental Biophysics
- Russian Academy of Sciences
- Pushchino
- Russia
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
| | - Victor P. Kutyshenko
- Institute of Theoretical and Experimental Biophysics
- Russian Academy of Sciences
- Pushchino
- Russia
| |
Collapse
|
4
|
Cilia E, Pancsa R, Tompa P, Lenaerts T, Vranken WF. From protein sequence to dynamics and disorder with DynaMine. Nat Commun 2014; 4:2741. [PMID: 24225580 DOI: 10.1038/ncomms3741] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 10/10/2013] [Indexed: 11/09/2022] Open
Abstract
Protein function and dynamics are closely related; however, accurate dynamics information is difficult to obtain. Here based on a carefully assembled data set derived from experimental data for proteins in solution, we quantify backbone dynamics properties on the amino-acid level and develop DynaMine--a fast, high-quality predictor of protein backbone dynamics. DynaMine uses only protein sequence information as input and shows great potential in distinguishing regions of different structural organization, such as folded domains, disordered linkers, molten globules and pre-structured binding motifs of different sizes. It also identifies disordered regions within proteins with an accuracy comparable to the most sophisticated existing predictors, without depending on prior disorder knowledge or three-dimensional structural information. DynaMine provides molecular biologists with an important new method that grasps the dynamical characteristics of any protein of interest, as we show here for human p53 and E1A from human adenovirus 5.
Collapse
Affiliation(s)
- Elisa Cilia
- 1] MLG, Département d'Informatique, Université Libre de Bruxelles, Boulevard du Triomphe, CP 212, 1050 Brussels, Belgium [2] Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, BC building, 6th floor, CP 263, 1050 Brussels, Belgium
| | | | | | | | | |
Collapse
|
5
|
|
6
|
Kutyshenko VP, Prokhorov DA, Molochkov NV, Sharapov MG, Kolesnikov I, Uversky VN. Dancing retro: solution structure and micelle interactions of the retro-SH3-domain, retro-SHH-'Bergerac'. J Biomol Struct Dyn 2013; 32:257-72. [PMID: 23527530 DOI: 10.1080/07391102.2012.762724] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A protein with the reversed direction of its polypeptide chain, retro-SHH, was analyzed by several spectroscopic techniques including circular dichroism and high-resolution NMR to understand its solution structure and structural consequences of interaction with the micelles formed by the zwitterionic detergent dodecylphosphocholine (DPC). This analysis revealed that retro-SHH does not contain rigid 3-D structure, but is characterized by the presence of residual secondary structure. Intriguingly, interaction with the DPC micelles affected the structures of SHH and retro-SHH very differently. In fact, micelles induce pronounced folding of retro-SHH, whereas micelle-bound SHH was noticeably disordered. Finally, we performed a disorder prediction with the PONDR-FIT algorithm and discovered that the reversal of the chain direction almost does not affect the propensity of a polypeptide for intrinsic disorder, since the disorder plot for retro-SHH was almost a mirror image of that for the normal SHH.
Collapse
Affiliation(s)
- Victor P Kutyshenko
- a Institute of Theoretical and Experimental Biophysics of Russian Academy of Science , Pushchino , Moscow Region , 142290 , Russia
| | | | | | | | | | | |
Collapse
|
7
|
Fedotoff O, Mikheeva LM, Chait A, Uversky VN, Zaslavsky BY. Influence of Serum Proteins on Conformation of Prostate-Specific Antigen. J Biomol Struct Dyn 2012; 29:1051-64. [DOI: 10.1080/073911012010525030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
8
|
Melnik BS, Povarnitsyna TV, Glukhov AS, Melnik TN, Uversky VN. SS-Stabilizing Proteins Rationally: Intrinsic Disorder-Based Design of Stabilizing Disulphide Bridges in GFP. J Biomol Struct Dyn 2012; 29:815-24. [DOI: 10.1080/07391102.2012.10507414] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
9
|
Daughdrill GW, Borcherds WM, Wu H. Disorder predictors also predict backbone dynamics for a family of disordered proteins. PLoS One 2011; 6:e29207. [PMID: 22195023 PMCID: PMC3240651 DOI: 10.1371/journal.pone.0029207] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 11/22/2011] [Indexed: 01/04/2023] Open
Abstract
Several algorithms have been developed that use amino acid sequences to predict whether or not a protein or a region of a protein is disordered. These algorithms make accurate predictions for disordered regions that are 30 amino acids or longer, but it is unclear whether the predictions can be directly related to the backbone dynamics of individual amino acid residues. The nuclear Overhauser effect between the amide nitrogen and hydrogen (NHNOE) provides an unambiguous measure of backbone dynamics at single residue resolution and is an excellent tool for characterizing the dynamic behavior of disordered proteins. In this report, we show that the NHNOE values for several members of a family of disordered proteins are highly correlated with the output from three popular algorithms used to predict disordered regions from amino acid sequence. This is the first test between an experimental measure of residue specific backbone dynamics and disorder predictions. The results suggest that some disorder predictors can accurately estimate the backbone dynamics of individual amino acids in a long disordered region.
Collapse
Affiliation(s)
- Gary W Daughdrill
- Department of Cell Biology, Microbiology and Molecular Biology and Center for Drug Discovery and Innovation, University of South Florida, Tampa, Florida, United States of America.
| | | | | |
Collapse
|
10
|
Melnik BS, Molochkov NV, Prokhorov DA, Uversky VN, Kutyshenko VP. Molecular mechanisms of the anomalous thermal aggregation of green fluorescent protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1930-9. [DOI: 10.1016/j.bbapap.2011.07.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 07/19/2011] [Accepted: 07/19/2011] [Indexed: 11/27/2022]
|
11
|
Melnik TN, Povarnitsyna TV, Glukhov AS, Uversky VN, Melnik BS. Sequential Melting of Two Hydrophobic Clusters within the Green Fluorescent Protein GFP-cycle3. Biochemistry 2011; 50:7735-44. [DOI: 10.1021/bi2006674] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tatiana N. Melnik
- Institute
of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Tatiana V. Povarnitsyna
- Institute
of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Anatoly S. Glukhov
- Institute
of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Vladimir N. Uversky
- Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, Florida 33612,
United States
| | - Bogdan S. Melnik
- Institute
of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| |
Collapse
|
12
|
Kutyshenko VP, Gushchina LV, Khristoforov VS, Prokhorov DA, Timchenko MA, Kudrevatykh YA, Fedyukina DV, Filimonov VV. NMR structure and dynamics of the chimeric protein SH3-F2. Mol Biol 2010. [DOI: 10.1134/s0026893310060129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
13
|
Khristoforov VS, Prokhorov DA, Timchenko MA, Kudrevatykh YA, Gushchina LV, Filimonov VV, Kutyshenko VP. Chimeric SHA-D domain “SH3-Bergerac“: 3D structure and dynamics studies. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010. [DOI: 10.1134/s1068162010040059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|