1
|
Alalmaie A, Khashan R. Mechanistic Insight Into the Conformational Changes of Cas8 Upon Binding to Different PAM Sequences in the Transposon-Encoded Type I-F CRISPR-Cas System. Proteins 2024. [PMID: 39171866 DOI: 10.1002/prot.26730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 07/02/2024] [Indexed: 08/23/2024]
Abstract
The INTEGRATE system is a gene-editing approach that offers advantages over the widely used CRISPR-Cas9 system. It does not introduce double strand breaks in the target DNA but rather integrates the desired DNA sequence directly into it. The first step in the integration process is PAM recognition, which is critical to understanding and optimizing the system. Experimental testing revealed varying integration efficiencies of different PAM mutants, and computational simulations were carried out to gain mechanistic insight into the conformational changes of Cas8 during PAM recognition. Our results showed that the interaction between Arg246 and guanine at position (-1) of the target strand is critical for PAM recognition. We found that unfavorable interactions in the 5'-AC-3' PAM mutant disrupted this interaction and may be responsible for its 0% integration efficiency. Additionally, we discovered that PAM sequences not only initiate the integration process but also regulate it through an allosteric mechanism that connects the N-terminal domain and the helical bundle of Cas8. This allosteric regulation was present in all PAMs tested, even those with lower integration efficiencies, such as 5'-TC-3' and 5'-AC-3'. We identified the Cas8 residues that are involved in this regulation. Our findings provide valuable insights into PAM recognition mechanisms in the INTEGRATE system and can help improve the gene-editing technology.
Collapse
Affiliation(s)
- Amnah Alalmaie
- Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, Saint Joseph University, Philadelphia, PA, USA
| | - Raed Khashan
- Division of Pharmaceutical Sciences, Collage of Pharmacy, Long Island University, Brooklyn, New York, USA
| |
Collapse
|
2
|
McCullagh M, Zeczycki TN, Kariyawasam CS, Durie CL, Halkidis K, Fitzkee NC, Holt JM, Fenton AW. What is allosteric regulation? Exploring the exceptions that prove the rule! J Biol Chem 2024; 300:105672. [PMID: 38272229 PMCID: PMC10897898 DOI: 10.1016/j.jbc.2024.105672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
"Allosteric" was first introduced to mean the other site (i.e., a site distinct from the active or orthosteric site), an adjective for "regulation" to imply a regulatory outcome resulting from ligand binding at another site. That original idea outlines a system with two ligand-binding events at two distinct locations on a macromolecule (originally a protein system), which defines a four-state energy cycle. An allosteric energy cycle provides a quantifiable allosteric coupling constant and focuses our attention on the unique properties of the four equilibrated protein complexes that constitute the energy cycle. Because many observed phenomena have been referenced as "allosteric regulation" in the literature, the goal of this work is to use literature examples to explore which systems are and are not consistent with the two-ligand thermodynamic energy cycle-based definition of allosteric regulation. We emphasize the need for consistent language so comparisons can be made among the ever-increasing number of allosteric systems. Building on the mutually exclusive natures of an energy cycle definition of allosteric regulation versus classic two-state models, we conclude our discussion by outlining how the often-proposed Rube-Goldberg-like mechanisms are likely inconsistent with an energy cycle definition of allosteric regulation.
Collapse
Affiliation(s)
- Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Tonya N Zeczycki
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
| | - Chathuri S Kariyawasam
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | - Clarissa L Durie
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Konstantine Halkidis
- Department of Hematologic Malignancies and Cellular Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas, USA; Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | - Jo M Holt
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA.
| |
Collapse
|
3
|
Sulyman AO, Fulcher J, Crossley S, Fatokun AA, Olorunniji FJ. Shikonin and Juglone Inhibit Mycobacterium tuberculosis Low-Molecular-Weight Protein Tyrosine Phosphatase a (Mt-PTPa). BIOTECH 2023; 12:59. [PMID: 37754203 PMCID: PMC10526854 DOI: 10.3390/biotech12030059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 08/21/2023] [Accepted: 09/12/2023] [Indexed: 09/28/2023] Open
Abstract
Low-molecular-weight protein tyrosine phosphatases (LMW-PTPs) are involved in promoting the intracellular survival of Mycobacterium tuberculosis (Mtb), the causative organism of tuberculosis. These PTPs directly alter host signalling pathways to evade the hostile environment of macrophages and avoid host clearance. Among these, protein tyrosine phosphatase A (Mt-PTPa) is implicated in phagosome acidification failure, thereby inhibiting phagosome maturation to promote Mycobacterium tuberculosis (Mtb) survival. In this study, we explored Mt-PTPa as a potential drug target for treating Mtb. We started by screening a library of 502 pure natural compounds against the activities of Mt-PTPa in vitro, with a threshold of 50% inhibition of activity via a <500 µM concentration of the candidate drugs. The initial screen identified epigallocatechin, myricetin, rosmarinic acid, and shikonin as hits. Among these, the naphthoquinone, shikonin (5, 8-dihydroxy-2-[(1R)-1-hydroxy-4-methyl-3-pentenyl]-1,4-naphthoquinone), showed the strongest inhibition (IC50 33 µM). Further tests showed that juglone (5-hydroxy-1,4-naphthalenedione), another naphthoquinone, displayed similar potent inhibition of Mt-PTPa to shikonin. Kinetic analysis of the inhibition patterns suggests a non-competitive inhibition mechanism for both compounds, with inhibitor constants (Ki) of 8.5 µM and 12.5 µM for shikonin and juglone, respectively. Our findings are consistent with earlier studies suggesting that Mt-PTPa is susceptible to specific allosteric modulation via a non-competitive or mixed inhibition mechanism.
Collapse
Affiliation(s)
- Abdulhakeem O. Sulyman
- Department of Biochemistry, Faculty of Pure and Applied Sciences, Kwara State University, Malete 241103, Nigeria
- School of Pharmacy & Biomolecular Sciences, Faculty of Science, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Jessie Fulcher
- School of Pharmacy & Biomolecular Sciences, Faculty of Science, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Samuel Crossley
- School of Pharmacy & Biomolecular Sciences, Faculty of Science, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Amos A. Fatokun
- School of Pharmacy & Biomolecular Sciences, Faculty of Science, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Femi J. Olorunniji
- School of Pharmacy & Biomolecular Sciences, Faculty of Science, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| |
Collapse
|
4
|
Maschietto F, Allen B, Kyro GW, Batista VS. MDiGest: A Python package for describing allostery from molecular dynamics simulations. J Chem Phys 2023; 158:215103. [PMID: 37272574 PMCID: PMC10769569 DOI: 10.1063/5.0140453] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/04/2023] [Indexed: 06/06/2023] Open
Abstract
Many biological processes are regulated by allosteric mechanisms that communicate with distant sites in the protein responsible for functionality. The binding of a small molecule at an allosteric site typically induces conformational changes that propagate through the protein along allosteric pathways regulating enzymatic activity. Elucidating those communication pathways from allosteric sites to orthosteric sites is, therefore, essential to gain insights into biochemical processes. Targeting the allosteric pathways by mutagenesis can allow the engineering of proteins with desired functions. Furthermore, binding small molecule modulators along the allosteric pathways is a viable approach to target reactions using allosteric inhibitors/activators with temporal and spatial selectivity. Methods based on network theory can elucidate protein communication networks through the analysis of pairwise correlations observed in molecular dynamics (MD) simulations using molecular descriptors that serve as proxies for allosteric information. Typically, single atomic descriptors such as α-carbon displacements are used as proxies for allosteric information. Therefore, allosteric networks are based on correlations revealed by that descriptor. Here, we introduce a Python software package that provides a comprehensive toolkit for studying allostery from MD simulations of biochemical systems. MDiGest offers the ability to describe protein dynamics by combining different approaches, such as correlations of atomic displacements or dihedral angles, as well as a novel approach based on the correlation of Kabsch-Sander electrostatic couplings. MDiGest allows for comparisons of networks and community structures that capture physical information relevant to allostery. Multiple complementary tools for studying essential dynamics include principal component analysis, root mean square fluctuation, as well as secondary structure-based analyses.
Collapse
Affiliation(s)
- Federica Maschietto
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Brandon Allen
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Gregory W. Kyro
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Victor S. Batista
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| |
Collapse
|
5
|
Berezovsky IN, Nussinov R. Multiscale Allostery: Basic Mechanisms and Versatility in Diagnostics and Drug Design. J Mol Biol 2022; 434:167751. [PMID: 35863488 DOI: 10.1016/j.jmb.2022.167751] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore; Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore.
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboraory, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| |
Collapse
|