1
|
Luu DD, Ramesh N, Kazan IC, Shah KH, Lahiri G, Mana MD, Ozkan SB, Van Horn WD. Evidence that the cold- and menthol-sensing functions of the human TRPM8 channel evolved separately. SCIENCE ADVANCES 2024; 10:eadm9228. [PMID: 38905339 PMCID: PMC11192081 DOI: 10.1126/sciadv.adm9228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/16/2024] [Indexed: 06/23/2024]
Abstract
Transient receptor potential melastatin 8 (TRPM8) is a temperature- and menthol-sensitive ion channel that contributes to diverse physiological roles, including cold sensing and pain perception. Clinical trials targeting TRPM8 have faced repeated setbacks predominantly due to the knowledge gap in unraveling the molecular underpinnings governing polymodal activation. A better understanding of the molecular foundations between the TRPM8 activation modes may aid the development of mode-specific, thermal-neutral therapies. Ancestral sequence reconstruction was used to explore the origins of TRPM8 activation modes. By resurrecting key TRPM8 nodes along the human evolutionary trajectory, we gained valuable insights into the trafficking, stability, and function of these ancestral forms. Notably, this approach unveiled the differential emergence of cold and menthol sensitivity over evolutionary time, providing a fresh perspective on complex polymodal behavior. These studies provide a paradigm for understanding polymodal behavior in TRPM8 and other proteins with the potential to enhance our understanding of sensory receptor biology and pave the way for innovative therapeutic interventions.
Collapse
Affiliation(s)
- Dustin D. Luu
- School of Molecular Sciences and The Virginia G. Piper Biodesign Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Nikhil Ramesh
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - I. Can Kazan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Karan H. Shah
- School of Molecular Sciences and The Virginia G. Piper Biodesign Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Gourab Lahiri
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Miyeko D. Mana
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - S. Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Wade D. Van Horn
- School of Molecular Sciences and The Virginia G. Piper Biodesign Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| |
Collapse
|
2
|
Ose NJ, Campitelli P, Modi T, Kazan IC, Kumar S, Ozkan SB. Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics. eLife 2024; 12:RP92063. [PMID: 38713502 PMCID: PMC11076047 DOI: 10.7554/elife.92063] [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] [Indexed: 05/08/2024] Open
Abstract
We integrate evolutionary predictions based on the neutral theory of molecular evolution with protein dynamics to generate mechanistic insight into the molecular adaptations of the SARS-COV-2 spike (S) protein. With this approach, we first identified candidate adaptive polymorphisms (CAPs) of the SARS-CoV-2 S protein and assessed the impact of these CAPs through dynamics analysis. Not only have we found that CAPs frequently overlap with well-known functional sites, but also, using several different dynamics-based metrics, we reveal the critical allosteric interplay between SARS-CoV-2 CAPs and the S protein binding sites with the human ACE2 (hACE2) protein. CAPs interact far differently with the hACE2 binding site residues in the open conformation of the S protein compared to the closed form. In particular, the CAP sites control the dynamics of binding residues in the open state, suggesting an allosteric control of hACE2 binding. We also explored the characteristic mutations of different SARS-CoV-2 strains to find dynamic hallmarks and potential effects of future mutations. Our analyses reveal that Delta strain-specific variants have non-additive (i.e., epistatic) interactions with CAP sites, whereas the less pathogenic Omicron strains have mostly additive mutations. Finally, our dynamics-based analysis suggests that the novel mutations observed in the Omicron strain epistatically interact with the CAP sites to help escape antibody binding.
Collapse
Affiliation(s)
- Nicholas James Ose
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - Tushar Modi
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - I Can Kazan
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple UniversityPhiladelphiaUnited States
- Department of Biology, Temple UniversityPhiladelphiaUnited States
- Center for Genomic Medicine Research, King Abdulaziz UniversityJeddahSaudi Arabia
| | - Sefika Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| |
Collapse
|
3
|
Ose NJ, Campitelli P, Modi T, Can Kazan I, Kumar S, Banu Ozkan S. Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.14.557827. [PMID: 37745560 PMCID: PMC10515954 DOI: 10.1101/2023.09.14.557827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
We integrate evolutionary predictions based on the neutral theory of molecular evolution with protein dynamics to generate mechanistic insight into the molecular adaptations of the SARS-COV-2 Spike (S) protein. With this approach, we first identified Candidate Adaptive Polymorphisms (CAPs) of the SARS-CoV-2 Spike protein and assessed the impact of these CAPs through dynamics analysis. Not only have we found that CAPs frequently overlap with well-known functional sites, but also, using several different dynamics-based metrics, we reveal the critical allosteric interplay between SARS-CoV-2 CAPs and the S protein binding sites with the human ACE2 (hACE2) protein. CAPs interact far differently with the hACE2 binding site residues in the open conformation of the S protein compared to the closed form. In particular, the CAP sites control the dynamics of binding residues in the open state, suggesting an allosteric control of hACE2 binding. We also explored the characteristic mutations of different SARS-CoV-2 strains to find dynamic hallmarks and potential effects of future mutations. Our analyses reveal that Delta strain-specific variants have non-additive (i.e., epistatic) interactions with CAP sites, whereas the less pathogenic Omicron strains have mostly additive mutations. Finally, our dynamics-based analysis suggests that the novel mutations observed in the Omicron strain epistatically interact with the CAP sites to help escape antibody binding.
Collapse
Affiliation(s)
- Nicholas J. Ose
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Tushar Modi
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - I. Can Kazan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
- Center for Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - S. Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| |
Collapse
|
4
|
Lu J, Rahman MI, Kazan IC, Halloran NR, Bobkov AA, Ozkan SB, Ghirlanda G. Engineering gain-of-function mutants of a WW domain by dynamics and structural analysis. Protein Sci 2023; 32:e4759. [PMID: 37574787 PMCID: PMC10464296 DOI: 10.1002/pro.4759] [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: 03/22/2023] [Revised: 07/17/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
Proteins gain optimal fitness such as foldability and function through evolutionary selection. However, classical studies have found that evolutionarily designed protein sequences alone cannot guarantee foldability, or at least not without considering local contacts associated with the initial folding steps. We previously showed that foldability and function can be restored by removing frustration in the folding energy landscape of a model WW domain protein, CC16, which was designed based on Statistical Coupling Analysis (SCA). Substitutions ensuring the formation of five local contacts identified as "on-path" were selected using the closest homolog native folded sequence, N21. Surprisingly, the resulting sequence, CC16-N21, bound to Group I peptides, while N21 did not. Here, we identified single-point mutations that enable N21 to bind a Group I peptide ligand through structure and dynamic-based computational design. Comparison of the docked position of the CC16-N21/ligand complex with the N21 structure showed that residues at positions 9 and 19 are important for peptide binding, whereas the dynamic profiles identified position 10 as allosterically coupled to the binding site and exhibiting different dynamics between N21 and CC16-N21. We found that swapping these positions in N21 with matched residues from CC16-N21 recovers nature-like binding affinity to N21. This study validates the use of dynamic profiles as guiding principles for affecting the binding affinity of small proteins.
Collapse
Affiliation(s)
- Jin Lu
- Department of Physics and Center for Biological PhysicsArizona State UniversityTempeArizonaUSA
| | | | - I. Can Kazan
- Department of Physics and Center for Biological PhysicsArizona State UniversityTempeArizonaUSA
| | | | - Andrey A. Bobkov
- Conrad Prebys Center for Chemical GenomicsSanford Burnham Prebys Medical Discovery InstituteCaliforniaUSA
| | - S. Banu Ozkan
- Department of Physics and Center for Biological PhysicsArizona State UniversityTempeArizonaUSA
| | | |
Collapse
|
5
|
Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles. Comput Struct Biotechnol J 2023; 21:1390-1402. [PMID: 36817953 PMCID: PMC9929209 DOI: 10.1016/j.csbj.2023.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/29/2023] Open
Abstract
We present the second update of Wordom, a user-friendly and efficient program for manipulation and analysis of conformational ensembles from molecular simulations. The actual update expands some of the existing modules and adds 21 new modules to the update 1 published in 2011. The new adds can be divided into three sets that: 1) analyze atomic fluctuations and structural communication; 2) explore ion-channel conformational dynamics and ionic translocation; and 3) compute geometrical indices of structural deformation. Set 1 serves to compute correlations of motions, find geometrically stable domains, identify a dynamically invariant core, find changes in domain-domain separation and mutual orientation, perform wavelet analysis of large-scale simulations, process the output of principal component analysis of atomic fluctuations, perform functional mode analysis, infer regions of mechanical rigidity, analyze overall fluctuations, and perform the perturbation response scanning. Set 2 includes modules specific for ion channels, which serve to monitor the pore radius as well as water or ion fluxes, and measure functional collective motions like receptor twisting or tilting angles. Finally, set 3 includes tools to monitor structural deformations by computing angles, perimeter, area, volume, β-sheet curvature, radial distribution function, and center of mass. The ring perception module is also included, helpful to monitor supramolecular self-assemblies. This update places Wordom among the most suitable, complete, user-friendly, and efficient software for the analysis of biomolecular simulations. The source code of Wordom and the relative documentation are available under the GNU general public license at http://wordom.sf.net.
Collapse
|
6
|
Stevens AO, Kazan IC, Ozkan B, He Y. Investigating the allosteric response of the PICK1 PDZ domain to different ligands with all-atom simulations. Protein Sci 2022; 31:e4474. [PMID: 36251217 PMCID: PMC9667829 DOI: 10.1002/pro.4474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/27/2022] [Accepted: 10/11/2022] [Indexed: 12/13/2022]
Abstract
The PDZ family is comprised of small modular domains that play critical roles in the allosteric modulation of many cellular signaling processes by binding to the C-terminal tail of different proteins. As dominant modular proteins that interact with a diverse set of peptides, it is of particular interest to explore how different binding partners induce different allosteric effects on the same PDZ domain. Because the PICK1 PDZ domain can bind different types of ligands, it is an ideal test case to answer this question and explore the network of interactions that give rise to dynamic allostery. Here, we use all-atom molecular dynamics simulations to explore dynamic allostery in the PICK1 PDZ domain by modeling two PICK1 PDZ systems: PICK1 PDZ-DAT and PICK1 PDZ-GluR2. Our results suggest that ligand binding to the PICK1 PDZ domain induces dynamic allostery at the αA helix that is similar to what has been observed in other PDZ domains. We found that the PICK1 PDZ-ligand distance is directly correlated with both dynamic changes of the αA helix and the distance between the αA helix and βB strand. Furthermore, our work identifies a hydrophobic core between DAT/GluR2 and I35 as a key interaction in inducing such dynamic allostery. Finally, the unique interaction patterns between different binding partners and the PICK1 PDZ domain can induce unique dynamic changes to the PICK1 PDZ domain. We suspect that unique allosteric coupling patterns with different ligands may play a critical role in how PICK1 performs its biological functions in various signaling networks.
Collapse
Affiliation(s)
- Amy O. Stevens
- Department of Chemistry and Chemical BiologyThe University of New MexicoAlbuquerqueNew MexicoUSA
| | - I. Can Kazan
- Department of Physics, Center for Biological PhysicsArizona State UniversityTempeArizonaUSA
| | - Banu Ozkan
- Department of Physics, Center for Biological PhysicsArizona State UniversityTempeArizonaUSA
| | - Yi He
- Department of Chemistry and Chemical BiologyThe University of New MexicoAlbuquerqueNew MexicoUSA
| |
Collapse
|
7
|
Shahabadi N, Hadidi S. Cu(I)-Phospine complex exhibits temperature-dependent DNA intercalative binding: Insights from spectroscopic and molecular modeling studies. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
8
|
Zhang M, Xue J, Chen X, Elsaid FG, Salem ET, Ghanem RA, El‐kott AF, Xu Z. Bioactivity of hamamelitannin, flavokawain A, and triacetyl resveratrol as natural compounds: Molecular docking study, anti‐colon cancer and anti‐Alzheimer potentials. Biotechnol Appl Biochem 2022; 70:730-745. [PMID: 35933706 DOI: 10.1002/bab.2394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/24/2022] [Indexed: 11/07/2022]
Abstract
In this study, we worked on anticolon cancer effects and anti-Alzheimer's disease with molecular docking studies. Hamamelitannin, flavokawain A, and triacetyl resveratrol compounds showed good inhibitory activities on acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) enzymes. The inhibition effects of flavokawain A, hamamelitannin, and triacetyl resveratrol on AChE and BuChE enzymes were determined spectrophotometrically conforming to Ellman. IC50 values of these enzymes were ranging between 0.95 ± 0.12 and 93.27 ± 8.14 nM for AChE and 5.71 ± 0.77 and 52.10 ± 8.41 nM for BuChE. The inhibitory activities of some chemical compounds such as flavokawain A, hamamelitannin, and triacetyl resveratrol were assessed by performing the molecular docking study in the presence of AChE and BuChE. Also, the features of the ligand-enzyme complex had value of -7.722 kcal/mol for flavokawain A against AChE and -5.530 kcal/mol against BuChE. The molecular docking calculations indicated the probable interactions and their characteristics at an atomic level. Due to the outcomes gained from docking, the affinity of the chemical compounds to the enzymes was considerable. In vitro cell viabilities of flavokawain A, hamamelitannin, and triacetyl resveratrol with various concentrations on SW620, DLD-1, HT29, HCT8, and HCT116 were investigated by MTT assay with Doxorubicin as the control compound.
Collapse
Affiliation(s)
- Ming Zhang
- Department of Gastroenterology The Second Affiliated Hospital of Xi'an Medical College Xi'an Shaanxi 710038 China
| | - Jiao Xue
- Health Management Center QingDao Municipal Hospital, ShanDong province QingDao 266000 China
| | - Xiao Chen
- Second Department of Encephalopathy Xi'an Chinese Medicine Hospital Xi'an Shaanxi 710032 China
| | - Fahmy G. Elsaid
- Department of Biology, Science College King Khalid University Abha Saudi Arabia
- Department of Zoology, Faculty of Science Mansoura University Mansoura Egypt
| | - Eman T. Salem
- Department of Basic Science, Faculty of Physical Therapy Horus University‐Egypt New Damietta 34518 Egypt
| | - Reham A. Ghanem
- Department of Oral biology, faculty of oral and dental medicine Delta university for science and technology Gamasa Egypt
| | - Attalla F. El‐kott
- Department of Biology, College of Science King Khalid University Abha Saudi Arabia
- Department of Zoology, Faculty of Science Damanhour University Damanhour Egypt
| | - Zhongkai Xu
- Department of Gastrointestinal Surgery Jinan Central Hospital Affiliated to Shandong University, Shangdong Jinan 250013 China
| |
Collapse
|
9
|
Kazan IC, Sharma P, Rahman MI, Bobkov A, Fromme R, Ghirlanda G, Ozkan SB. Design of novel cyanovirin-N variants by modulation of binding dynamics through distal mutations. eLife 2022; 11:67474. [PMID: 36472898 PMCID: PMC9725752 DOI: 10.7554/elife.67474] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 11/28/2022] [Indexed: 12/07/2022] Open
Abstract
We develop integrated co-evolution and dynamic coupling (ICDC) approach to identify, mutate, and assess distal sites to modulate function. We validate the approach first by analyzing the existing mutational fitness data of TEM-1 β-lactamase and show that allosteric positions co-evolved and dynamically coupled with the active site significantly modulate function. We further apply ICDC approach to identify positions and their mutations that can modulate binding affinity in a lectin, cyanovirin-N (CV-N), that selectively binds to dimannose, and predict binding energies of its variants through Adaptive BP-Dock. Computational and experimental analyses reveal that binding enhancing mutants identified by ICDC impact the dynamics of the binding pocket, and show that rigidification of the binding residues compensates for the entropic cost of binding. This work suggests a mechanism by which distal mutations modulate function through dynamic allostery and provides a blueprint to identify candidates for mutagenesis in order to optimize protein function.
Collapse
Affiliation(s)
- I Can Kazan
- Center for Biological Physics and Department of Physics, Arizona State UniversityTempeUnited States,School of Molecular Sciences, Arizona State UniversityTempeUnited States
| | - Prerna Sharma
- School of Molecular Sciences, Arizona State UniversityTempeUnited States
| | | | - Andrey Bobkov
- Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State UniversityTempeUnited States
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State UniversityTempeUnited States
| | - S Banu Ozkan
- Center for Biological Physics and Department of Physics, Arizona State UniversityTempeUnited States
| |
Collapse
|
10
|
|
11
|
Modi T, Risso VA, Martinez-Rodriguez S, Gavira JA, Mebrat MD, Van Horn WD, Sanchez-Ruiz JM, Banu Ozkan S. Hinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity. Nat Commun 2021; 12:1852. [PMID: 33767175 PMCID: PMC7994827 DOI: 10.1038/s41467-021-22089-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 02/01/2021] [Indexed: 01/31/2023] Open
Abstract
TEM-1 β-lactamase degrades β-lactam antibiotics with a strong preference for penicillins. Sequence reconstruction studies indicate that it evolved from ancestral enzymes that degraded a variety of β-lactam antibiotics with moderate efficiency. This generalist to specialist conversion involved more than 100 mutational changes, but conserved fold and catalytic residues, suggesting a role for dynamics in enzyme evolution. Here, we develop a conformational dynamics computational approach to rationally mold a protein flexibility profile on the basis of a hinge-shift mechanism. By deliberately weighting and altering the conformational dynamics of a putative Precambrian β-lactamase, we engineer enzyme specificity that mimics the modern TEM-1 β-lactamase with only 21 amino acid replacements. Our conformational dynamics design thus re-enacts the evolutionary process and provides a rational allosteric approach for manipulating function while conserving the enzyme active site.
Collapse
Affiliation(s)
- Tushar Modi
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Valeria A Risso
- Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain
- Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada, Spain
| | - Sergio Martinez-Rodriguez
- Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain
- Departamento de Bioquimica, Biologia Molecular III e Inmunologia, Universidad de Granada, Granada, Spain
| | - Jose A Gavira
- Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada, Spain
- Laboratorio de Estudios Cristalograficos, Instituto Andaluz de Ciencias de la Tierra, CSIC, Universidad de Granada, Granada, Armilla, Spain
| | - Mubark D Mebrat
- The Biodesign Institute Virginia G. Piper Center for Personalized Diagnostics, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Wade D Van Horn
- The Biodesign Institute Virginia G. Piper Center for Personalized Diagnostics, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Jose M Sanchez-Ruiz
- Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain.
- Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada, Spain.
| | - S Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA.
| |
Collapse
|
12
|
The Role of Rigid Residues in Modulating TEM-1 β-Lactamase Function and Thermostability. Int J Mol Sci 2021; 22:ijms22062895. [PMID: 33809335 PMCID: PMC7999226 DOI: 10.3390/ijms22062895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 01/18/2023] Open
Abstract
The relationship between protein motions (i.e., dynamics) and enzymatic function has begun to be explored in β-lactamases as a way to advance our understanding of these proteins. In a recent study, we analyzed the dynamic profiles of TEM-1 (a ubiquitous class A β-lactamase) and several ancestrally reconstructed homologues. A chief finding of this work was that rigid residues that were allosterically coupled to the active site appeared to have profound effects on enzyme function, even when separated from the active site by many angstroms. In the present work, our aim was to further explore the implications of protein dynamics on β-lactamase function by altering the dynamic profile of TEM-1 using computational protein design methods. The Rosetta software suite was used to mutate amino acids surrounding either rigid residues that are highly coupled to the active site or to flexible residues with no apparent communication with the active site. Experimental characterization of ten designed proteins indicated that alteration of residues surrounding rigid, highly coupled residues, substantially affected both enzymatic activity and stability; in contrast, native-like activities and stabilities were maintained when flexible, uncoupled residues, were targeted. Our results provide additional insight into the structure-function relationship present in the TEM family of β-lactamases. Furthermore, the integration of computational protein design methods with analyses of protein dynamics represents a general approach that could be used to extend our understanding of the relationship between dynamics and function in other enzyme classes.
Collapse
|
13
|
Modi T, Campitelli P, Kazan IC, Ozkan SB. Protein folding stability and binding interactions through the lens of evolution: a dynamical perspective. Curr Opin Struct Biol 2020; 66:207-215. [PMID: 33388636 DOI: 10.1016/j.sbi.2020.11.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/02/2020] [Accepted: 11/26/2020] [Indexed: 01/06/2023]
Abstract
While the function of a protein depends heavily on its ability to fold into a correct 3D structure, billions of years of evolution have tailored proteins from highly stable objects to flexible molecules as they adapted to environmental changes. Nature maintains the fine balance of protein folding and stability while still evolving towards new function through generations of fine-tuning necessary interactions with other proteins and small molecules. Here we focus on recent computational and experimental studies that shed light onto how evolution molds protein folding and the functional landscape from a conformational dynamics' perspective. Particularly, we explore the importance of dynamic allostery throughout protein evolution and discuss how the protein anisotropic network can give rise to allosteric and epistatic interactions.
Collapse
Affiliation(s)
- Tushar Modi
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Ismail Can Kazan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Sefika Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287-1504, USA.
| |
Collapse
|
14
|
Larrimore KE, Kannan L, Kendle RP, Jamal T, Barcus M, Stefanko K, Kilbourne J, Brimijoin S, Zhan CG, Neisewander J, Mor TS. A plant-derived cocaine hydrolase prevents cocaine overdose lethality and attenuates cocaine-induced drug seeking behavior. Prog Neuropsychopharmacol Biol Psychiatry 2020; 102:109961. [PMID: 32387315 PMCID: PMC7398606 DOI: 10.1016/j.pnpbp.2020.109961] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 05/01/2020] [Accepted: 05/02/2020] [Indexed: 12/21/2022]
Abstract
Cocaine use disorders include short-term and acute pathologies (e.g. overdose) and long-term and chronic disorders (e.g. intractable addiction and post-abstinence relapse). There is currently no available treatment that can effectively reduce morbidity and mortality associated with cocaine overdose or that can effectively prevent relapse in recovering addicts. One recently developed approach to treat these problems is the use of enzymes that rapidly break down the active cocaine molecule into inactive metabolites. In particular, rational design and site-directed mutagenesis transformed human serum recombinant butyrylcholinesterase (BChE) into a highly efficient cocaine hydrolase with drastically improved catalytic efficiency toward (-)-cocaine. A current drawback preventing the clinical application of this promising enzyme-based therapy is the lack of a cost-effective production strategy that is also flexible enough to rapidly scale-up in response to continuous improvements in enzyme design. Plant-based expression systems provide a unique solution as this platform is designed for fast scalability, low cost and the advantage of performing eukaryotic protein modifications such as glycosylation. A Plant-derived form of the Cocaine Super Hydrolase (A199S/F227A/S287G/A328W/Y332G) we designate PCocSH protects mice from cocaine overdose, counters the lethal effects of acute cocaine overdose, and prevents reinstatement of extinguished drug-seeking behavior in mice that underwent place conditioning with cocaine. These results demonstrate that the novel PCocSH enzyme may well serve as an effective therapeutic for cocaine use disorders in a clinical setting.
Collapse
Affiliation(s)
| | - Latha Kannan
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA; Center of Immunotherapy, Vaccines, and Virotherapy, Biodesign Institute, Arizona State University, Tempe, AZ 85287-4501, USA.
| | - R Player Kendle
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA.
| | - Tameem Jamal
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA.
| | - Matthew Barcus
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA.
| | - Kathryn Stefanko
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
| | - Jacquelyn Kilbourne
- Center of Immunotherapy, Vaccines, and Virotherapy, Biodesign Institute, Arizona State University, Tempe, AZ 85287-4501, USA.
| | - Stephen Brimijoin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.
| | - Chang-Guo Zhan
- Molecular Modeling and Biopharmaceutical Center and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA.
| | - Janet Neisewander
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA.
| | - Tsafrir S Mor
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA; Center of Immunotherapy, Vaccines, and Virotherapy, Biodesign Institute, Arizona State University, Tempe, AZ 85287-4501, USA.
| |
Collapse
|
15
|
Allostery and Epistasis: Emergent Properties of Anisotropic Networks. ENTROPY 2020; 22:e22060667. [PMID: 33286439 PMCID: PMC7517209 DOI: 10.3390/e22060667] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/02/2020] [Accepted: 06/08/2020] [Indexed: 11/17/2022]
Abstract
Understanding the underlying mechanisms behind protein allostery and non-additivity of substitution outcomes (i.e., epistasis) is critical when attempting to predict the functional impact of mutations, particularly at non-conserved sites. In an effort to model these two biological properties, we extend the framework of our metric to calculate dynamic coupling between residues, the Dynamic Coupling Index (DCI) to two new metrics: (i) EpiScore, which quantifies the difference between the residue fluctuation response of a functional site when two other positions are perturbed with random Brownian kicks simultaneously versus individually to capture the degree of cooperativity of these two other positions in modulating the dynamics of the functional site and (ii) DCIasym, which measures the degree of asymmetry between the residue fluctuation response of two sites when one or the other is perturbed with a random force. Applied to four independent systems, we successfully show that EpiScore and DCIasym can capture important biophysical properties in dual mutant substitution outcomes. We propose that allosteric regulation and the mechanisms underlying non-additive amino acid substitution outcomes (i.e., epistasis) can be understood as emergent properties of an anisotropic network of interactions where the inclusion of the full network of interactions is critical for accurate modeling. Consequently, mutations which drive towards a new function may require a fine balance between functional site asymmetry and strength of dynamic coupling with the functional sites. These two tools will provide mechanistic insight into both understanding and predicting the outcome of dual mutations.
Collapse
|
16
|
Campitelli P, Modi T, Kumar S, Ozkan SB. The Role of Conformational Dynamics and Allostery in Modulating Protein Evolution. Annu Rev Biophys 2020; 49:267-288. [PMID: 32075411 DOI: 10.1146/annurev-biophys-052118-115517] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Advances in sequencing techniques and statistical methods have made it possible not only to predict sequences of ancestral proteins but also to identify thousands of mutations in the human exome, some of which are disease associated. These developments have motivated numerous theories and raised many questions regarding the fundamental principles behind protein evolution, which have been traditionally investigated horizontally using the tip of the phylogenetic tree through comparative studies of extant proteins within a family. In this article, we review a vertical comparison of the modern and resurrected ancestral proteins. We focus mainly on the dynamical properties responsible for a protein's ability to adapt new functions in response to environmental changes. Using the Dynamic Flexibility Index and the Dynamic Coupling Index to quantify the relative flexibility and dynamic coupling at a site-specific, single-amino-acid level, we provide evidence that the migration of hinges, which are often functionally critical rigid sites, is a mechanism through which proteins can rapidly evolve. Additionally, we show that disease-associated mutations in proteins often result in flexibility changes even at positions distal from mutational sites, particularly in the modulation of active site dynamics.
Collapse
Affiliation(s)
- Paul Campitelli
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona 85281, USA; , ,
| | - Tushar Modi
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona 85281, USA; , ,
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania 19122, USA; .,Department of Biology, Temple University, Philadelphia, Pennsylvania 19122, USA.,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - S Banu Ozkan
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona 85281, USA; , ,
| |
Collapse
|
17
|
Soares A, Niedermaier S, Faro R, Loos A, Manadas B, Faro C, Huesgen PF, Cheung AY, Simões I. An atypical aspartic protease modulates lateral root development in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2157-2171. [PMID: 30778561 DOI: 10.1093/jxb/erz059] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/05/2019] [Indexed: 05/25/2023]
Abstract
Few atypical aspartic proteases (APs) present in plants have been functionally studied to date despite having been implicated in developmental processes and stress responses. Here we characterize a novel atypical AP that we name Atypical Aspartic Protease in Roots 1 (ASPR1), denoting its expression in Arabidopsis roots. Recombinant ASPR1 produced by transient expression in Nicotiana benthamiana was active and displayed atypical properties, combining optimum acidic pH, partial sensitivity to pepstatin, pronounced sensitivity to redox agents, and unique specificity preferences resembling those of fungal APs. ASPR1 overexpression suppressed primary root growth and lateral root development, implying a previously unknown biological role for an AP. Quantitative comparison of wild-type and aspr1 root proteomes revealed deregulation of proteins associated with both reactive oxygen species and auxin homeostasis in the mutant. Together, our findings on ASPR1 reinforce the diverse pattern of enzymatic properties and biological roles of atypical APs and raise exciting questions on how these distinctive features impact functional specialization among these proteases.
Collapse
Affiliation(s)
- André Soares
- PhD Programme in Experimental Biology and Biomedicine, Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
- Institute for Interdisciplinary Research, University of Coimbra, Portugal
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
| | - Stefan Niedermaier
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Rosário Faro
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - Andreas Loos
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Bruno Manadas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - Carlos Faro
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Alice Y Cheung
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
| | - Isaura Simões
- Institute for Interdisciplinary Research, University of Coimbra, Portugal
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| |
Collapse
|
18
|
Mutations Utilize Dynamic Allostery to Confer Resistance in TEM-1 β-lactamase. Int J Mol Sci 2018; 19:ijms19123808. [PMID: 30501088 PMCID: PMC6321620 DOI: 10.3390/ijms19123808] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 11/27/2018] [Accepted: 11/27/2018] [Indexed: 12/20/2022] Open
Abstract
β-lactamases are enzymes produced by bacteria to hydrolyze β-lactam antibiotics as a common mechanism of resistance. Evolution in such enzymes has been rendering a wide variety of antibiotics impotent, therefore posing a major threat. Clinical and in vitro studies of evolution in TEM-1 β-lactamase have revealed a large number of single point mutations that are responsible for driving resistance to antibiotics and/or inhibitors. The distal locations of these mutations from the active sites suggest that these allosterically modulate the antibiotic resistance. We investigated the effects of resistance driver mutations on the conformational dynamics of the enzyme to provide insights about the mechanism of their long-distance interactions. Through all-atom molecular dynamics (MD) simulations, we obtained the dynamic flexibility profiles of the variants and compared those with that of the wild type TEM-1. While the mutational sites in the variants did not have any direct van der Waals interactions with the active site position S70 and E166, we observed a change in the flexibility of these sites, which play a very critical role in hydrolysis. Such long distance dynamic interactions were further confirmed by dynamic coupling index (DCI) analysis as the sites involved in resistance driving mutations exhibited high dynamic coupling with the active sites. A more exhaustive dynamic analysis, using a selection pressure for ampicillin and cefotaxime resistance on all possible types of substitutions in the amino acid sequence of TEM-1, further demonstrated the observed mechanism. Mutational positions that play a crucial role for the emergence of resistance to new antibiotics exhibited high dynamic coupling with the active site irrespective of their locations. These dynamically coupled positions were neither particularly rigid nor particularly flexible, making them more evolvable positions. Nature utilizes these sites to modulate the dynamics of the catalytic sites instead of mutating the highly rigid positions around the catalytic site.
Collapse
|
19
|
Modi T, Huihui J, Ghosh K, Ozkan SB. Ancient thioredoxins evolved to modern-day stability-function requirement by altering native state ensemble. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170184. [PMID: 29735738 PMCID: PMC5941179 DOI: 10.1098/rstb.2017.0184] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2018] [Indexed: 02/06/2023] Open
Abstract
Thioredoxins (THRXs)-small globular proteins that reduce other proteins-are ubiquitous in all forms of life, from Archaea to mammals. Although ancestral thioredoxins share sequential and structural similarity with the modern-day (extant) homologues, they exhibit significantly different functional activity and stability. We investigate this puzzle by comparative studies of their (ancient and modern-day THRXs') native state ensemble, as quantified by the dynamic flexibility index (DFI), a metric for the relative resilience of an amino acid to perturbations in the rest of the protein. Clustering proteins using DFI profiles strongly resemble an alternative classification scheme based on their activity and stability. The DFI profiles of the extant proteins are substantially different around the α3, α4 helices and catalytic regions. Likewise, allosteric coupling of the active site with the rest of the protein is different between ancient and extant THRXs, possibly explaining the decreased catalytic activity at low pH with evolution. At a global level, we note that the population of low-flexibility (called hinges) and high-flexibility sites increases with evolution. The heterogeneity (quantified by the variance) in DFI distribution increases with the decrease in the melting temperature typically associated with the evolution of ancient proteins to their modern-day counterparts.This article is part of a discussion meeting issue 'Allostery and molecular machines'.
Collapse
Affiliation(s)
- Tushar Modi
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85281, USA
| | - Jonathan Huihui
- Department of Physics and Astronomy, University of Denver, Denver, CO 80209, USA
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, CO 80209, USA
| | - S Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85281, USA
| |
Collapse
|
20
|
Masson P, Lushchekina S. Analysis of Apparent Catalytic Parameters of Multiple Molecular Forms of Human Plasma Butyrylcholinesterase by Activity Gel-Scanning Following Non-denaturing Electrophoresis. BIONANOSCIENCE 2018. [DOI: 10.1007/s12668-017-0489-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
21
|
Campitelli P, Guo J, Zhou HX, Ozkan SB. Hinge-Shift Mechanism Modulates Allosteric Regulations in Human Pin1. J Phys Chem B 2018; 122:5623-5629. [PMID: 29361231 DOI: 10.1021/acs.jpcb.7b11971] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allostery, which is regulation from distant sites, plays a major role in biology. While traditional allostery is described in terms of conformational change upon ligand binding as an underlying principle, it is possible to have allosteric regulations without significant conformational change through modulating the conformational dynamics by altering the local effective elastic modulus of the protein upon ligand binding. Pin1 utilizes this dynamic allostery to regulate its function. It is a modular protein containing a WW domain and a larger peptidyl prolyl isomerase domain (PPIase) that isomerizes phosphoserine/threonine-proline (pS/TP) motifs. The WW domain serves as a docking module, whereas catalysis solely takes place within the PPIase domain. Here, we analyze the change in the dynamic flexibility profile of the PPIase domain upon ligand binding to the WW domain. Substrate binding to the WW domain induces the formation of a new rigid hinge site around the interface of the two domains and loosens the flexibility of a rigid site existing in the Apo form around the catalytic site. This hinge-shift mechanism enhances the dynamic coupling of the catalytic positions with the PPIase domain, where the rest of the domain can cooperatively respond to the local conformational changes around the catalytic site, leading to an increase in catalytic efficiency.
Collapse
Affiliation(s)
- Paul Campitelli
- Department of Physics and Center for Biological Physics , Arizona State University , Tempe , Arizona 85287 , United States
| | - Jingjing Guo
- School of Chemistry and Chemical Engineering , Henan Normal University , Xinxiang , China
| | - Huan-Xiang Zhou
- Department of Chemistry and Department of Physics , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
| | - S Banu Ozkan
- Department of Physics and Center for Biological Physics , Arizona State University , Tempe , Arizona 85287 , United States
| |
Collapse
|