1
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Has C, Das SL. The Functionality of Membrane-Inserting Proteins and Peptides: Curvature Sensing, Generation, and Pore Formation. J Membr Biol 2023; 256:343-372. [PMID: 37650909 DOI: 10.1007/s00232-023-00289-7] [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: 01/17/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
Proteins and peptides with hydrophobic and amphiphilic segments are responsible for many biological functions. The sensing and generation of membrane curvature are the functions of several protein domains or motifs. While some specific membrane proteins play an essential role in controlling the curvature of distinct intracellular membranes, others participate in various cellular processes such as clathrin-mediated endocytosis, where several proteins sort themselves at the neck of the membrane bud. A few membrane-inserting proteins form nanopores that permeate selective ions and water to cross the membrane. In addition, many natural and synthetic small peptides and protein toxins disrupt the membrane by inducing nonspecific pores in the membrane. The pore formation causes cell death through the uncontrolled exchange between interior and exterior cellular contents. In this article, we discuss the insertion depth and orientation of protein/peptide helices, and their role as a sensor and inducer of membrane curvature as well as a pore former in the membrane. We anticipate that this extensive review will assist biophysicists to gain insight into curvature sensing, generation, and pore formation by membrane insertion.
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Affiliation(s)
- Chandra Has
- Department of Chemical Engineering, GSFC University, Vadodara, 391750, Gujarat, India.
| | - Sovan Lal Das
- Physical and Chemical Biology Laboratory and Department of Mechanical Engineering, Indian Institute of Technology, Palakkad, 678623, Kerala, India
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2
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Tyagi C, Marik T, Szekeres A, Vágvölgyi C, Kredics L, Ötvös F. Modeling the Effect on a Novel Fungal Peptaibol Placed in an All-Atom Bacterial Membrane Mimicking System via Accelerated Molecular Dynamics Simulations. Life (Basel) 2023; 13:2288. [PMID: 38137889 PMCID: PMC10744397 DOI: 10.3390/life13122288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
We previously reported on a novel peptaibol, named Tripleurin XIIc (TPN), an 18-residue long sequence produced by the fungus Trichoderma pleuroti. We elucidated its 3D structure via classical and accelerated molecular dynamics simulation (aMD) methods and reported the folding dynamics of TPN in water and chloroform solvents. Peptaibols, in general, are insoluble in water, as they are amphipathic and may prefer hydrophobic environments like transmembrane regions. In this study, we attempted to use aMD simulations to model an all-atom bacterial membrane system while placing a TPN molecule in its vicinity. The results highlighted that TPN was able to introduce some disorder into the membrane and caused lipid clustering. It could also enter the transmembrane region from the water-bilayer interface. The structural dynamics of TPN in the transmembrane region revealed a single energetically stable conformation similar to the one obtained from water and chloroform solvent simulations reported by us previously. However, this linear structure was found to be at the local energy minimum (stable) in water but at a metastable intermediate state (higher energy) in chloroform. Therefore, it could be said that the water solvent can be successfully used for folding simulations of peptaibols.
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Affiliation(s)
- Chetna Tyagi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (A.S.); (C.V.); (L.K.)
| | - Tamás Marik
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (A.S.); (C.V.); (L.K.)
| | - András Szekeres
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (A.S.); (C.V.); (L.K.)
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (A.S.); (C.V.); (L.K.)
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (A.S.); (C.V.); (L.K.)
| | - Ferenc Ötvös
- Institute of Biochemistry, Biological Research Centre, Temesvári krt. 62, H-6726 Szeged, Hungary;
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3
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Pereira-Dias L, Oliveira-Pinto PR, Fernandes JO, Regalado L, Mendes R, Teixeira C, Mariz-Ponte N, Gomes P, Santos C. Peptaibiotics: Harnessing the potential of microbial secondary metabolites for mitigation of plant pathogens. Biotechnol Adv 2023; 68:108223. [PMID: 37536466 DOI: 10.1016/j.biotechadv.2023.108223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
Agricultural systems are in need of low-cost, safe antibiotics to protect crops from pests and diseases. Peptaibiotics, a family of linear, membrane-active, amphipathic polypeptides, have been shown to exhibit antibacterial, antifungal, and antiviral activity, and to be inducers of plant resistance against a wide range of phytopathogens. Peptaibiotics belong to the new generation of alternatives to agrochemicals, aligned with the United Nations Sustainable Development Goals and the One Health approach toward ensuring global food security and safety. Despite that, these fungi-derived, non-ribosomal peptides remain surprisingly understudied, especially in agriculture, where only a small number has been tested against a reduced number of phytopathogens. This lack of adoption stems from peptaibiotics' poor water solubility and the difficulty to synthesize and purify them in vitro, which compromises their delivery and inclusion in formulations. In this review, we offer a comprehensive analysis of peptaibiotics' classification, biosynthesis, relevance to plant protection, and mode of action against phytopathogens, along with the techniques enabling researchers to extract, purify, and elucidate their structure, and the databases holding such valuable data. It is also discussed how chemical synthesis and ionic liquids could increase their solubility, how genetic engineering and epigenetics could boost in vitro production, and how omics can reduce screenings' workload through in silico selection of the best candidates. These strategies could turn peptaibiotics into effective, ultra-specific, biodegradable tools for phytopathogen control.
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Affiliation(s)
- Leandro Pereira-Dias
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022, Valencia, Spain.
| | - Paulo R Oliveira-Pinto
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Juliana O Fernandes
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Laura Regalado
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rafael Mendes
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Cátia Teixeira
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Nuno Mariz-Ponte
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Paula Gomes
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Conceição Santos
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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4
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Gracia Carmona O, Oostenbrink C. Flexible Gaussian Accelerated Molecular Dynamics to Enhance Biological Sampling. J Chem Theory Comput 2023; 19:6521-6531. [PMID: 37649349 PMCID: PMC10536968 DOI: 10.1021/acs.jctc.3c00619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Indexed: 09/01/2023]
Abstract
Molecular dynamics simulations often struggle to obtain sufficient sampling to study complex molecular events due to high energy barriers separating the minima of interest. Multiple enhanced sampling techniques have been developed and improved over the years to tackle this issue. Gaussian accelerated molecular dynamics (GaMD) is a recently developed enhanced sampling technique that works by adding a biasing potential, lifting the energy landscape up, and decreasing the height of its barriers. GaMD allows one to increase the sampling of events of interest without the need of a priori knowledge of the system or the relevant coordinates. All required acceleration parameters can be obtained from a previous search run. Upon its development, several improvements for the methodology have been proposed, among them selective GaMD in which the boosting potential is selectively applied to the region of interest. There are currently four selective GaMD methods that have shown promising results. However, all of these methods are constrained on the number, location, and scenarios in which this selective boosting potential can be applied to ligands, peptides, or protein-protein interactions. In this work, we showcase a GROMOS implementation of the GaMD methodology with a fully flexible selective GaMD approach that allows the user to define, in a straightforward way, multiple boosting potentials for as many regions as desired. We show and analyze the advantages of this flexible selective approach on two previously used test systems, the alanine dipeptide and the chignolin peptide, and extend these examples to study its applicability and potential to study conformational changes of glycans and glycosylated proteins.
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Affiliation(s)
- Oriol Gracia Carmona
- Institute
for Molecular Modeling and Simulation, Department of Material Sciences
and Process Engineering, University of Natural
Resources and Life Sciences, Vienna. Muthgasse 18, 1190 Vienna, Austria
| | - Chris Oostenbrink
- Institute
for Molecular Modeling and Simulation, Department of Material Sciences
and Process Engineering, University of Natural
Resources and Life Sciences, Vienna. Muthgasse 18, 1190 Vienna, Austria
- Christian
Doppler Laboratory for Molecular Informatics in the Biosciences, University of Natural Resources and Life Sciences, Vienna. Muthgasse 18, 1190 Vienna, Austria
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5
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Coppa C, Bazzoli A, Barkhordari M, Contini A. Accelerated Molecular Dynamics for Peptide Folding: Benchmarking Different Combinations of Force Fields and Explicit Solvent Models. J Chem Inf Model 2023; 63:3030-3042. [PMID: 37163419 DOI: 10.1021/acs.jcim.3c00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Accelerated molecular dynamics (aMD) protocols were assessed on predicting the secondary structure of eight peptides, of which two are helical, three are β-hairpins, and three are disordered. Protocols consisted of combinations of three force fields (ff99SB, ff14SB, ff19SB) and two explicit solvation models (TIP3P and OPC), and were evaluated in two independent aMD simulations, one starting from an extended conformation, the other starting from a misfolded conformation. The results of these analyses indicate that all three combinations performed well on helical peptides. As for β-hairpins, ff19SB performed well with both solvation methods, with a slight preference for the TIP3P solvation model, even though performance was dependent on both peptide sequence and initial conformation. The ff19SB/OPC combination had the best performance on intrinsically disordered peptides. In general, ff14SB/TIP3P suffered the strongest helical bias.
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Affiliation(s)
- Crescenzo Coppa
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano, Via Venezian, 21, 20133 Milano, Italy
| | - Andrea Bazzoli
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano, Via Venezian, 21, 20133 Milano, Italy
| | - Maral Barkhordari
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano, Via Venezian, 21, 20133 Milano, Italy
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano, Via Venezian, 21, 20133 Milano, Italy
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6
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Zhao Y, Zhang J, Zhang H, Gu S, Deng Y, Tu Y, Hou T, Kang Y. Sigmoid Accelerated Molecular Dynamics: An Efficient Enhanced Sampling Method for Biosystems. J Phys Chem Lett 2023; 14:1103-1112. [PMID: 36700836 DOI: 10.1021/acs.jpclett.2c03688] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Gaussian accelerated molecular dynamics (GaMD) is recognized as a popular enhanced sampling method for tackling long-standing challenges in biomolecular simulations. Inspired by GaMD, Sigmoid accelerated molecular dynamics (SaMD) is proposed in this work by adding a Sigmoid boost potential to improve the balance between the highest acceleration and accurate reweighting. Compared with GaMD, SaMD extends the accessible time scale and improves the computational efficiency as tested in three tasks. In the alanine dipeptide task, SaMD can produce the free energy landscape with better accuracy and efficiency. In the chignolin folding task, the estimated Gibbs free energy difference can converge to the experimental value ∼30% faster. In the protein-ligand binding task, the bound conformations are closer to the crystal structure with a minimal ligand root-mean-square deviation of 1.7 Å. The binding of the ligand XK263 to the HIV protease is reproduced by SaMD in ∼60% less simulation time.
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Affiliation(s)
- Yihao Zhao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou310058, Zhejiang, China
| | - Jintu Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou310058, Zhejiang, China
- CarbonSilicon AI Technology Company, Ltd., Hangzhou310018, Zhejiang, China
| | - Haotian Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou310058, Zhejiang, China
- CarbonSilicon AI Technology Company, Ltd., Hangzhou310018, Zhejiang, China
| | - Shukai Gu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou310058, Zhejiang, China
| | - Yafeng Deng
- CarbonSilicon AI Technology Company, Ltd., Hangzhou310018, Zhejiang, China
| | - Yaoquan Tu
- Division of Theoretical Chemistry and Biology, Department of Chemistry, KTH Royal Institute of Technology, 114 28Stockholm, Sweden
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou310058, Zhejiang, China
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou310058, Zhejiang, China
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7
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Balázs D, Marik T, Szekeres A, Vágvölgyi C, Kredics L, Tyagi C. Structure-activity correlations for peptaibols obtained from clade Longibrachiatum of Trichoderma: A combined experimental and computational approach. Comput Struct Biotechnol J 2023; 21:1860-1873. [PMID: 36915379 PMCID: PMC10006723 DOI: 10.1016/j.csbj.2023.02.046] [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: 07/26/2022] [Revised: 02/23/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Integrated disease management and plant protection have been discussed with much fervor in the past decade due to the rising environmental concerns of using industrially produced pesticides. Members of the genus Trichoderma are a subject of considerable research today due to their several properties as biocontrol agents. In our study, the peptaibol production of Trichoderma longibrachiatum SZMC 1775, T. longibrachiatum f. bissettii SZMC 12546, T. reesei SZMC 22616, T. reesei SZMC 22614, T. saturnisporum SZMC 22606 and T. effusum SZMC 22611 were investigated to elucidate structure-activity relationships (SARs) between the properties of peptaibols and their 3D structures. The effects of peptaibol mixtures obtained from every Trichoderma strain were examined against nine commonly known bacteria. The lowest minimum inhibitory concentrations (MIC, mg ml-1) were exerted by T. longibrachiatum f. bissettii SZMC 12546 against Gram-positive bacteria, which was also able to inhibit the plant pathogenic Gram-negative Rhizobium radiobacter. Accelerated molecular dynamics (aMD) simulations were performed in aqueous solvent to explore the folding dynamics of 12 selected peptaibol sequences. The most characteristic difference between the peptaibols from group A and B relies in the 'Gly-Leu-Aib-Pro' and 'Gly-Aib-Aib-Pro' motifs ('Aib' stands for α-aminoisobutyric acid), which imparted a significant effect on the folding dynamics in water and might be correlated with their expressed bioactivity. In our aMD simulation experiments, Group A peptaibols showed more restricted folding dynamics with well-folded helical conformations as the most stable representative structures. This structural stability and dynamics may contribute to their bioactivity against the selected bacterial species.
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Affiliation(s)
- Dóra Balázs
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.,Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Tamás Marik
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - András Szekeres
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Chetna Tyagi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
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Perini DA, Aguilella-Arzo M, Alcaraz A, Perálvarez-Marín A, Queralt-Martín M. Dynorphin A induces membrane permeabilization by formation of proteolipidic pores. Insights from electrophysiology and computational simulations. Comput Struct Biotechnol J 2022; 20:230-240. [PMID: 35024095 PMCID: PMC8718563 DOI: 10.1016/j.csbj.2021.12.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 01/14/2023] Open
Abstract
Dynorphins are endogenous neuropeptides that function as ligands for the κ-opioid receptor. In addition to opioid activity, dynorphins can induce several pathological effects such as neurological dysfunctions and cell death. Previous studies have suggested that Dynorphin A (DynA) mediates some pathogenic actions through formation of transient pores in lipid domains of the plasma membrane. Here, we use planar bilayer electrophysiology to show that DynA induces pore formation in negatively charged membranes. We find a large variability in pore conformations showing equilibrium conductance fluctuations, what disregards electroporation as the dominant mechanism of pore formation. Ion selectivity measurements showing cationic selectivity indicate that positive protein charges of DynA are stabilized by phosphatidyl serine negative charges in the formation of combined structures. We complement our study with computational simulations that assess the stability of diverse peptide arrangements in the hydrophobic core of the bilayer. We show that DynA is capable of assembling in charged membranes to form water-filled pores that conduct ions.
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Affiliation(s)
- D Aurora Perini
- Laboratory of Molecular Biophysics. Department of Physics. Universitat Jaume I, 12071 Castellón, Spain
| | - Marcel Aguilella-Arzo
- Laboratory of Molecular Biophysics. Department of Physics. Universitat Jaume I, 12071 Castellón, Spain
| | - Antonio Alcaraz
- Laboratory of Molecular Biophysics. Department of Physics. Universitat Jaume I, 12071 Castellón, Spain
| | - Alex Perálvarez-Marín
- Biophysics Unit, Department of Biochemistry and Molecular Biology, School of Medicine, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Institute of Neuroscience, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - María Queralt-Martín
- Laboratory of Molecular Biophysics. Department of Physics. Universitat Jaume I, 12071 Castellón, Spain
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9
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Pawnikar S, Bhattarai A, Wang J, Miao Y. Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives. Adv Appl Bioinform Chem 2022; 15:1-19. [PMID: 35023931 PMCID: PMC8747661 DOI: 10.2147/aabc.s247950] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/20/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular recognition such as binding of small molecules, nucleic acids, peptides and proteins to their target receptors plays key roles in cellular function and has been targeted for therapeutic drug design. Molecular dynamics (MD) is a computational approach to analyze these binding processes at an atomistic level, which provides valuable understandings of the mechanisms of biomolecular recognition. However, the rather slow biomolecular binding events often present challenges for conventional MD (cMD), due to limited simulation timescales (typically over hundreds of nanoseconds to tens of microseconds). In this regard, enhanced sampling methods, particularly accelerated MD (aMD), have proven useful to bridge the gap and enable all-atom simulations of biomolecular binding events. Here, we will review the recent method developments of Gaussian aMD (GaMD), ligand GaMD (LiGaMD) and peptide GaMD (Pep-GaMD), which have greatly expanded our capabilities to simulate biomolecular binding processes. Spontaneous binding of various biomolecules to their receptors has been successfully simulated by GaMD. Microsecond LiGaMD and Pep-GaMD simulations have captured repetitive binding and dissociation of small-molecule ligands and highly flexible peptides, and thus enabled ligand/peptide binding thermodynamics and kinetics calculations. We will also present relevant application studies in simulations of important drug targets and future perspectives for rational computer-aided drug design.
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Affiliation(s)
- Shristi Pawnikar
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Apurba Bhattarai
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
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10
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Gavryushina IA, Georgieva ML, Kuvarina AE, Sadykova VS. Peptaibols as Potential Antifungal and Anticancer Antibiotics: Current and Foreseeable Development (Review). APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821050070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Wang J, Arantes PR, Bhattarai A, Hsu RV, Pawnikar S, Huang YMM, Palermo G, Miao Y. Gaussian accelerated molecular dynamics (GaMD): principles and applications. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2021; 11:e1521. [PMID: 34899998 PMCID: PMC8658739 DOI: 10.1002/wcms.1521] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/28/2021] [Indexed: 12/20/2022]
Abstract
Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for simultaneous unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost potential to smooth biomolecular potential energy surface and reduce energy barriers. GaMD greatly accelerates biomolecular simulations by orders of magnitude. Without the need to set predefined reaction coordinates or collective variables, GaMD provides unconstrained enhanced sampling and is advantageous for simulating complex biological processes. The GaMD boost potential exhibits a Gaussian distribution, thereby allowing for energetic reweighting via cumulant expansion to the second order (i.e., "Gaussian approximation"). This leads to accurate reconstruction of free energy landscapes of biomolecules. Hybrid schemes with other enhanced sampling methods, such as the replica exchange GaMD (rex-GaMD) and replica exchange umbrella sampling GaMD (GaREUS), have also been introduced, further improving sampling and free energy calculations. Recently, new "selective GaMD" algorithms including the ligand GaMD (LiGaMD) and peptide GaMD (Pep-GaMD) enabled microsecond simulations to capture repetitive dissociation and binding of small-molecule ligands and highly flexible peptides. The simulations then allowed highly efficient quantitative characterization of the ligand/peptide binding thermodynamics and kinetics. Taken together, GaMD and its innovative variants are applicable to simulate a wide variety of biomolecular dynamics, including protein folding, conformational changes and allostery, ligand binding, peptide binding, protein-protein/nucleic acid/carbohydrate interactions, and carbohydrate/nucleic acid interactions. In this review, we present principles of the GaMD algorithms and recent applications in biomolecular simulations and drug design.
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Affiliation(s)
- Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, 2030 Becker Dr., Lawrence, KS, 66047, United States
| | - Pablo R Arantes
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 92512, United States
| | - Apurba Bhattarai
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, 2030 Becker Dr, Lawrence, KS, 66047, United States
| | - Rohaine V Hsu
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 92512, United States
| | - Shristi Pawnikar
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, 2030 Becker Dr., Lawrence, KS, 66047, United States
| | - Yu-Ming M Huang
- Department of Physics & Astronomy, Wayne State University, 666 W Hancock St, Detroit, MI 48207, USA
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 92512, United States
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, 2030 Becker Dr., Lawrence, Kansas 66047, United States
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Li J, Hu S, Jian W, Xie C, Yang X. Plant antimicrobial peptides: structures, functions, and applications. BOTANICAL STUDIES 2021; 62:5. [PMID: 33914180 PMCID: PMC8085091 DOI: 10.1186/s40529-021-00312-x] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/13/2021] [Indexed: 05/20/2023]
Abstract
Antimicrobial peptides (AMPs) are a class of short, usually positively charged polypeptides that exist in humans, animals, and plants. Considering the increasing number of drug-resistant pathogens, the antimicrobial activity of AMPs has attracted much attention. AMPs with broad-spectrum antimicrobial activity against many gram-positive bacteria, gram-negative bacteria, and fungi are an important defensive barrier against pathogens for many organisms. With continuing research, many other physiological functions of plant AMPs have been found in addition to their antimicrobial roles, such as regulating plant growth and development and treating many diseases with high efficacy. The potential applicability of plant AMPs in agricultural production, as food additives and disease treatments, has garnered much interest. This review focuses on the types of plant AMPs, their mechanisms of action, the parameters affecting the antimicrobial activities of AMPs, and their potential applications in agricultural production, the food industry, breeding industry, and medical field.
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Affiliation(s)
- Junpeng Li
- College of Life Science, Chongqing Normal University, Chongqing, 401331, China
| | - Shuping Hu
- College of Life Science, Chongqing Normal University, Chongqing, 401331, China
| | - Wei Jian
- College of Life Science, Chongqing Normal University, Chongqing, 401331, China
| | - Chengjian Xie
- College of Life Science, Chongqing Normal University, Chongqing, 401331, China.
| | - Xingyong Yang
- College of Life Science, Chongqing Normal University, Chongqing, 401331, China.
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Ermakova EA, Makshakova ON, Zuev YF, Sedov IA. Fibril fragments from the amyloid core of lysozyme: An accelerated molecular dynamics study. J Mol Graph Model 2021; 106:107917. [PMID: 33887522 DOI: 10.1016/j.jmgm.2021.107917] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 10/21/2022]
Abstract
Protein aggregation and formation of amyloid fibrils are associated with many diseases and present a ubiquitous problem in protein science. Hen egg white lysozyme (HEWL) can form fibrils both from the full length protein and from its fragments. In the present study, we simulated unfolding of the amyloidogenic fragment of HEWL encompassing residues 49-101 to study the conformational aspects of amyloidogenesis. The accelerated molecular dynamics approach was used to speed up the sampling of the fragment conformers under enhanced temperature. Analysis of conformational transformation and intermediate structures was performed. During the unfolding, the novel short-living and long-living β-structures are formed along with the unstructured random coils. Such β-structure enriched monomers can interact with each other and propagate into fibril-like forms. The stability of oligomers assembled from these monomers was evaluated in the course of MD simulations with explicit water. The residues playing a key role in fibril stabilization were determined. The work provides new insights into the processes occurring at the early stages of amyloid fibril assembly.
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Affiliation(s)
- Elena A Ermakova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia; Sirius University of Science and Technology, Olympic Ave, 1, 354340, Sochi, Russia.
| | - Olga N Makshakova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia; Sirius University of Science and Technology, Olympic Ave, 1, 354340, Sochi, Russia
| | - Yuriy F Zuev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia
| | - Igor A Sedov
- Kazan Federal University, Kremlevskaya Str.,18, 420111, Kazan, Russia; Sirius University of Science and Technology, Olympic Ave, 1, 354340, Sochi, Russia
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Tyagi C, Marik T, Vágvölgyi C, Kredics L, Ötvös F. Correction: Tyagi, C., et al. Accelerated Molecular Dynamics Applied to the Peptaibol Folding Problem. International Journal of Molecular Sciences, 2019, 20, 4268. Int J Mol Sci 2021; 22:ijms22073707. [PMID: 33918535 PMCID: PMC8038155 DOI: 10.3390/ijms22073707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 08/05/2020] [Indexed: 11/16/2022] Open
Affiliation(s)
- Chetna Tyagi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (C.V.); (L.K.)
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Correspondence: ; Tel.: +36-705251491
| | - Tamás Marik
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (C.V.); (L.K.)
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (C.V.); (L.K.)
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (C.V.); (L.K.)
| | - Ferenc Ötvös
- Institute of Biochemistry, Biological Research Centre, Szeged, Temesvári krt. 62., H-6726 Szeged, Hungary;
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Bertrand B, Garduño-Juárez R, Munoz-Garay C. Estimation of pore dimensions in lipid membranes induced by peptides and other biomolecules: A review. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183551. [PMID: 33465367 DOI: 10.1016/j.bbamem.2021.183551] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/31/2020] [Accepted: 01/04/2021] [Indexed: 02/07/2023]
Abstract
The cytoplasmic membrane is one of the most frequent cell targets of antimicrobial peptides (AMPs) and other biomolecules. Understanding the mechanism of action of AMPs at the molecular level is of utmost importance for designing of new membrane-specific molecules. In particular, the formation of pores, the structure and size of these pores are of great interest and require nanoscale resolution approaches, therefore, biophysical strategies are essential to achieve an understanding of these processes at this scale. In the case of membrane active peptides, pore formation or general membrane disruption is usually the last step before cell death, and so, pore size is generally directly associated to pore structure and stability and loss of cellular homeostasis, implicated in overall peptide activity. Up to date, there has not been a critical review discussing the methods that can be used specifically for estimating the pore dimensions induced by membrane active peptides. In this review we discuss the scope, relevance and popularity of the different biophysical techniques such as liposome leakage experiments, advanced microscopy, neutron or X-ray scattering, electrophysiological techniques and molecular dynamics studies, all of them useful for determining pore structure and dimension.
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Affiliation(s)
- Brandt Bertrand
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México (ICF-UNAM), Avenida Universidad 2001, Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Ramón Garduño-Juárez
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México (ICF-UNAM), Avenida Universidad 2001, Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Carlos Munoz-Garay
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México (ICF-UNAM), Avenida Universidad 2001, Chamilpa, 62210 Cuernavaca, Morelos, Mexico.
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