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Min J, Rong X, Zhang J, Su R, Wang Y, Qi W. Computational Design of Peptide Assemblies. J Chem Theory Comput 2024; 20:532-550. [PMID: 38206800 DOI: 10.1021/acs.jctc.3c01054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
With the ongoing development of peptide self-assembling materials, there is growing interest in exploring novel functional peptide sequences. From short peptides to long polypeptides, as the functionality increases, the sequence space is also expanding exponentially. Consequently, attempting to explore all functional sequences comprehensively through experience and experiments alone has become impractical. By utilizing computational methods, especially artificial intelligence enhanced molecular dynamics (MD) simulation and de novo peptide design, there has been a significant expansion in the exploration of sequence space. Through these methods, a variety of supramolecular functional materials, including fibers, two-dimensional arrays, nanocages, etc., have been designed by meticulously controlling the inter- and intramolecular interactions. In this review, we first provide a brief overview of the current main computational methods and then focus on the computational design methods for various self-assembled peptide materials. Additionally, we introduce some representative protein self-assemblies to offer guidance for the design of self-assembling peptides.
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Affiliation(s)
- Jiwei Min
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Xi Rong
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Jiaxing Zhang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300072, P. R. China
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300072, P. R. China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300072, P. R. China
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Drori R, Stevens CA. Divergent Mechanisms of Ice Growth Inhibition by Antifreeze Proteins. Methods Mol Biol 2024; 2730:169-181. [PMID: 37943458 DOI: 10.1007/978-1-0716-3503-2_12] [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] [Indexed: 11/10/2023]
Abstract
Antifreeze proteins (AFPs) are biomolecules that can bind to ice and hinder its growth, thus holding significant potential for biotechnological and biomedical applications. AFPs are a subset of ice-binding proteins (IBPs) and are found in various organisms across different life kingdoms. This mini-review investigates the underlying mechanisms by which AFPs impede ice growth, emphasizing the disparities between hyperactive and moderate AFPs. Hyperactive AFPs exhibit heightened thermal hysteresis (TH) activity and can bind to both the basal and prism planes of ice crystals, enabling them to endure extremely cold temperatures. In contrast, moderate AFPs predominantly bind to the prism/pyramidal planes and demonstrate lower TH activity. The structural diversity of AFPs and the presence of ordered water molecules on their ice-binding sites (IBS) have been subjects of debate among researchers. Multiple hypotheses have been proposed concerning the significance of ordered water molecules in ice binding. Gaining insights into the binding dynamics and the factors influencing TH activity in AFPs is crucial for the development of efficient synthetic compounds and the establishment of comprehensive models to elucidate ice growth inhibition. Here we emphasize the necessity for further research to unravel the mechanisms of AFPs and presents a pathway for constructing models capable of comprehensively explaining their inhibitory effects on ice growth.
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Affiliation(s)
- Ran Drori
- Department of Chemistry and Biochemistry, Yeshiva University, New York, NY, USA.
| | - Corey A Stevens
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Zielkiewicz J. Mechanism of antifreeze protein functioning and the "anchored clathrate water" concept. J Chem Phys 2023; 159:085101. [PMID: 37622597 DOI: 10.1063/5.0158590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
In liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case, the interactions of water molecules with the protein surface shift the equilibrium of the process. In this paper, we analyze the structural properties of the solvation water in antifreeze proteins (AFPs). The results of molecular dynamics analysis with the use of various parameters related to the structure of solvation water on the protein surface are presented. We found that in the vicinity of the active region responsible for the binding of AFPs to ice, the equilibrium is clearly shifted toward the formation of "ice-like aggregates," and the solvation water has a more ordered ice-like structure. We have demonstrated that a reduction in the tendency to create "ice-like aggregates" results in a significant reduction in the antifreeze activity of the protein. We conclude that shifting the equilibrium in favor of the formation of "ice-like aggregates" in the solvation water in the active region is a prerequisite for the biological functionality of AFPs, at least for AFPs having a well-defined ice binding area. In addition, our results fully confirm the validity of the "anchored clathrate water" concept, formulated by Garnham et al. [Proc. Natl. Acad. Sci. U. S. A. 108, 7363 (2011)].
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Affiliation(s)
- Jan Zielkiewicz
- Faculty of Chemistry, Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
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Zhang W, Liu H, Fu H, Shao X, Cai W. Revealing the Mechanism of Irreversible Binding of Antifreeze Glycoproteins to Ice. J Phys Chem B 2022; 126:10637-10645. [PMID: 36513495 DOI: 10.1021/acs.jpcb.2c06183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Antifreeze glycoproteins (AFGPs) are a special kind of antifreeze proteins with strong flexibility. Whether their antifreeze activity is achieved by reversibly or irreversibly binding to ice is widely debated, and the molecular mechanism of irreversible binding remains unclear. In this work, the antifreeze mechanism of the smallest AFGP isoform, AFGP8, is investigated at the atomic level. The results indicate that AFGP8 can bind to ice both reversibly through its hydrophobic methyl groups (peptide binding) and irreversibly through its hydrophilic disaccharide moieties (saccharide binding). Although peptide binding occurs faster than saccharide binding, free-energy calculations indicate that the latter is energetically more favorable. In saccharide binding, at least one disaccharide moiety is frozen in the grown ice, resulting in irreversible binding, while the other moieties significantly perturb the water hydrogen-bonding network, thus inhibiting ice growth more effectively. The present study reveals the coexistence of reversible and irreversible bindings of AFGP8, both contributing to the inhibition of ice growth and further provides molecular mechanism of irreversible binding.
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Affiliation(s)
- Weijia Zhang
- Research Center for Analytical Sciences, Haihe Laboratory of Sustainable Chemical Transformations, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin300071, China
| | - Han Liu
- Research Center for Analytical Sciences, Haihe Laboratory of Sustainable Chemical Transformations, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin300071, China
| | - Haohao Fu
- Research Center for Analytical Sciences, Haihe Laboratory of Sustainable Chemical Transformations, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin300071, China
| | - Xueguang Shao
- Research Center for Analytical Sciences, Haihe Laboratory of Sustainable Chemical Transformations, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin300071, China
| | - Wensheng Cai
- Research Center for Analytical Sciences, Haihe Laboratory of Sustainable Chemical Transformations, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin300071, China
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Pal P, Aich R, Chakraborty S, Jana B. Molecular Factors of Ice Growth Inhibition for Hyperactive and Globular Antifreeze Proteins: Insights from Molecular Dynamics Simulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:15132-15144. [PMID: 36450094 DOI: 10.1021/acs.langmuir.2c02149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The molecular mechanism behind the ice growth inhibition by antifreeze proteins (AFPs) is yet to be understood completely. Also, what physical parameters differentiate between the AFP and non-AFP are largely unknown. Thus, to get an atomistic overview of the differential antifreeze activities of different classes of AFPs, we have studied ice growth from different ice surfaces in the presence of a moderately active globular type III AFP and a hyperactive spruce budworm (sbw) AFP. Results are compared with the observations of ice growth simulations in the presence of topologically similar non-AFPs using all-atom molecular dynamics simulations. Simulation data suggest that the ice surface coverage is a critical factor in ice growth inhibition. Due to the presence of an ice binding surface (IBS), AFPs form a high affinity complex with ice, accompanied by a transition of hydration water around the IBS from clathrate-like to ice-like. Several residues around the periphery of the IBS anchor the AFP to the curved ice surface mediated by multiple strong hydrogen bonds, stabilizing the complex immensely. In the high surface coverage regime, the slow unbinding kinetics dominates over the ice growth kinetics and thus facilitates the ice growth inhibition. Due to the non-availability of a proper IBS, non-AFPs form a low-affinity complex with the growing ice surface. As a result, the non-AFPs are continuously repelled by the surface. If the concentration of AFPs is low, then the effective surface coverage is reduced significantly. In this low surface coverage regime, AFPs can also behave like impurities and are engulfed by the growing ice crystal.
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Affiliation(s)
- Prasun Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Rahul Aich
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Sandipan Chakraborty
- Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS), Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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Wei GW, Soares TA, Wahab H, Zhu F. Computational Chemistry in Asia. J Chem Inf Model 2022; 62:5035-5037. [DOI: 10.1021/acs.jcim.2c01050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Cui S, Zhang W, Shao X, Cai W. Do antifreeze proteins generally possess the potential to promote ice growth? Phys Chem Chem Phys 2022; 24:7901-7908. [PMID: 35311839 DOI: 10.1039/d1cp05431g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding of antifreeze proteins (AFPs) to ice needs to be mediated by interfacial water molecules. Our previous study of the effect of AFPs on the dynamics of the interfacial water of freezing at its initial stage has shown that AFPs can promote the growth of ice before binding to it. However, whether different AFPs can promote the freezing of water molecules on the basal and the prismatic surfaces of ice still needs further study. In the present contribution, five representative natural AFPs with different structures and different activities that can be adsorbed on the basal and/or prismatic surfaces of ice are investigated at the atomic level. Our results show that the phenomenon of promoting the growth of ice crystals is not universal. Only hyperactive AFPs (hypAFPs) can promote the growth of the basal plane of ice, while moderately active AFPs cannot. Moreover, this significant promotion is not observed on the prismatic plane regardless of their activity. Further analysis indicates that this promotion may result from the thicker ice/water interface of the basal plane, and the synergy of hypAFPs with ice crystals.
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Affiliation(s)
- Shaoli Cui
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China.
| | - Weijia Zhang
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China.
| | - Xueguang Shao
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China.
| | - Wensheng Cai
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China.
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