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Beck J, Shanmugaratnam S, Höcker B. Diversifying de novo TIM barrels by hallucination. Protein Sci 2024; 33:e5001. [PMID: 38723111 PMCID: PMC11081422 DOI: 10.1002/pro.5001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/26/2024] [Accepted: 04/10/2024] [Indexed: 05/13/2024]
Abstract
De novo protein design expands the protein universe by creating new sequences to accomplish tailor-made enzymes in the future. A promising topology to implement diverse enzyme functions is the ubiquitous TIM-barrel fold. Since the initial de novo design of an idealized four-fold symmetric TIM barrel, the family of de novo TIM barrels is expanding rapidly. Despite this and in contrast to natural TIM barrels, these novel proteins lack cavities and structural elements essential for the incorporation of binding sites or enzymatic functions. In this work, we diversified a de novo TIM barrel by extending multiple βα-loops using constrained hallucination. Experimentally tested designs were found to be soluble upon expression in Escherichia coli and well-behaved. Biochemical characterization and crystal structures revealed successful extensions with defined α-helical structures. These diversified de novo TIM barrels provide a framework to explore a broad spectrum of functions based on the potential of natural TIM barrels.
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Affiliation(s)
- Julian Beck
- Department of BiochemistryUniversity of BayreuthBayreuthGermany
| | | | - Birte Höcker
- Department of BiochemistryUniversity of BayreuthBayreuthGermany
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2
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Chen M, Jin T, Nian B, Cheng W. Solvent Tolerance Improvement of Lipases Enhanced Their Applications: State of the Art. Molecules 2024; 29:2444. [PMID: 38893320 PMCID: PMC11173743 DOI: 10.3390/molecules29112444] [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: 04/15/2024] [Revised: 05/08/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Lipases, crucial catalysts in biochemical synthesis, find extensive applications across industries such as food, medicine, and cosmetics. The efficiency of lipase-catalyzed reactions is significantly influenced by the choice of solvents. Polar organic solvents often result in a decrease, or even loss, of lipase activity. Conversely, nonpolar organic solvents induce excessive rigidity in lipases, thereby affecting their activity. While the advent of new solvents like ionic liquids and deep eutectic solvents has somewhat improved the activity and stability of lipases, it fails to address the fundamental issue of lipases' poor solvent tolerance. Hence, the rational design of lipases for enhanced solvent tolerance can significantly boost their industrial performance. This review provides a comprehensive summary of the structural characteristics and properties of lipases in various solvent systems and emphasizes various strategies of protein engineering for non-aqueous media to improve lipases' solvent tolerance. This study provides a theoretical foundation for further enhancing the solvent tolerance and industrial properties of lipases.
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Affiliation(s)
| | | | | | - Wenjun Cheng
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China; (M.C.); (T.J.); (B.N.)
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3
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Jaufer AM, Bouhadana A, Fanucci GE. Hydrophobic Clusters Regulate Surface Hydration Dynamics of Bacillus subtilis Lipase A. J Phys Chem B 2024; 128:3919-3928. [PMID: 38628066 DOI: 10.1021/acs.jpcb.4c00405] [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: 04/26/2024]
Abstract
The surface hydration diffusivity of Bacillus subtilis Lipase A (BSLA) has been characterized by low-field Overhauser dynamic nuclear polarization (ODNP) relaxometry using a series of spin-labeled constructs. Sites for spin-label incorporation were previously designed via an atomistic computational approach that screened for surface exposure, reflective of the surface hydration comparable to other proteins studied by this method, as well as minimal impact on protein function, dynamics, and structure of BSLA by excluding any surface site that participated in greater than 30% occupancy of a hydrogen bonding network within BSLA. Experimental ODNP relaxometry coupling factor results verify the overall surface hydration behavior for these BSLA spin-labeled sites similar to other globular proteins. Here, by plotting the ODNP parameters of relative diffusive water versus the relative bound water, we introduce an effective "phase-space" analysis, which provides a facile visual comparison of the ODNP parameters of various biomolecular systems studied to date. We find notable differences when comparing BSLA to other systems, as well as when comparing different clusters on the surface of BSLA. Specifically, we find a grouping of sites that correspond to the spin-label surface location within the two main hydrophobic core clusters of the branched aliphatic amino acids isoleucine, leucine, and valine cores observed in the BSLA crystal structure. The results imply that hydrophobic clustering may dictate local surface hydration properties, perhaps through modulation of protein conformations and samplings of the unfolded states, providing insights into how the dynamics of the hydration shell is coupled to protein motion and fluctuations.
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Affiliation(s)
- Afnan M Jaufer
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
- George and Josephine Butler Polymer Research Laboratory, University of Florida, Gainesville, Florida 32611, United States
| | - Adam Bouhadana
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
- George and Josephine Butler Polymer Research Laboratory, University of Florida, Gainesville, Florida 32611, United States
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4
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Koch J, Romero‐Romero S, Höcker B. Stepwise introduction of stabilizing mutations reveals nonlinear additive effects in de novo TIM barrels. Protein Sci 2024; 33:e4926. [PMID: 38380781 PMCID: PMC10880431 DOI: 10.1002/pro.4926] [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: 11/05/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/22/2024]
Abstract
Over the past decades, the TIM-barrel fold has served as a model system for the exploration of how changes in protein sequences affect their structural, stability, and functional characteristics, and moreover, how this information can be leveraged to design proteins from the ground up. After numerous attempts to design de novo proteins with this specific fold, sTIM11 was the first validated de novo design of an idealized four-fold symmetric TIM barrel. Subsequent efforts to enhance the stability of this initial design resulted in the development of DeNovoTIMs, a family of de novo TIM barrels with various stabilizing mutations. In this study, we present an investigation into the biophysical and thermodynamic effects upon introducing a varying number of stabilizing mutations per quarter along the sequence of a four-fold symmetric TIM barrel. We compared the base design DeNovoTIM0 without any stabilizing mutations with variants containing mutations in one, two, three, and all four quarters-designated TIM1q, TIM2q, TIM3q, and DeNovoTIM6, respectively. This analysis revealed a stepwise and nonlinear change in the thermodynamic properties that correlated with the number of mutated quarters, suggesting positive nonadditive effects. To shed light on the significance of the location of stabilized quarters, we engineered two variants of TIM2q which contain the same number of mutations but positioned in different quarter locations. Characterization of these TIM2q variants revealed that the mutations exhibit varying effects on the overall protein stability, contingent upon the specific region in which they are introduced. These findings emphasize that the amount and location of stabilized interfaces among the four quarters play a crucial role in shaping the conformational stability of these four-fold symmetric TIM barrels. Analysis of de novo proteins, as described in this study, enhances our understanding of how sequence variations can finely modulate stability in both naturally occurring and computationally designed proteins.
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Affiliation(s)
| | | | - Birte Höcker
- Department of BiochemistryUniversity of BayreuthBayreuthGermany
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5
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Ghaedizadeh S, Zeinali M, Dabirmanesh B, Rasekh B, Khajeh K, Banaei-Moghaddam AM. Rational design engineering of a more thermostable Sulfurihydrogenibium yellowstonense carbonic anhydrase for potential application in carbon dioxide capture technologies. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140962. [PMID: 37716447 DOI: 10.1016/j.bbapap.2023.140962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/18/2023] [Accepted: 09/06/2023] [Indexed: 09/18/2023]
Abstract
Implementing hyperthermostable carbonic anhydrases into CO2 capture and storage technologies in order to increase the rate of CO2 absorption from the industrial flue gases is of great importance from technical and economical points of view. The present study employed a combination of in silico tools to further improve thermostability of a known thermostable carbonic anhydrase from Sulfurihydrogenibium yellowstonense. Experimental results showed that our rationally engineered K100G mutant not only retained the overall structure and catalytic efficiency but also showed a 3 °C increase in the melting temperature and a two-fold improvement in the enzyme half-life at 85 °C. Based on the molecular dynamics simulation results, rearrangement of salt bridges and hydrogen interactions network causes a reduction in local flexibility of the K100G variant. In conclusion, our study demonstrated that thermostability can be improved through imposing local structural rigidity by engineering a single-point mutation on the surface of the enzyme.
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Affiliation(s)
- Shima Ghaedizadeh
- Laboratory of Genomics and Epigenomics (LGE), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Majid Zeinali
- Microbiology and Biotechnology Research Group, Research Institute of Petroleum Industry (RIPI), Tehran, Iran.
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Behnam Rasekh
- Microbiology and Biotechnology Research Group, Research Institute of Petroleum Industry (RIPI), Tehran, Iran
| | - Khosrow Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Mohammad Banaei-Moghaddam
- Laboratory of Genomics and Epigenomics (LGE), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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Kordes S, Beck J, Shanmugaratnam S, Flecks M, Höcker B. Physics-based approach to extend a de novo TIM barrel with rationally designed helix-loop-helix motifs. Protein Eng Des Sel 2023; 36:gzad012. [PMID: 37707513 DOI: 10.1093/protein/gzad012] [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: 07/31/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023] Open
Abstract
Computational protein design promises the ability to build tailor-made proteins de novo. While a range of de novo proteins have been constructed so far, the majority of these designs have idealized topologies that lack larger cavities which are necessary for the incorporation of small molecule binding sites or enzymatic functions. One attractive target for enzyme design is the TIM-barrel fold, due to its ubiquity in nature and capability to host versatile functions. With the successful de novo design of a 4-fold symmetric TIM barrel, sTIM11, an idealized, minimalistic scaffold was created. In this work, we attempted to extend this de novo TIM barrel by incorporating a helix-loop-helix motif into its βα-loops by applying a physics-based modular design approach using Rosetta. Further diversification was performed by exploiting the symmetry of the scaffold to integrate two helix-loop-helix motifs into the scaffold. Analysis with AlphaFold2 and biochemical characterization demonstrate the formation of additional α-helical secondary structure elements supporting the successful extension as intended.
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Affiliation(s)
- Sina Kordes
- Department of Biochemistry, University of Bayreuth, Bayreuth 95447, Germany
| | - Julian Beck
- Department of Biochemistry, University of Bayreuth, Bayreuth 95447, Germany
| | | | - Merle Flecks
- Department of Biochemistry, University of Bayreuth, Bayreuth 95447, Germany
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, Bayreuth 95447, Germany
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Chu AE, Fernandez D, Liu J, Eguchi RR, Huang PS. De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design. BIODESIGN RESEARCH 2022; 2022:9842315. [PMID: 37850141 PMCID: PMC10521652 DOI: 10.34133/2022/9842315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/26/2022] [Indexed: 10/19/2023] Open
Abstract
The ability to finely control the structure of protein folds is an important prerequisite to functional protein design. The TIM barrel fold is an important target for these efforts as it is highly enriched for diverse functions in nature. Although a TIM barrel protein has been designed de novo, the ability to finely alter the curvature of the central beta barrel and the overall architecture of the fold remains elusive, limiting its utility for functional design. Here, we report the de novo design of a TIM barrel with ovoid (twofold) symmetry, drawing inspiration from natural beta and TIM barrels with ovoid curvature. We use an autoregressive backbone sampling strategy to implement our hypothesis for elongated barrel curvature, followed by an iterative enrichment sequence design protocol to obtain sequences which yield a high proportion of successfully folding designs. Designed sequences are highly stable and fold to the designed barrel curvature as determined by a 2.1 Å resolution crystal structure. The designs show robustness to drastic mutations, retaining high melting temperatures even when multiple charged residues are buried in the hydrophobic core or when the hydrophobic core is ablated to alanine. As a scaffold with a greater capacity for hosting diverse hydrogen bonding networks and installation of binding pockets or active sites, the ovoid TIM barrel represents a major step towards the de novo design of functional TIM barrels.
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Affiliation(s)
- Alexander E Chu
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Daniel Fernandez
- Program in Chemistry, Engineering, And Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
- Stanford ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Stanford, CA, USA
| | - Jingjia Liu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Raphael R Eguchi
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Stanford ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Po-Ssu Huang
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Stanford ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Stanford, CA, USA
- Bio-X Institute, Stanford University, Stanford, CA, USA
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ProtGPT2 is a deep unsupervised language model for protein design. Nat Commun 2022; 13:4348. [PMID: 35896542 PMCID: PMC9329459 DOI: 10.1038/s41467-022-32007-7] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/13/2022] [Indexed: 11/29/2022] Open
Abstract
Protein design aims to build novel proteins customized for specific purposes, thereby holding the potential to tackle many environmental and biomedical problems. Recent progress in Transformer-based architectures has enabled the implementation of language models capable of generating text with human-like capabilities. Here, motivated by this success, we describe ProtGPT2, a language model trained on the protein space that generates de novo protein sequences following the principles of natural ones. The generated proteins display natural amino acid propensities, while disorder predictions indicate that 88% of ProtGPT2-generated proteins are globular, in line with natural sequences. Sensitive sequence searches in protein databases show that ProtGPT2 sequences are distantly related to natural ones, and similarity networks further demonstrate that ProtGPT2 is sampling unexplored regions of protein space. AlphaFold prediction of ProtGPT2-sequences yields well-folded non-idealized structures with embodiments and large loops and reveals topologies not captured in current structure databases. ProtGPT2 generates sequences in a matter of seconds and is freely available. Protein design aims to build novel proteins customized for specific purposes, thereby holding the potential to tackle many environmental and biomedical problems. Here the authors apply some of the latest advances in natural language processing, generative Transformers, to train ProtGPT2, a language model that explores unseen regions of the protein space while designing proteins with nature-like properties.
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Khersonsky O, Fleishman SJ. What Have We Learned from Design of Function in Large Proteins? BIODESIGN RESEARCH 2022; 2022:9787581. [PMID: 37850148 PMCID: PMC10521758 DOI: 10.34133/2022/9787581] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 02/21/2022] [Indexed: 10/19/2023] Open
Abstract
The overarching goal of computational protein design is to gain complete control over protein structure and function. The majority of sophisticated binders and enzymes, however, are large and exhibit diverse and complex folds that defy atomistic design calculations. Encouragingly, recent strategies that combine evolutionary constraints from natural homologs with atomistic calculations have significantly improved design accuracy. In these approaches, evolutionary constraints mitigate the risk from misfolding and aggregation, focusing atomistic design calculations on a small but highly enriched sequence subspace. Such methods have dramatically optimized diverse proteins, including vaccine immunogens, enzymes for sustainable chemistry, and proteins with therapeutic potential. The new generation of deep learning-based ab initio structure predictors can be combined with these methods to extend the scope of protein design, in principle, to any natural protein of known sequence. We envision that protein engineering will come to rely on completely computational methods to efficiently discover and optimize biomolecular activities.
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Affiliation(s)
- Olga Khersonsky
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarel J. Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
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