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Guan A, He Z, Wang X, Jia ZJ, Qin J. Engineering the next-generation synthetic cell factory driven by protein engineering. Biotechnol Adv 2024; 73:108366. [PMID: 38663492 DOI: 10.1016/j.biotechadv.2024.108366] [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: 11/02/2023] [Revised: 03/21/2024] [Accepted: 04/22/2024] [Indexed: 05/09/2024]
Abstract
Synthetic cell factory offers substantial advantages in economically efficient production of biofuels, chemicals, and pharmaceutical compounds. However, to create a high-performance synthetic cell factory, precise regulation of cellular material and energy flux is essential. In this context, protein components including enzymes, transcription factor-based biosensors and transporters play pivotal roles. Protein engineering aims to create novel protein variants with desired properties by modifying or designing protein sequences. This review focuses on summarizing the latest advancements of protein engineering in optimizing various aspects of synthetic cell factory, including: enhancing enzyme activity to eliminate production bottlenecks, altering enzyme selectivity to steer metabolic pathways towards desired products, modifying enzyme promiscuity to explore innovative routes, and improving the efficiency of transporters. Furthermore, the utilization of protein engineering to modify protein-based biosensors accelerates evolutionary process and optimizes the regulation of metabolic pathways. The remaining challenges and future opportunities in this field are also discussed.
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Affiliation(s)
- Ailin Guan
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Zixi He
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Xin Wang
- West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Zhi-Jun Jia
- West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Jiufu Qin
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China.
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2
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Weinstein JJ, Saikia C, Karbat I, Goldenzweig A, Reuveny E, Fleishman SJ. One-shot design elevates functional expression levels of a voltage-gated potassium channel. Protein Sci 2024; 33:e4995. [PMID: 38747377 PMCID: PMC11094769 DOI: 10.1002/pro.4995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 05/19/2024]
Abstract
Membrane proteins play critical physiological roles as receptors, channels, pumps, and transporters. Despite their importance, however, low expression levels often hamper the experimental characterization of membrane proteins. We present an automated and web-accessible design algorithm called mPROSS (https://mPROSS.weizmann.ac.il), which uses phylogenetic analysis and an atomistic potential, including an empirical lipophilicity scale, to improve native-state energy. As a stringent test, we apply mPROSS to the Kv1.2-Kv2.1 paddle chimera voltage-gated potassium channel. Four designs, encoding 9-26 mutations relative to the parental channel, were functional and maintained potassium-selective permeation and voltage dependence in Xenopus oocytes with up to 14-fold increase in whole-cell current densities. Additionally, single-channel recordings reveal no significant change in the channel-opening probability nor in unitary conductance, indicating that functional expression levels increase without impacting the activity profile of individual channels. Our results suggest that the expression levels of other dynamic channels and receptors may be enhanced through one-shot design calculations.
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Affiliation(s)
- Jonathan Jacob Weinstein
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
- Present address:
Scala Biodesign LtdTel AvivIsrael
| | - Chandamita Saikia
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
- Present address:
Institute for BiochemistryUniversity of LübeckLübeckGermany
| | - Izhar Karbat
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | | | - Eitan Reuveny
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
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3
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Saikia B, Baruah A. In silico design of misfolding resistant proteins: the role of structural similarity of a competing conformational ensemble in the optimization of frustration. SOFT MATTER 2024; 20:3283-3298. [PMID: 38529658 DOI: 10.1039/d4sm00171k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Most state-of-the-art in silico design methods fail due to misfolding of designed sequences to a conformation other than the target. Thus, a method to design misfolding resistant proteins will provide a better understanding of the misfolding phenomenon and will also increase the success rate of in silico design methods. In this work, we optimize the conformational ensemble to be selected for negative design purposes based on the similarity of the conformational ensemble to the target. Five ensembles with different degrees of similarity to the target are created and destabilized and the target is stabilized while designing sequences using mean field theory and Monte Carlo simulation methods. The results suggest that the degree of similarity of the non-native conformations to the target plays a prominent role in designing misfolding resistant protein sequences. The design procedures that destabilize the conformational ensemble with moderate similarity to the target have proven to be more promising. Incorporation of either highly similar or highly dissimilar conformations to the target conformation into the non-native ensemble to be destabilized may lead to sequences with a higher misfolding propensity. This will significantly reduce the conformational space to be considered in any protein design procedure. Interestingly, the results suggest that a sequence with higher frustration in the target structure does not necessarily lead to a misfold prone sequence. A successful design method may purposefully choose a frustrated sequence in the target conformation if that sequence is even more frustrated in the competing non-native conformations.
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Affiliation(s)
- Bondeepa Saikia
- Department of Chemistry, Dibrugarh University, Dibrugarh 786004, India.
| | - Anupaul Baruah
- Department of Chemistry, Dibrugarh University, Dibrugarh 786004, India.
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4
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Listov D, Goverde CA, Correia BE, Fleishman SJ. Opportunities and challenges in design and optimization of protein function. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00718-y. [PMID: 38565617 DOI: 10.1038/s41580-024-00718-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calculations, as well as machine learning tools, have dramatically improved protein engineering and design. In this Review, we discuss how these methods have enabled the design of increasingly complex structures and therapeutically relevant activities. Additionally, protein optimization methods have improved the stability and activity of complex eukaryotic proteins. Thanks to their increased reliability, computational design methods have been applied to improve therapeutics and enzymes for green chemistry and have generated vaccine antigens, antivirals and drug-delivery nano-vehicles. Moreover, the high success of design methods reflects an increased understanding of basic rules that govern the relationships among protein sequence, structure and function. However, de novo design is still limited mostly to α-helix bundles, restricting its potential to generate sophisticated enzymes and diverse protein and small-molecule binders. Designing complex protein structures is a challenging but necessary next step if we are to realize our objective of generating new-to-nature activities.
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Affiliation(s)
- Dina Listov
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Casper A Goverde
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bruno E Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Sarel Jacob Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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5
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Kheirollahi A, Sadeghi S, Orandi S, Moayedi K, Khajeh K, Khoobi M, Golestani A. Chondroitinase as a therapeutic enzyme: Prospects and challenges. Enzyme Microb Technol 2024; 172:110348. [PMID: 37898093 DOI: 10.1016/j.enzmictec.2023.110348] [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: 05/22/2023] [Revised: 09/28/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023]
Abstract
The chondroitinases (Chase) are bacterial lyases that specifically digest chondroitin sulfate and/or dermatan sulfate glycosaminoglycans via a β-elimination reaction and generate unsaturated disaccharides. In recent decades, these enzymes have attracted the attention of many researchers due to their potential applications in various aspects of medicine from the treatment of spinal cord injury to use as an analytical tool. In spite of this diverse spectrum, the application of Chase is faced with several limitations and challenges such as thermal instability and lack of a suitable delivery system. In the current review, we address potential therapeutic applications of Chase with emphasis on the challenges ahead. Then, we summarize the latest achievements to overcome the problems by considering the studies carried out in the field of enzyme engineering, drug delivery, and combination-based therapy.
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Affiliation(s)
- Asma Kheirollahi
- Department of Comparative Biosciences, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Solmaz Sadeghi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Shirin Orandi
- Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Kiana Moayedi
- Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
| | - Mehdi Khoobi
- Department of Radiopharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; Department of Pharmaceutical Biomaterials and Medical Biomaterials Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Abolfazl Golestani
- Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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Milton AJ, Kwok JC, McClellan J, Randall SG, Lathia JD, Warren PM, Silver DJ, Silver J. Recovery of Forearm and Fine Digit Function After Chronic Spinal Cord Injury by Simultaneous Blockade of Inhibitory Matrix Chondroitin Sulfate Proteoglycan Production and the Receptor PTPσ. J Neurotrauma 2023; 40:2500-2521. [PMID: 37606910 PMCID: PMC10698859 DOI: 10.1089/neu.2023.0117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023] Open
Abstract
Spinal cord injuries (SCI), for which there are limited effective treatments, result in enduring paralysis and hypoesthesia, in part because of the inhibitory microenvironment that develops and limits regeneration/sprouting, especially during chronic stages. Recently, we discovered that targeted enzymatic removal of the inhibitory chondroitin sulfate proteoglycan (CSPG) component of the extracellular and perineuronal net (PNN) matrix via Chondroitinase ABC (ChABC) rapidly restored robust respiratory function to the previously paralyzed hemi-diaphragm after remarkably long times post-injury (up to 1.5 years) following a cervical level 2 lateral hemi-transection. Importantly, ChABC treatment at cervical level 4 in this chronic model also elicited improvements in gross upper arm function. In the present study, we focused on arm and hand function, seeking to highlight and optimize crude as well as fine motor control of the forearm and digits at lengthy chronic stages post-injury. However, instead of using ChABC, we utilized a novel and more clinically relevant systemic combinatorial treatment strategy designed to simultaneously reduce and overcome inhibitory CSPGs. Following a 3-month upper cervical spinal hemi-lesion using adult female Sprague Dawley rats, we show that the combined treatment had a profound effect on functional recovery of the chronically paralyzed forelimb and paw, as well as on precision movements of the digits. The regenerative and immune system related events that we describe deepen our basic understanding of the crucial role of CSPG-mediated inhibition via the PTPσ receptor in constraining functional synaptic plasticity at lengthy time points following SCI, hopefully leading to clinically relevant translational benefits.
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Affiliation(s)
- Adrianna J. Milton
- Department of Neurosciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jessica C.F. Kwok
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Institute of Experimental Medicine, Czech Academy of Science, Prague, Czech Republic
| | - Jacob McClellan
- Department of Neurosciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Sabre G. Randall
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA
| | - Justin D. Lathia
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, Ohio, USA
| | - Philippa M. Warren
- Department of Neurosciences, Case Western Reserve University, Cleveland, Ohio, USA
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Daniel J. Silver
- Department of Neurosciences, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, Ohio, USA
| | - Jerry Silver
- Department of Neurosciences, Case Western Reserve University, Cleveland, Ohio, USA
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Damle SR, Krzyzanowska AK, Korsun MK, Morse KW, Gilbert S, Kim HJ, Boachie-Adjei O, Rawlins BA, van der Meulen MCH, Greenblatt MB, Hidaka C, Cunningham ME. Inducing Angiogenesis in the Nucleus Pulposus. Cells 2023; 12:2488. [PMID: 37887332 PMCID: PMC10605635 DOI: 10.3390/cells12202488] [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: 07/31/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Bone morphogenetic protein (BMP) gene delivery to Lewis rat lumbar intervertebral discs (IVDs) drives bone formation anterior and external to the IVD, suggesting the IVD is inhospitable to osteogenesis. This study was designed to determine if IVD destruction with a proteoglycanase, and/or generating an IVD blood supply by gene delivery of an angiogenic growth factor, could render the IVD permissive to intra-discal BMP-driven osteogenesis and fusion. Surgical intra-discal delivery of naïve or gene-programmed cells (BMP2/BMP7 co-expressing or VEGF165 expressing) +/- purified chondroitinase-ABC (chABC) in all permutations was performed between lumbar 4/5 and L5/6 vertebrae, and radiographic, histology, and biomechanics endpoints were collected. Follow-up anti-sFlt Western blotting was performed. BMP and VEGF/BMP treatments had the highest stiffness, bone production and fusion. Bone was induced anterior to the IVD, and was not intra-discal from any treatment. chABC impaired BMP-driven osteogenesis, decreased histological staining for IVD proteoglycans, and made the IVD permissive to angiogenesis. A soluble fragment of VEGF Receptor-1 (sFlt) was liberated from the IVD matrix by incubation with chABC, suggesting dysregulation of the sFlt matrix attachment is a possible mechanism for the chABC-mediated IVD angiogenesis we observed. Based on these results, the IVD can be manipulated to foster vascular invasion, and by extension, possibly osteogenesis.
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Affiliation(s)
- Sheela R. Damle
- HSS Research Institute, Hospital for Special Surgery, 515 E 71st Street, New York, NY 10021, USA
| | - Agata K. Krzyzanowska
- HSS Research Institute, Hospital for Special Surgery, 515 E 71st Street, New York, NY 10021, USA
| | - Maximilian K. Korsun
- HSS Research Institute, Hospital for Special Surgery, 515 E 71st Street, New York, NY 10021, USA
| | - Kyle W. Morse
- HSS Research Institute, Hospital for Special Surgery, 515 E 71st Street, New York, NY 10021, USA
| | - Susannah Gilbert
- HSS Research Institute, Hospital for Special Surgery, 515 E 71st Street, New York, NY 10021, USA
| | - Han Jo Kim
- HSS Research Institute, Hospital for Special Surgery, 515 E 71st Street, New York, NY 10021, USA
- Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Oheneba Boachie-Adjei
- HSS Research Institute, Hospital for Special Surgery, 515 E 71st Street, New York, NY 10021, USA
- Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Bernard A. Rawlins
- HSS Research Institute, Hospital for Special Surgery, 515 E 71st Street, New York, NY 10021, USA
- Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Marjolein C. H. van der Meulen
- HSS Research Institute, Hospital for Special Surgery, 515 E 71st Street, New York, NY 10021, USA
- Meinig School of Biomedical Engineering and Sibley School of Mechanical & Aerospace Engineering, Cornell University, Ithaca, NY 14853, USA
| | | | - Chisa Hidaka
- HSS Research Institute, Hospital for Special Surgery, 515 E 71st Street, New York, NY 10021, USA
- Department of Genetic Medicine and Belfer Gene Therapy Core Facility, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Matthew E. Cunningham
- HSS Research Institute, Hospital for Special Surgery, 515 E 71st Street, New York, NY 10021, USA
- Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
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8
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Miao H, Xiang X, Han N, Wu Q, Huang Z. Improving the Thermostability of Serine Protease PB92 from Bacillus alcalophilus via Site-Directed Mutagenesis Based on Semi-Rational Design. Foods 2023; 12:3081. [PMID: 37628080 PMCID: PMC10453622 DOI: 10.3390/foods12163081] [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: 07/20/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Proteases have been widely employed in many industrial processes. In this work, we aimed to improve the thermostability of the serine protease PB92 from Bacillus alcalophilus to meet the high-temperature requirements of biotechnological treatments. Eight mutation sites (N18, S97-S101, E110, and R143) were identified, and 21 mutants were constructed from B-factor comparison and multiple sequence alignment and expressed via Bacillus subtilis. Among them, fifteen mutants exhibited increased half-life (t1/2) values at 65 °C (1.13-31.61 times greater than that of the wild type). Based on the composite score of enzyme activity and thermostability, six complex mutants were implemented. The t1/2 values of these six complex mutants were 2.12-10.05 times greater than that of the wild type at 65 °C. In addition, structural analysis revealed that the increased thermal stability of complex mutants may be related to the formation of additional hydrophobic interactions due to increased hydrophobicity and the decreased flexibility of the structure. In brief, the thermal stability of the complex mutants N18L/R143L/S97A, N18L/R143L/S99L, and N18L/R143L/G100A was increased 4-fold, which reveals application potential in industry.
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Affiliation(s)
- Huabiao Miao
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, China
- School of Life Science, Yunnan Normal University, Kunming 650500, China
| | - Xia Xiang
- School of Life Science, Yunnan Normal University, Kunming 650500, China
| | - Nanyu Han
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, China
- School of Life Science, Yunnan Normal University, Kunming 650500, China
| | - Qian Wu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, China
- School of Life Science, Yunnan Normal University, Kunming 650500, China
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, China
- School of Life Science, Yunnan Normal University, Kunming 650500, China
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Huang X, Sun Y, Osawa Y, Chen YE, Zhang H. Computational redesign of cytochrome P450 CYP102A1 for highly stereoselective omeprazole hydroxylation by UniDesign. J Biol Chem 2023; 299:105050. [PMID: 37451479 PMCID: PMC10413352 DOI: 10.1016/j.jbc.2023.105050] [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: 05/24/2023] [Revised: 07/03/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023] Open
Abstract
Cytochrome P450 CYP102A1 is a prototypic biocatalyst that has great potential in chemical synthesis, drug discovery, and biotechnology. CYP102A1 variants engineered by directed evolution and/or rational design are capable of catalyzing the oxidation of a wide range of organic compounds. However, it is difficult to foresee the outcome of engineering CYP102A1 for a compound of interest. Here, we introduce UniDesign as a computational framework for enzyme design and engineering. We tested UniDesign by redesigning CYP102A1 for stereoselective metabolism of omeprazole (OMP), a proton pump inhibitor, starting from an active but nonstereoselective triple mutant (TM: A82F/F87V/L188Q). To shift stereoselectivity toward (R)-OMP, we computationally scanned three active site positions (75, 264, and 328) for mutations that would stabilize the binding of the transition state of (R)-OMP while destabilizing that of (S)-OMP and picked three variants, namely UD1 (TM/L75I), UD2 (TM/A264G), and UD3 (TM/A328V), for experimentation, based on computed energy scores and models. UD1, UD2, and UD3 exhibit high turnover rates of 55 ± 4.7, 84 ± 4.8, and 79 ± 5.7 min-1, respectively, for (R)-OMP hydroxylation, whereas the corresponding rates for (S)-OMP are only 2.2 ± 0.19, 6.0 ± 0.68, and 14 ± 2.8 min-1, yielding an enantiomeric excess value of 92, 87, and 70%, respectively. These results suggest the critical roles of L75I, A264G, and A328V in steering OMP in the optimal orientation for stereoselective oxidation and demonstrate the utility of UniDesign for engineering CYP102A1 to produce drug metabolites of interest. The results are discussed in the context of protein structures.
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Affiliation(s)
- Xiaoqiang Huang
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.
| | - Yudong Sun
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yoichi Osawa
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, USA
| | - Y Eugene Chen
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Haoming Zhang
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, USA.
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Huang X, Zhou J, Yang D, Zhang J, Xia X, Chen YE, Xu J. Decoding CRISPR-Cas PAM recognition with UniDesign. Brief Bioinform 2023; 24:bbad133. [PMID: 37078688 PMCID: PMC10199764 DOI: 10.1093/bib/bbad133] [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: 12/20/2022] [Revised: 02/09/2023] [Accepted: 03/16/2023] [Indexed: 04/21/2023] Open
Abstract
The critical first step in Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated (CRISPR-Cas) protein-mediated gene editing is recognizing a preferred protospacer adjacent motif (PAM) on target DNAs by the protein's PAM-interacting amino acids (PIAAs). Thus, accurate computational modeling of PAM recognition is useful in assisting CRISPR-Cas engineering to relax or tighten PAM requirements for subsequent applications. Here, we describe a universal computational protein design framework (UniDesign) for designing protein-nucleic acid interactions. As a proof of concept, we applied UniDesign to decode the PAM-PIAA interactions for eight Cas9 and two Cas12a proteins. We show that, given native PIAAs, the UniDesign-predicted PAMs are largely identical to the natural PAMs of all Cas proteins. In turn, given natural PAMs, the computationally redesigned PIAA residues largely recapitulated the native PIAAs (74% and 86% in terms of identity and similarity, respectively). These results demonstrate that UniDesign faithfully captures the mutual preference between natural PAMs and native PIAAs, suggesting it is a useful tool for engineering CRISPR-Cas and other nucleic acid-interacting proteins. UniDesign is open-sourced at https://github.com/tommyhuangthu/UniDesign.
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Affiliation(s)
- Xiaoqiang Huang
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Jun Zhou
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Dongshan Yang
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Jifeng Zhang
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Xiaofeng Xia
- Research & Development, ATGC Inc., 100 E Lancaster Avenue, LIMR Building Lab 129, Wynnewood, PA 19096, USA
| | - Yuqing Eugene Chen
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Jie Xu
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
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11
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Teal CJ, Ho MT, Huo L, Harada H, Bahlmann LC, Léveillard T, Monnier PP, Ramachandran A, Shoichet MS. Affinity-controlled release of rod-derived cone viability factor enhances cone photoreceptor survival. Acta Biomater 2023; 161:37-49. [PMID: 36898472 DOI: 10.1016/j.actbio.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/11/2023]
Abstract
Retinitis pigmentosa (RP) is a group of genetic diseases that results in rod photoreceptor cell degeneration, which subsequently leads to cone photoreceptor cell death, impaired vision and eventual blindness. Rod-derived cone viability factor (RdCVF) is a protein which has two isoforms: a short form (RdCVF) and a long form (RdCVFL) which act on cone photoreceptors in the retina. RdCVFL protects photoreceptors by reducing hyperoxia in the retina; however, sustained delivery of RdCVFL remains challenging. We developed an affinity-controlled release strategy for RdCVFL. An injectable physical blend of hyaluronan and methylcellulose (HAMC) was covalently modified with a peptide binding partner of the Src homology 3 (SH3) domain. This domain was expressed as a fusion protein with RdCVFL, thereby enabling its controlled release from HAMC-binding peptide. Sustained release of RdCVFL was demonstrated for the first time as RdCVFL-SH3 from HAMC-binding peptide for 7 d in vitro. To assess bioactivity, chick retinal dissociates were harvested and treated with the affinity-released recombinant protein from the HAMC-binding peptide vehicle. After 6 d in culture, cone cell viability was greater when cultured with released RdCVFL-SH3 relative to controls. We utilized computational fluid dynamics to model release of RdCVFL-SH3 from our delivery vehicle in the vitreous of the human eye. We demonstrate that our delivery vehicle can prolong the bioavailability of RdCVFL-SH3 in the retina, potentially enhancing its therapeutic effects. Our affinity-based system constitutes a versatile delivery platform for ultimate intraocular injection in the treatment of retinal degenerative diseases. STATEMENT OF SIGNIFICANCE: Retinitis pigmentosa (RP) is the leading cause of inherited blindness in the world. Rod-derived cone viability factor (RdCVF), a novel protein paracrine factor, is effective in preclinical models of RP. To extend its therapeutic effects, we developed an affinity-controlled release strategy for the long form of RdCVF, RdCVFL. We expressed RdCVFL as a fusion protein with an Src homology 3 domain (SH3). We then utilized a hydrogel composed of hyaluronan and methylcellulose (HAMC) and modified it with SH3 binding peptides to investigate its release in vitro. Furthermore, we designed a mathematical model of the human eye to investigate delivery of the protein from the delivery vehicle. This work paves the way for future investigation of controlled release RdCVF.
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Affiliation(s)
- Carter J Teal
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, M5S 3G9 Toronto, Ontario, Canada; Donnelly Centre, University of Toronto, 160 College Street, M5S3E1 Toronto, Ontario, Canada
| | - Margaret T Ho
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, M5S 3G9 Toronto, Ontario, Canada; Donnelly Centre, University of Toronto, 160 College Street, M5S3E1 Toronto, Ontario, Canada
| | - Lia Huo
- Donnelly Centre, University of Toronto, 160 College Street, M5S3E1 Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, 1 King's College Circle, M5S 1A8 Toronto, Ontario, Canada
| | - Hidekiyo Harada
- Donald K. Johnson Research Institute, Krembil Research Institute, Krembil Discovery Tower, Toronto, Ontario, Canada
| | - Laura C Bahlmann
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, M5S 3G9 Toronto, Ontario, Canada; Donnelly Centre, University of Toronto, 160 College Street, M5S3E1 Toronto, Ontario, Canada
| | - Thierry Léveillard
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France
| | - Philippe P Monnier
- Donald K. Johnson Research Institute, Krembil Research Institute, Krembil Discovery Tower, Toronto, Ontario, Canada; Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Arun Ramachandran
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, M5S 3E5 Toronto, Ontario, Canada
| | - Molly S Shoichet
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, M5S 3G9 Toronto, Ontario, Canada; Donnelly Centre, University of Toronto, 160 College Street, M5S3E1 Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, 1 King's College Circle, M5S 1A8 Toronto, Ontario, Canada; Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, M5S 3E5 Toronto, Ontario, Canada; Department of Chemistry, University of Toronto, 80 Saint George Street, M5S 3H6 Toronto, Ontario, Canada.
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12
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Enzyme Kinetics Features of the Representative Engineered Recombinants of Chondroitinase ABC I. Protein J 2023; 42:55-63. [PMID: 36715784 DOI: 10.1007/s10930-023-10093-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2023] [Indexed: 01/31/2023]
Abstract
Chondroitinase ABC I (cABC I) from Proteus vulgaris is an important enzyme in medicinal biotechnology due to its ability to help axon regeneration after spinal cord injury. Its practical application involves solving several problems at the molecular and cellular levels. Structurally, most residues at the C-terminal domain of cABC I are arranged as organized strands, and only a small fraction of residues have helical conformation. The structural and functional features of modified residues on two specific helix fragments have previously been reported. The single mutant M889K has been combined with L679S and L679D mutants to make enzyme variants containing simultaneously modified helix. Here, the pH stability and temperature-based analysis of the transition state structure for the catalysis reaction were investigated. We found that double mutant L679D/M889K is the better choice to use in physiological conditions due to its higher pH stability at physiological pH as well as its different optimum temperature as compared with the (wild-type) WT protein. According to Arrhenius's analysis, the values of the Gibbs free energy of the transition state (∆G#) are not changed upon mutation. However, the relative contribution and absolute values of the enthalpy and entropy change to the total value of ∆G#, varied between the WT and mutants.
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13
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Miao H, Zhe Y, Xiang X, Cao Y, Han N, Wu Q, Huang Z. Enhanced Extracellular Expression of a Ca 2+- and Mg 2+-Dependent Hyperthermostable Protease EA1 in Bacillus subtilis via Systematic Screening of Optimal Signal Peptides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:15830-15839. [PMID: 36480738 DOI: 10.1021/acs.jafc.2c06741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Proteases have been widely applied in various industries, including tanning, silk, feed, medicine, food, and environmental protection. Herein, the protease EA1 (GenBank accession no. U25630.1) was successfully expressed in Bacillus subtilis and demonstrated to function as a Ca2+- and Mg2+-dependent hyperthermostable neutral protease. At 80 °C, its half-life (t1/2) in the presence of 10 mM Mg2+ and Ca2+ was 50.4-fold longer than that in their absence (7.4 min), which can be explained by structural analysis. Compared with the currently available commercial proteases, protease EA1 has obvious advantages in heat resistance. The largest peptide library was used to enhance the extracellular expression of protease EA1 via constructing and screening 244 signal peptides (SPs). Eleven SPs with high yields of protease EA1 were identified from 5000 clones using a high-throughput assay. Specifically, the enzyme activity of protease produced by the strain (217.6 U/mL) containing the SP XynD was 5.2-fold higher than that of the strain with the initial SP. In brief, the protease is a potential candidate for future use in the high-temperature industry.
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Affiliation(s)
- Huabiao Miao
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, China
- School of Life Science, Yunnan Normal University, Kunming 650500, China
| | - Yuanyuan Zhe
- School of Life Science, Yunnan Normal University, Kunming 650500, China
| | - Xia Xiang
- School of Life Science, Yunnan Normal University, Kunming 650500, China
| | - Yan Cao
- School of Life Science, Yunnan Normal University, Kunming 650500, China
| | - Nanyu Han
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, China
- School of Life Science, Yunnan Normal University, Kunming 650500, China
| | - Qian Wu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, China
- School of Life Science, Yunnan Normal University, Kunming 650500, China
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, China
- School of Life Science, Yunnan Normal University, Kunming 650500, China
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14
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Zappe A, Miller RL, Struwe WB, Pagel K. State-of-the-art glycosaminoglycan characterization. MASS SPECTROMETRY REVIEWS 2022; 41:1040-1071. [PMID: 34608657 DOI: 10.1002/mas.21737] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/02/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Glycosaminoglycans (GAGs) are heterogeneous acidic polysaccharides involved in a range of biological functions. They have a significant influence on the regulation of cellular processes and the development of various diseases and infections. To fully understand the functional roles that GAGs play in mammalian systems, including disease processes, it is essential to understand their structural features. Despite having a linear structure and a repetitive disaccharide backbone, their structural analysis is challenging and requires elaborate preparative and analytical techniques. In particular, the extent to which GAGs are sulfated, as well as variation in sulfate position across the entire oligosaccharide or on individual monosaccharides, represents a major obstacle. Here, we summarize the current state-of-the-art methodologies used for GAG sample preparation and analysis, discussing in detail liquid chromatograpy and mass spectrometry-based approaches, including advanced ion activation methods, ion mobility separations and infrared action spectroscopy of mass-selected species.
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Affiliation(s)
- Andreas Zappe
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Rebecca L Miller
- Department of Cellular and Molecular Medicine, Copenhagen Centre for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | | | - Kevin Pagel
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
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15
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Khalil AS, Hellenbrand D, Reichl K, Umhoefer J, Filipp M, Choe J, Hanna A, Murphy WL. A Localized Materials-Based Strategy to Non-Virally Deliver Chondroitinase ABC mRNA Improves Hindlimb Function in a Rat Spinal Cord Injury Model. Adv Healthc Mater 2022; 11:e2200206. [PMID: 35882512 PMCID: PMC10031873 DOI: 10.1002/adhm.202200206] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 07/14/2022] [Indexed: 01/27/2023]
Abstract
Spinal cord injury often results in devastating consequences for those afflicted, with very few therapeutic options. A central element of spinal cord injuries is astrogliosis, which forms a glial scar that inhibits neuronal regeneration post-injury. Chondroitinase ABC (ChABC) is an enzyme capable of degrading chondroitin sulfate proteoglycan (CSPG), the predominant extracellular matrix component of the glial scar. However, poor protein stability remains a challenge in its therapeutic use. Messenger RNA (mRNA) delivery is an emerging gene therapy technology for in vivo production of difficult-to-produce therapeutic proteins. Here, mineral-coated microparticles as an efficient, non-viral mRNA delivery vehicles to produce exogenous ChABC in situ within a spinal cord lesion are used. ChABC production reduces the deposition of CSPGs in an in vitro model of astrogliosis, and direct injection of these microparticles within a glial scar forces local overexpression of ChABC and improves recovery of motor function seven weeks post-injury.
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Affiliation(s)
- Andrew S. Khalil
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53705
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, WI 53705
| | - Daniel Hellenbrand
- Department of Neurosurgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53705
| | - Kaitlyn Reichl
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53705
| | - Jennifer Umhoefer
- Department of Biology, University of Wisconsin-Madison, Madison, WI 53705
| | - Mallory Filipp
- Department of Neurosurgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53705
| | - Joshua Choe
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53705
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, WI 53705
- Medical Scientist Training Program, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53705
| | - Amgad Hanna
- Department of Neurosurgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53705
| | - William L. Murphy
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53705
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, WI 53705
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, WI 53705
- Forward BIO Institute, University of Wisconsin-Madison, Madison, WI 53705
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16
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Girão AF, Serrano MC, Completo A, Marques PAAP. Is Graphene Shortening the Path toward Spinal Cord Regeneration? ACS NANO 2022; 16:13430-13467. [PMID: 36000717 PMCID: PMC9776589 DOI: 10.1021/acsnano.2c04756] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Along with the development of the next generation of biomedical platforms, the inclusion of graphene-based materials (GBMs) into therapeutics for spinal cord injury (SCI) has potential to nourish topmost neuroprotective and neuroregenerative strategies for enhancing neural structural and physiological recovery. In the context of SCI, contemplated as one of the most convoluted challenges of modern medicine, this review first provides an overview of its characteristics and pathophysiological features. Then, the most relevant ongoing clinical trials targeting SCI, including pharmaceutical, robotics/neuromodulation, and scaffolding approaches, are introduced and discussed in sequence with the most important insights brought by GBMs into each particular topic. The current role of these nanomaterials on restoring the spinal cord microenvironment after injury is critically contextualized, while proposing future concepts and desirable outputs for graphene-based technologies aiming to reach clinical significance for SCI.
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Affiliation(s)
- André F. Girão
- Centre
for Mechanical Technology and Automation (TEMA), Department of Mechanical
Engineering, University of Aveiro (UA), Aveiro, 3810-193, Portugal
- Instituto
de Ciencia de Materiales de Madrid (ICMM), Consejo Superior de Investigaciones Científicas (CSIC), Calle Sor Juana Inés de la
Cruz 3, Madrid, 28049, Spain
- (A.F.G.)
| | - María Concepcion Serrano
- Instituto
de Ciencia de Materiales de Madrid (ICMM), Consejo Superior de Investigaciones Científicas (CSIC), Calle Sor Juana Inés de la
Cruz 3, Madrid, 28049, Spain
- (M.C.S.)
| | - António Completo
- Centre
for Mechanical Technology and Automation (TEMA), Department of Mechanical
Engineering, University of Aveiro (UA), Aveiro, 3810-193, Portugal
| | - Paula A. A. P. Marques
- Centre
for Mechanical Technology and Automation (TEMA), Department of Mechanical
Engineering, University of Aveiro (UA), Aveiro, 3810-193, Portugal
- (P.A.A.P.M.)
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17
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Bostock C, Teal CJ, Dang M, Golinski AW, Hackel BJ, Shoichet MS. Affibody-mediated controlled release of fibroblast growth factor 2. J Control Release 2022; 350:815-828. [PMID: 36087800 DOI: 10.1016/j.jconrel.2022.09.004] [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: 05/17/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 10/14/2022]
Abstract
Protein therapeutics possess high target affinity and specificity, yet short residence times, which limit their broad utility. To overcome this challenge, we used affinity interactions to modulate protein release from a hydrogel delivery vehicle thereby prolonging therapeutic availability. Specifically, we designed an affibody-modified hyaluronan (HA)-based hydrogel as a delivery platform for fibroblast growth factor 2 (FGF2), a neuroprotective and neuroregenerative factor in the central nervous system (CNS). We identified a highly specific affibody binding partner with moderate affinity for FGF2 using yeast surface display and flow cytometry-based screening. Importantly, we demonstrated controlled release of bioactive FGF2 from the hydrogel by varying the ratio of affibody to protein and showed increased thermal stability of FGF2 in the presence of affibody. This versatile delivery platform will allow the distinct, simultaneous release of multiple proteins based on specific affinity interactions.
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Affiliation(s)
- Chiara Bostock
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Carter J Teal
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada; Institute of Biomedical Engineering, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Mickael Dang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Alex W Golinski
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Avenue Southeast, 356 Amundson Hall, Minneapolis, MN 55455, United States
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Avenue Southeast, 356 Amundson Hall, Minneapolis, MN 55455, United States
| | - Molly S Shoichet
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada; Institute of Biomedical Engineering, 164 College Street, Toronto, Ontario M5S 3G9, Canada.
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18
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Luo F, Wang J, Zhang Z, You Z, Bedolla A, Okwubido-Williams F, Huang LF, Silver J, Luo Y. Inhibition of CSPG receptor PTPσ promotes migration of newly born neuroblasts, axonal sprouting, and recovery from stroke. Cell Rep 2022; 40:111137. [PMID: 35905716 DOI: 10.1016/j.celrep.2022.111137] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/16/2022] [Accepted: 07/05/2022] [Indexed: 12/12/2022] Open
Abstract
In addition to neuroprotective strategies, neuroregenerative processes could provide targets for stroke recovery. However, the upregulation of inhibitory chondroitin sulfate proteoglycans (CSPGs) impedes innate regenerative efforts. Here, we examine the regulatory role of PTPσ (a major proteoglycan receptor) in dampening post-stroke recovery. Use of a receptor modulatory peptide (ISP) or Ptprs gene deletion leads to increased neurite outgrowth and enhanced NSCs migration upon inhibitory CSPG substrates. Post-stroke ISP treatment results in increased axonal sprouting as well as neuroblast migration deeply into the lesion scar with a transcriptional signature reflective of repair. Lastly, peptide treatment post-stroke (initiated acutely or more chronically at 7 days) results in improved behavioral recovery in both motor and cognitive functions. Therefore, we propose that CSPGs induced by stroke play a predominant role in the regulation of neural repair and that blocking CSPG signaling pathways will lead to enhanced neurorepair and functional recovery in stroke.
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Affiliation(s)
- Fucheng Luo
- Department of Molecular Genetics, Biochemistry, and Microbiology, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Jiapeng Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Zhen Zhang
- Department of Molecular Genetics, Biochemistry, and Microbiology, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Zhen You
- Division of Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Alicia Bedolla
- Department of Molecular Genetics, Biochemistry, and Microbiology, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - FearGod Okwubido-Williams
- Department of Molecular Genetics, Biochemistry, and Microbiology, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - L Frank Huang
- Division of Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Jerry Silver
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Yu Luo
- Department of Molecular Genetics, Biochemistry, and Microbiology, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA.
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19
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Dong F, Zhang M, Ma R, Lu C, Xu F. Insights of conformational dynamics on catalytic activity in the computational stability design of Bacillus subtilis LipA. Arch Biochem Biophys 2022; 722:109196. [PMID: 35339426 DOI: 10.1016/j.abb.2022.109196] [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: 11/23/2021] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 11/18/2022]
Abstract
In protein engineering, the contributions of individual mutations to designed combinatorial mutants are unpredictable. Screening designed mutations that affect enzyme catalytic activity enables evolutions towards efficient activities. Here, Bacillus subtilis LipA (BSLA) was selected as a model protein for thermostabilization designs, and the circular dichroism measurements showed six combinatorial designs with improved stability (from 5.81 °C to 13.61 °C). Based on molecular dynamic simulations, the conformational dynamics of the mutants revealed that mutations alter the populations of conformational states and the increased ensembles of inactive conformations might lead to a reduction in activity. We further demonstrated that the mutations responsible for the reduced enzyme catalytic activity involved a short dynamic correlation path to disturbing the equilibrium conformation of active sites. By removing N82V, which had a close dynamic correlation to the active sites in mutant D3, the redesigned mutant RD3 had an increased activity of 57.6%. By combining computational simulation with experimental verification, this work established that essential sites to counteract the activity-stability trade-off in multipoint combinatorial mutants could be computationally predicted and thus provide a possible strategy by which to indirectly or directly guide protein design.
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Affiliation(s)
- Fangying Dong
- Ministry of Education Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, 214122, Wuxi, China
| | - Meng Zhang
- Ministry of Education Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, 214122, Wuxi, China
| | - Rui Ma
- Ministry of Education Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, 214122, Wuxi, China
| | - Cheng Lu
- Ministry of Education Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, 214122, Wuxi, China.
| | - Fei Xu
- Ministry of Education Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, 214122, Wuxi, China.
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20
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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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21
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Lemay-St-Denis C, Doucet N, Pelletier JN. Integrating dynamics into enzyme engineering. Protein Eng Des Sel 2022; 35:6842866. [PMID: 36416215 DOI: 10.1093/protein/gzac015] [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: 06/21/2022] [Revised: 11/02/2022] [Accepted: 11/06/2022] [Indexed: 11/24/2022] Open
Abstract
Enzyme engineering has become a widely adopted practice in research labs and industry. In parallel, the past decades have seen tremendous strides in characterizing the dynamics of proteins, using a growing array of methodologies. Importantly, links have been established between the dynamics of proteins and their function. Characterizing the dynamics of an enzyme prior to, and following, its engineering is beginning to inform on the potential of 'dynamic engineering', i.e. the rational modification of protein dynamics to alter enzyme function. Here we examine the state of knowledge at the intersection of enzyme engineering and protein dynamics, describe current challenges and highlight pioneering work in the nascent area of dynamic engineering.
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Affiliation(s)
- Claudèle Lemay-St-Denis
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
| | - Nicolas Doucet
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, QC, Canada
| | - Joelle N Pelletier
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
- Chemistry Department, Université de Montréal, Montreal, QC, Canada
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22
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Yu Z, Yu H, Xu J, Wang Z, Wang Z, Kang T, Chen K, Pu Z, Wu J, Yang LR, Xu G. Enhancing Thermostability of Lipase from Pseudomonas alcaligenes for producing L-menthol by the CREATE Strategy. Catal Sci Technol 2022. [DOI: 10.1039/d2cy00082b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Lipase from Pseudomonas alcaligenes (PaL) catalyzes the hydrolysis of racemic menthol propionate to produce L-menthol, one of the most important flavoring agents in food, cosmetics and pharmaceuticals industries. However,...
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23
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Cioni P, Gabellieri E, Campanini B, Bettati S, Raboni S. Use of Exogenous Enzymes in Human Therapy: Approved Drugs and Potential Applications. Curr Med Chem 2021; 29:411-452. [PMID: 34259137 DOI: 10.2174/0929867328666210713094722] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/05/2021] [Accepted: 03/17/2021] [Indexed: 11/22/2022]
Abstract
The development of safe and efficacious enzyme-based human therapies has increased greatly in the last decades, thanks to remarkable advances in the understanding of the molecular mechanisms responsible for different diseases, and the characterization of the catalytic activity of relevant exogenous enzymes that may play a remedial effect in the treatment of such pathologies. Several enzyme-based biotherapeutics have been approved by FDA (the U.S. Food and Drug Administration) and EMA (the European Medicines Agency) and many are undergoing clinical trials. Apart from enzyme replacement therapy in human genetic diseases, which is not discussed in this review, approved enzymes for human therapy find applications in several fields, from cancer therapy to thrombolysis and the treatment, e.g., of clotting disorders, cystic fibrosis, lactose intolerance and collagen-based disorders. The majority of therapeutic enzymes are of microbial origin, the most convenient source due to fast, simple and cost-effective production and manipulation. The use of microbial recombinant enzymes has broadened prospects for human therapy but some hurdles such as high immunogenicity, protein instability, short half-life and low substrate affinity, still need to be tackled. Alternative sources of enzymes, with reduced side effects and improved activity, as well as genetic modification of the enzymes and novel delivery systems are constantly searched. Chemical modification strategies, targeted- and/or nanocarrier-mediated delivery, directed evolution and site-specific mutagenesis, fusion proteins generated by genetic manipulation are the most explored tools to reduce toxicity and improve bioavailability and cellular targeting. This review provides a description of exogenous enzymes that are presently employed for the therapeutic management of human diseases with their current FDA/EMA-approved status, along with those already experimented at the clinical level and potential promising candidates.
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Affiliation(s)
- Patrizia Cioni
- Institute of Biophysics, National Research Council, Via Moruzzi 1, 56124 Pisa. Italy
| | - Edi Gabellieri
- Institute of Biophysics, National Research Council, Via Moruzzi 1, 56124 Pisa. Italy
| | - Barbara Campanini
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma. Italy
| | - Stefano Bettati
- Institute of Biophysics, National Research Council, Via Moruzzi 1, 56124 Pisa. Italy
| | - Samanta Raboni
- Institute of Biophysics, National Research Council, Via Moruzzi 1, 56124 Pisa. Italy
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24
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Hlavac N, Seroski DT, Agrawal NK, Astrab L, Liu R, Hudalla GA, Schmidt CE. Chondroitinase ABC/galectin-3 fusion proteins with hyaluronan-based hydrogels stabilize enzyme and provide targeted enzyme activity for neural applications. J Neural Eng 2021; 18. [PMID: 34082409 DOI: 10.1088/1741-2552/ac07bf] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/03/2021] [Indexed: 12/22/2022]
Abstract
Objective. Chondroitinase ABC (ChABC) has emerged as a promising therapeutic agent for central nervous system regeneration. Despite multiple beneficial outcomes for regeneration, translation of this enzyme is challenged by poor pharmacokinetics, localization, and stability.Approach. This study explored the function andin vitroapplication of engineered ChABC fused to galectin-3 (Gal3). Two previously developed ChABC-Gal3 oligomers (monomeric and trimeric) were evaluated for functionality and kinetics, then applied to anin vitrocellular outgrowth model using dorsal root ganglia (DRGs). The fusions were combined with two formulations of hyaluronan (HA)-based scaffolds to determine the extent of active enzyme release compared to wild type (WT) ChABC.Main Results. Monomeric and trimeric ChABC-Gal3 maintained digestive capabilities with kinetic properties that were substrate-dependent for chondroitin sulfates A, B, and C. The fusions had longer half-lives at 37 °C on the order of seven fold for monomer and twelve fold for trimer compared to WT. Both fusions were also effective at restoring DRG outgrowthin vitro. To create a combination approach, two triple-component hydrogels containing modified HA were formulated to match the mechanical properties of native spinal cord tissue and to support astrocyte viability (>80%) and adhesion. The hydrogels included collagen-I and laminin mixed with either 5 mg ml-1of glycidyl methacrylate HA or 3 mg ml-1Hystem. When combined with scaffolds, ChABC-Gal3 release time was lengthened compared to WT. Both fusions had measurable enzymatic activity for at least 10 d when incorporated in gels, compared to WT that lost activity after 1 d. These longer term release products from gels maintained adequate function to promote DRG outgrowth.Significance. Results of this study demonstrated cohesive benefits of two stabilized ChABC-Gal3 oligomers in combination with HA-based scaffolds for neural applications. Significant improvements to ChABC stability and release were achieved, meriting future studies of ChABC-Gal3/hydrogel combinations to target neural regeneration.
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Affiliation(s)
- Nora Hlavac
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States of America
| | - Dillon T Seroski
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States of America
| | - Nikunj K Agrawal
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States of America
| | - Leilani Astrab
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States of America
| | - Renjie Liu
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States of America
| | - Gregory A Hudalla
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States of America
| | - Christine E Schmidt
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States of America
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Dorogin J, Townsend JM, Hettiaratchi MH. Biomaterials for protein delivery for complex tissue healing responses. Biomater Sci 2021; 9:2339-2361. [PMID: 33432960 DOI: 10.1039/d0bm01804j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Tissue repair requires a complex cascade of events mediated by a variety of cells, proteins, and matrix molecules; however, the healing cascade can be easily disrupted by numerous factors, resulting in impaired tissue regeneration. Recent advances in biomaterials for tissue regeneration have increased the ability to tailor the delivery of proteins and other biomolecules to injury sites to restore normal healing cascades and stimulate robust tissue repair. In this review, we discuss the evolution of the field toward creating biomaterials that precisely control protein delivery to stimulate tissue regeneration, with a focus on addressing complex and dynamic injury environments. We highlight biomaterials that leverage different mechanisms to deliver and present proteins involved in healing cascades, tissue targeting and mimicking strategies, materials that can be triggered by environmental cues, and integrated strategies that combine multiple biomaterial properties to improve protein delivery. Improvements in biomaterial design to address complex injury environments will expand our understanding of both normal and aberrant tissue repair processes and ultimately provide a better standard of patient care.
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Affiliation(s)
- Jonathan Dorogin
- Knight Campus for Accelerating Scientific Impact, University of Oregon, 6321 University of Oregon, Eugene, OR 97401, USA.
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26
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Bretherton RC, DeForest CA. The Art of Engineering Biomimetic Cellular Microenvironments. ACS Biomater Sci Eng 2021; 7:3997-4008. [PMID: 33523625 DOI: 10.1021/acsbiomaterials.0c01549] [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] [Indexed: 11/29/2022]
Abstract
Cells and their surrounding microenvironment exist in dynamic reciprocity, where bidirectional feedback and feedforward crosstalk drives essential processes in development, homeostasis, and disease. With the ongoing explosion of customizable biomaterial innovation for dynamic cell culture, an ever-expanding suite of user-programmable scaffolds now exists to probe cell fate in response to spatiotemporally controlled biophysical and biochemical cues. Here, we highlight emerging trends in these efforts, emphasizing strategies that offer tunability over complex network mechanics, present biomolecular cues anisotropically, and harness cells as physiochemical actuators of the pericellular niche. Altogether, these material advances will lead to breakthroughs in our basic understanding of how cells interact with, integrate signals from, and influence their surrounding microenvironment.
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Affiliation(s)
- Ross C Bretherton
- Department of Bioengineering, University of Washington, Seattle, Washington 98105, United States.,Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Cole A DeForest
- Department of Bioengineering, University of Washington, Seattle, Washington 98105, United States.,Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington 98109, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Department of Chemistry, University of Washington, Seattle, Washington 98195, United States.,Molecular Engineering & Sciences Institute, University of Washington, Seattle, Washington 98195, United States
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