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Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022; 122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.
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Affiliation(s)
- Rui Qing
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shilei Hao
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Eva Smorodina
- Department
of Immunology, University of Oslo and Oslo
University Hospital, Oslo 0424, Norway
| | - David Jin
- Avalon GloboCare
Corp., Freehold, New Jersey 07728, United States
| | - Arthur Zalevsky
- Laboratory
of Bioinformatics Approaches in Combinatorial Chemistry and Biology, Shemyakin−Ovchinnikov Institute of Bioorganic
Chemistry RAS, Moscow 117997, Russia
| | - Shuguang Zhang
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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2
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Puthumadathil N, Krishnan R S, Nair GS, Mahendran KR. Assembly of alpha-helical transmembrane pores through an intermediate state. NANOSCALE 2022; 14:6507-6517. [PMID: 35420118 DOI: 10.1039/d2nr00556e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Pore-forming alpha-helical proteins are well known for their dynamic assembly mechanism and it has been challenging to delineate the pore-forming structures in membranes. Previously, attempts have been made to elucidate their assembly mechanism and there is a large gap due to complex pathways by which these membrane-active pores impart their effect. Here we demonstrate a multi-step structural assembly pathway of alpha-helical peptide pores formed by a 37 amino acid synthetic peptide, pPorU, based on the natural porin from Corynebacterium urealyticum using single-channel electrical recordings. More specifically, we report detectable intermediate states during the membrane insertion and pore formation of pPorU. The fully assembled pore exhibited unusually large stable conductance, voltage-dependent gating, and functional blockage by cyclic sugars generally applicable to a range of transmembrane pores. Furthermore, we used rationally designed mutants to understand the role of specific amino acids in the assembly of these peptide pores. Mutant peptides that differ from wild-type peptides produced noisy and unstable intermediate states and low conductance pores, demonstrating sequence specificity in the pore-formation process supported by molecular dynamics simulations. We suggest that our study contributes to understanding the mechanism of action of naturally occurring alpha-helical pore-forming proteins and should be of broad interest to build peptide-based nanopore sensors.
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Affiliation(s)
- Neethu Puthumadathil
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.
- Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Smrithi Krishnan R
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.
- Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Greeshma S Nair
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.
| | - Kozhinjampara R Mahendran
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.
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Crnković A, Srnko M, Anderluh G. Biological Nanopores: Engineering on Demand. Life (Basel) 2021; 11:life11010027. [PMID: 33466427 PMCID: PMC7824896 DOI: 10.3390/life11010027] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 12/17/2022] Open
Abstract
Nanopore-based sensing is a powerful technique for the detection of diverse organic and inorganic molecules, long-read sequencing of nucleic acids, and single-molecule analyses of enzymatic reactions. Selected from natural sources, protein-based nanopores enable rapid, label-free detection of analytes. Furthermore, these proteins are easy to produce, form pores with defined sizes, and can be easily manipulated with standard molecular biology techniques. The range of possible analytes can be extended by using externally added adapter molecules. Here, we provide an overview of current nanopore applications with a focus on engineering strategies and solutions.
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Abstract
Protein pores play key roles in fundamental biological processes1 and biotechnological applications such as DNA nanopore sequencing2–4, and hence the design of pore-containing proteins is of considerable scientific and biotechnological interest. Synthetic amphiphilic peptides have been found to form ion channels5,6, and there have been recent advances in de novo membrane protein design7,8 and in redesigning naturally occurring channel-containing proteins9,10. However, the de novo design of stable, well-defined transmembrane protein pores capable of conducting ions selectively or large enough to allow passage of small-molecule fluorophores remains an outstanding challenge11,12. Here, we report the computational design of protein pores formed by two concentric rings of ɑ-helices that are stable and mono-disperse in both water-soluble and transmembrane forms. Crystal structures of the water-soluble forms of a 12 helical and a 16 helical pore are close to the computational design models. Patch-clamp electrophysiology experiments show that the transmembrane form of the 12-helix pore expressed in insect cells allows passage of ions across the membrane with high selectivity for potassium over sodium, which is blocked by specific chemical modification at the pore entrance. The transmembrane form of the 16-helix pore, but not the 12-helix pore, allows passage of biotinylated Alexa Fluor 488 when incorporated into liposomes using in vitro protein synthesis. A cryo-EM structure of the 16-helix transmembrane pore closely matches the design model. The ability to produce structurally and functionally well-defined transmembrane pores opens the door to the creation of designer pores for a wide variety of applications.
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5
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Monserrat-Martinez A, Gambin Y, Sierecki E. Thinking Outside the Bug: Molecular Targets and Strategies to Overcome Antibiotic Resistance. Int J Mol Sci 2019; 20:ijms20061255. [PMID: 30871132 PMCID: PMC6470534 DOI: 10.3390/ijms20061255] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/04/2019] [Accepted: 03/04/2019] [Indexed: 12/25/2022] Open
Abstract
Since their discovery in the early 20th century, antibiotics have been used as the primary weapon against bacterial infections. Due to their prophylactic effect, they are also used as part of the cocktail of drugs given to treat complex diseases such as cancer or during surgery, in order to prevent infection. This has resulted in a decrease of mortality from infectious diseases and an increase in life expectancy in the last 100 years. However, as a consequence of administering antibiotics broadly to the population and sometimes misusing them, antibiotic-resistant bacteria have appeared. The emergence of resistant strains is a global health threat to humanity. Highly-resistant bacteria like Staphylococcus aureus (methicillin-resistant) or Enterococcus faecium (vancomycin-resistant) have led to complications in intensive care units, increasing medical costs and putting patient lives at risk. The appearance of these resistant strains together with the difficulty in finding new antimicrobials has alarmed the scientific community. Most of the strategies currently employed to develop new antibiotics point towards novel approaches for drug design based on prodrugs or rational design of new molecules. However, targeting crucial bacterial processes by these means will keep creating evolutionary pressure towards drug resistance. In this review, we discuss antibiotic resistance and new options for antibiotic discovery, focusing in particular on new alternatives aiming to disarm the bacteria or empower the host to avoid disease onset.
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Affiliation(s)
- Ana Monserrat-Martinez
- European Molecular Biology Laboratory Australia (EMBL Australia) Node in Single Molecule Science, Sydney, NSW 2031, Australia.
- School of Medical Sciences, The University of New South Wales, Sydney, NSW 2031, Australia.
| | - Yann Gambin
- European Molecular Biology Laboratory Australia (EMBL Australia) Node in Single Molecule Science, Sydney, NSW 2031, Australia.
- School of Medical Sciences, The University of New South Wales, Sydney, NSW 2031, Australia.
| | - Emma Sierecki
- European Molecular Biology Laboratory Australia (EMBL Australia) Node in Single Molecule Science, Sydney, NSW 2031, Australia.
- School of Medical Sciences, The University of New South Wales, Sydney, NSW 2031, Australia.
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6
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Spruijt E, Tusk SE, Bayley H. DNA scaffolds support stable and uniform peptide nanopores. NATURE NANOTECHNOLOGY 2018; 13:739-745. [PMID: 29808001 DOI: 10.1038/s41565-018-0139-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/04/2018] [Indexed: 05/18/2023]
Abstract
The assembly of peptides into membrane-spanning nanopores might be promoted by scaffolds to pre-organize the structures. Such scaffolds could enable the construction of uniform pores of various sizes and pores with controlled permutations around a central axis. Here, we show that DNA nanostructures can serve as scaffolds to arrange peptides derived from the octameric polysaccharide transporter Wza to form uniform nanopores in planar lipid bilayers. Our ring-shaped DNA scaffold is assembled from short synthetic oligonucleotides that are connected to Wza peptides through flexible linkers. When scaffolded, the Wza peptides form conducting nanopores of which only octamers are stable and of uniform conductance. Removal of the DNA scaffold by cleavage of the linkers leads to a rapid loss of the nanopores from the lipid bilayer, which shows that the scaffold is essential for their stability. The DNA scaffold also adds functionality to the nanopores by enabling reversible and permanent binding of complementary tagged oligonucleotides near the nanopore entrance.
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Affiliation(s)
- Evan Spruijt
- Chemistry Research Laboratory, University of Oxford, Oxford, UK.
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
| | - Samuel E Tusk
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Hagan Bayley
- Chemistry Research Laboratory, University of Oxford, Oxford, UK.
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Pittman AE, Marsh BP, King GM. Conformations and Dynamic Transitions of a Melittin Derivative That Forms Macromolecule-Sized Pores in Lipid Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:8393-8399. [PMID: 29933696 DOI: 10.1021/acs.langmuir.8b00804] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Systematically evolved from the primary active component of bee venom, MelP5 is a lipophilic peptide with important physical properties that differ from wild-type melittin, including the ability to create large equilibrium pores in lipid bilayers at low peptide to lipid ratios. Self-assembly into stable membrane spanning pores makes MelP5 a promising candidate for future applications in the pharmaceutical arena. Despite significant interest, little is known about the mechanism by which MelP5 remodels the lipid bilayer upon binding. We demonstrate by direct atomic force microscope imaging of supported lipid bilayers in solution that MelP5 remodels 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphocholine (POPC) in one of two ways. It creates either highly localized voids in the bilayer or diffuse nonlocalized thinning. Thinning of the bilayer was measured to be 3.0 ± 1.4 Å (mean ± standard deviation) below the surface of the upper leaflet of the bilayer. Pores, defined as highly localized voids in the bilayer, exhibited several sizes. Approximately 20% of pores exhibited large footprint areas (47 ± 20 nm2) which appear capable of passing bulky macromolecules. The peptide-effected bilayer was observed to reversibly exchange between membrane-thinned and pore states in an apparent dynamic equilibrium. Analysis of time-lapsed images suggested upper and lower bounds (0.2 < τ < 180 s) on the characteristic time scale of transitions between the membrane-thinned and pore states. Moreover, pores were found to colocalize with membrane-thinned regions, a novel observation that is consistent with the notion of cooperativity among membrane-bound peptides when forming pores.
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Berezhkovskii AM, Bezrukov SM. Mapping Intrachannel Diffusive Dynamics of Interacting Molecules onto a Two-Site Model: Crossover in Flux Concentration Dependence. J Phys Chem B 2018; 122:10996-11001. [PMID: 29957941 DOI: 10.1021/acs.jpcb.8b04371] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study focuses on how interactions of solute molecules affect the concentration dependence of their flux through narrow membrane channels. It is assumed that the molecules cannot bypass each other because of their hard-core repulsion. In addition, other short- and long-range solute-solute interactions are included into consideration. These interactions make it impossible to develop an analytical theory for the flux in the framework of a diffusion model of solute dynamics in the channel. To overcome this difficulty, we course-grain the diffusion model by mapping it onto a two-site one, where the rate constants describing the solute dynamics are expressed in terms of the parameters of the initial diffusion model. This allows us (i) to find an analytical solution for the flux as a function of the solute concentration and (ii) to characterize the solute-solute interactions by two dimensionless parameters. Such a characterization proves to be very informative as it results in a clear classification of the effects of the solute-solute interactions on the concentration dependence of the flux. Unexpectedly, this dependence can be nonmonotonic, exhibiting a sharp maximum in a certain parameter range. We hypothesize that such a behavior may constitute an element of a regulatory mechanism, wherein maximal flux reports on the optimal solute concentration in the bulk near the channel entrance.
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Affiliation(s)
- Alexander M Berezhkovskii
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development , National Institutes of Health , Bethesda , Maryland 20892 , United States.,Mathematical and Statistical Computing Laboratory, Division for Computational Bioscience, Center for Information Technology , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Sergey M Bezrukov
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development , National Institutes of Health , Bethesda , Maryland 20892 , United States
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Bus T, Traeger A, Schubert US. The great escape: how cationic polyplexes overcome the endosomal barrier. J Mater Chem B 2018; 6:6904-6918. [DOI: 10.1039/c8tb00967h] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Endo-lysosomal escape strategies of cationic polymer-mediated gene delivery at a glance.
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Affiliation(s)
- Tanja Bus
- Laboratory of Organic Chemistry and Macromolecular Chemistry (IOMC)
- Friedrich Schiller University Jena
- 07743 Jena
- Germany
- Jena Center for Soft Matter (JCSM)
| | - Anja Traeger
- Laboratory of Organic Chemistry and Macromolecular Chemistry (IOMC)
- Friedrich Schiller University Jena
- 07743 Jena
- Germany
- Jena Center for Soft Matter (JCSM)
| | - Ulrich S. Schubert
- Laboratory of Organic Chemistry and Macromolecular Chemistry (IOMC)
- Friedrich Schiller University Jena
- 07743 Jena
- Germany
- Jena Center for Soft Matter (JCSM)
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