1
|
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.
Collapse
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
| |
Collapse
|
2
|
Le NT, Abe JI. MicroRNA 199a and the eNOS (Endothelial NO Synthase)/NO Pathway. Arterioscler Thromb Vasc Biol 2018; 38:2278-2280. [PMID: 30354226 DOI: 10.1161/atvbaha.118.311515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Nhat-Tu Le
- From the Department of Cardiovascular Sciences (N.-T.L.), Houston Methodist Research Institute, TX
| | - Jun-Ichi Abe
- Department of Cardiology (J.-i.A.), The University of Texas MD Anderson Cancer Center, Houston
| |
Collapse
|
3
|
Zuo C, Tang S, Zheng JS. Chemical synthesis and biophysical applications of membrane proteins. J Pept Sci 2014; 21:540-9. [DOI: 10.1002/psc.2721] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 10/30/2014] [Accepted: 10/31/2014] [Indexed: 12/16/2022]
Affiliation(s)
- Chao Zuo
- High Magnetic Field Laboratory; Chinese Academy of Sciences; Hefei 230031 China
- Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Shan Tang
- Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Ji-Shen Zheng
- High Magnetic Field Laboratory; Chinese Academy of Sciences; Hefei 230031 China
| |
Collapse
|
4
|
Folding energetics and oligomerization of polytopic α-helical transmembrane proteins. Arch Biochem Biophys 2014; 564:281-96. [DOI: 10.1016/j.abb.2014.07.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/26/2014] [Accepted: 07/14/2014] [Indexed: 01/06/2023]
|
5
|
Rowan F, Richards M, Widya M, Bayliss R, Blagg J. Diverse functionalization of Aurora-A kinase at specified surface and buried sites by native chemical modification. PLoS One 2014; 9:e103935. [PMID: 25093837 PMCID: PMC4122486 DOI: 10.1371/journal.pone.0103935] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 07/06/2014] [Indexed: 12/18/2022] Open
Abstract
The ability to obtain a homogeneous sample of protein is invaluable when studying the effect of alterations such as post-translational modifications (PTMs). Selective functionalization of a protein to investigate the effect of PTMs on its structure or activity can be achieved by chemical modification of cysteine residues. We demonstrate here that one such technique, which involves conversion of cysteine to dehydroalanine followed by thiol nucleophile addition, is suitable for the site-specific installation of a wide range of chemical mimics of PTMs, including acetylated and dimethylated lysine, and other unnatural amino acids. These reactions, optimized for the clinically relevant kinase Aurora-A, readily proceed to completion as revealed by intact protein mass spectrometry. Moreover, these reactions proceed under non-denaturing conditions, which is desirable when working with large protein substrates. We have determined reactivity trends for a diverse range of thiol nucleophile addition reactions at two separate sites on Aurora-A, and we also highlight limitations when using thiol nucleophiles that contain basic functional groups. We show that chemical modification of cysteine residues is possible not only on a flexible surface-exposed loop, but also within a deep active site pocket at the conserved DFG motif, which reveals the potential use of this method in exploring enzyme function through modification of catalytic site residues.
Collapse
Affiliation(s)
- Fiona Rowan
- Cancer Research U.K. Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
- Division of Structural Biology, The Institute of Cancer Research, London, United Kingdom
- * E-mail: (FR); (JB)
| | - Meirion Richards
- Cancer Research U.K. Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Marcella Widya
- Proteomics Core Facility, The Institute of Cancer Research, London, United Kingdom
| | - Richard Bayliss
- Division of Structural Biology, The Institute of Cancer Research, London, United Kingdom
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
| | - Julian Blagg
- Cancer Research U.K. Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
- * E-mail: (FR); (JB)
| |
Collapse
|
6
|
Zhou F, Millhauser GL. The Rich Electrochemistry and Redox Reactions of the Copper Sites in the Cellular Prion Protein. Coord Chem Rev 2012; 256:2285-2296. [PMID: 23144499 PMCID: PMC3491995 DOI: 10.1016/j.ccr.2012.04.035] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This paper reviews recent electrochemical studies of the copper complexes of prion protein (PrP) and its related peptides, and correlates their redox behavior to chemical and biologically relevant reactions. Particular emphasis is placed on the difference in redox properties between copper in the octarepeat (OR) and the non-OR domains of PrP, as well as differences between the high and low copper occupancy states in the OR domain. Several discrepancies in literature concerning these differences are discussed and reconciled. The PrP copper complexes, in comparison to copper complexes of other amyloidogenic proteins/peptides, display a more diverse and richer redox chemistry. The specific protocols and caveats that need to be considered in studying the electrochemistry and redox reactions of copper complexes of PrP, PrP-derived peptides, and other related amyloidogenic proteins are summarized.
Collapse
Affiliation(s)
- Feimeng Zhou
- Department of Chemistry and Biochemistry, California State University, Los Angeles, Los Angeles, California 90032
| | - Glenn L. Millhauser
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064
| |
Collapse
|
7
|
Janaratne TK, Okach L, Brock A, Lesley SA. Solubilization of native integral membrane proteins in aqueous buffer by noncovalent chelation with monomethoxy poly(ethylene glycol) (mPEG) polymers. Bioconjug Chem 2011; 22:1513-8. [PMID: 21740061 DOI: 10.1021/bc200019x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Highly hydrophobic integral membrane proteins (IMPs)are typically purified in excess detergent media, often resulting in rapid inactivation and denaturation of the protein. One promising approach to solve this problem is to couple hydrophilic polymers, such as monomethoxypolyethylene glycol (mPEG) to IMPs under mild conditions in place of detergents. However, the broad application of this approach is hampered by poor reaction efficiencies, low tolerance of detergent stabilized membrane proteins to reaction conditions, and a lack of proper site-specific reversible approaches. Here, we have developed a straightforward, efficient, and mild approach to site-specific noncovalent binding of long-chain polymers to recombinant IMPs. This method uses the hexa-histidine tag (His-Tag) often used for purification of recombinant proteins as an attachment site for mPEGs. Solubility studies performed using five different IMPs confirmed that all tested mPEG-bound IMPs were completely soluble and stable in detergent free aqueous buffer compared to their precipitated native proteins under the identical circumstances. Activity assays and circular dichroism (CD) spectroscopy confirmed the structural integrity of modified IMPs.
Collapse
Affiliation(s)
- Thamara K Janaratne
- The Joint Center for Structural Genomics and The Scripps Research Institute, Department of Molecular Biology, La Jolla, California 92037, United States
| | | | | | | |
Collapse
|
8
|
Shen F, Tang S, Liu L. Hexafluoro-2-propanol as a potent cosolvent for chemical ligation of membrane proteins. Sci China Chem 2011. [DOI: 10.1007/s11426-010-4188-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
9
|
Bonomo RP, Di Natale G, Rizzarelli E, Tabbì G, Vagliasindi LI. Copper(ii) complexes of prion protein PEG11-tetraoctarepeat fragment: spectroscopic and voltammetric studies. Dalton Trans 2009:2637-46. [DOI: 10.1039/b821727k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
10
|
Becker CFW, Marsac Y, Hazarika P, Moser J, Goody RS, Niemeyer CM. Functional immobilization of the small GTPase Rab6A on DNA-Gold nanoparticles by using a site-specifically attached poly(ethylene glycol) linker and thiol place-exchange reaction. Chembiochem 2007; 8:32-6. [PMID: 17121405 DOI: 10.1002/cbic.200600422] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Christian F W Becker
- Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
| | | | | | | | | | | |
Collapse
|
11
|
Roosild TP, Castronovo S, Choe S. Structure of anti-FLAG M2 Fab domain and its use in the stabilization of engineered membrane proteins. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:835-9. [PMID: 16946459 PMCID: PMC2242885 DOI: 10.1107/s1744309106029125] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Accepted: 07/27/2006] [Indexed: 11/10/2022]
Abstract
The inherent difficulties of stabilizing detergent-solubilized integral membrane proteins for biophysical or structural analysis demand the development of new methodologies to improve success rates. One proven strategy is the use of antibody fragments to increase the ;soluble' portion of any membrane protein, but this approach is limited by the difficulties and expense associated with producing monoclonal antibodies to an appropriate exposed epitope on the target protein. Here, the stabilization of a detergent-solubilized K(+) channel protein, KvPae, by engineering a FLAG-binding epitope into a known loop region of the protein and creating a complex with Fab fragments from commercially available anti-FLAG M2 monoclonal antibodies is reported. Although well diffracting crystals of the complex have not yet been obtained, during the course of crystallization trials the structure of the anti-FLAG M2 Fab domain was solved to 1.86 A resolution. This structure, which should aid future structure-determination efforts using this approach by facilitating molecular-replacement phasing, reveals that the binding pocket appears to be specific only for the first four amino acids of the traditional FLAG epitope, namely DYKD. Thus, the use of antibody fragments for improving the stability of target proteins can be rapidly applied to the study of membrane-protein structure by placing the short DKYD motif within a predicted peripheral loop of that protein and utilizing commercially available anti-FLAG M2 antibody fragments.
Collapse
Affiliation(s)
- Tarmo P. Roosild
- Structural Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Samantha Castronovo
- Structural Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Senyon Choe
- Structural Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| |
Collapse
|
12
|
Folgering JHA, Wolters JC, Poolman B. Engineering covalent oligomers of the mechanosensitive channel of large conductance from Escherichia coli with native conductance and gating characteristics. Protein Sci 2006; 14:2947-54. [PMID: 16322576 PMCID: PMC2253253 DOI: 10.1110/ps.051679005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
To obtain a gene construct for making single substitutions per channel and to determine the quaternary structure of the mechanosensitive channel MscL from Escherichia coli, covalent oligomers (monomer to hexamer) were engineered by gene fusion; up to six copies of the mscL gene were fused in tandem. All the multimeric tandem constructs yielded functional channels with wild-type conductance and dwell times. Importantly, only the covalent pentamer opened at the same relative pressure (compared to the pressure required to open MscS) as the wild-type MscL channel. The in vivo data strongly suggest that pentameric MscL represents the functional state of the channel.
Collapse
Affiliation(s)
- Joost H A Folgering
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | | | | |
Collapse
|
13
|
Du P, Loulakis P, Luo C, Mistry A, Simons SP, LeMotte PK, Rajamohan F, Rafidi K, Coleman KG, Geoghegan KF, Xie Z. Phosphorylation of serine residues in histidine-tag sequences attached to recombinant protein kinases: A cause of heterogeneity in mass and complications in function. Protein Expr Purif 2005; 44:121-9. [PMID: 15946859 DOI: 10.1016/j.pep.2005.04.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2005] [Revised: 04/18/2005] [Accepted: 04/26/2005] [Indexed: 10/25/2022]
Abstract
High-level recombinant expression of protein kinases in eukaryotic cells or Escherichia coli commonly gives products that are phosphorylated by autocatalysis or by the action of endogenous kinases. Here, we report that phosphorylation occurred on serine residues adjacent to hexahistidine affinity tags (His-tags) derived from several commercial expression vectors and fused to overexpressed kinases. The result was observed with a variety of recombinant kinases expressed in either insect cells or E. coli. Multiple phosphorylations of His-tagged full-length Aurora A, a protein serine/threonine kinase, were detected by mass spectrometry when it was expressed in insect cells in the presence of okadaic acid, a protein phosphatase inhibitor. Peptide mapping by liquid chromatography-mass spectrometry detected phosphorylations on all three serine residues in an N-terminal tag, alpha-N-acetyl-MHHHHHHSSGLPRGS. The same sequence was also phosphorylated, but only at a low level, when a His-tagged protein tyrosine kinase, Pyk2 was expressed in insect cells and activated in vitro. When catalytic domains of Aurora A and several other protein serine/threonine kinases were expressed in E. coli, serines in the affinity tag sequence GSSHHHHHHSSGLVPRGS were also variably phosphorylated. His-Aurora A with hyperphosphorylation of the serine residues in the tag aggregated and resisted thrombin-catalyzed removal of the tag. Treatment with alkaline phosphatase partly restored sensitivity to thrombin. The same His-tag sequence was also detected bearing alpha-N-d-gluconoylation in addition to multiple phosphorylations. The results show that histidine-tag sequences can receive complicated posttranslational modification, and that the hyperphosphorylation and resulting heterogeneity of the recombinant fusion proteins can interfere with downstream applications.
Collapse
Affiliation(s)
- Ping Du
- Pfizer Global Research and Development, Groton Laboratories, Groton, CT 06340, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|