Suppr超能文献

两种序列同一性为88%但结构和功能不同的蛋白质的设计与特性分析。

The design and characterization of two proteins with 88% sequence identity but different structure and function.

作者信息

Alexander Patrick A, He Yanan, Chen Yihong, Orban John, Bryan Philip N

机构信息

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA.

出版信息

Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):11963-8. doi: 10.1073/pnas.0700922104. Epub 2007 Jul 3.

Abstract

To identify a simplified code for conformational switching, we have redesigned two natural proteins to have 88% sequence identity but different tertiary structures: a 3-alpha helix fold and an alpha/beta fold. We describe the design of these homologous heteromorphic proteins, their structural properties as determined by NMR, their conformational stabilities, and their affinities for their respective ligands: IgG and serum albumin. Each of these proteins is completely folded at 25 degrees C, is monomeric, and retains the native binding activity. The complete binding epitope for both ligands is encoded within each of the proteins. The IgG-binding epitope is functional only in the alpha/beta fold, and the albumin-binding epitope is functional only in the 3-alpha fold. These results demonstrate that two monomeric folds and two different functions can be encoded with only 12% of the amino acids in a protein (7 of 56). The fact that 49 aa in these proteins are compatible with both folds shows that the essential information determining a fold can be highly concentrated in a few amino acids and that a very limited subset of interactions in the protein can tip the balance from one monomer fold to another. This delicate balance helps explain why protein structure prediction is so challenging. Furthermore, because a few mutations can result in both new conformation and new function, the evolution of new folds driven by natural selection for alternative functions may be much more probable than previously recognized.

摘要

为了确定构象转换的简化编码,我们重新设计了两种天然蛋白质,使其具有88%的序列同一性但三级结构不同:一种是3-α螺旋折叠,另一种是α/β折叠。我们描述了这些同源异形蛋白的设计、通过核磁共振确定的结构特性、它们的构象稳定性以及它们对各自配体(IgG和血清白蛋白)的亲和力。这些蛋白质在25摄氏度时均完全折叠,呈单体形式,并保留天然结合活性。两种配体的完整结合表位均编码在每种蛋白质中。IgG结合表位仅在α/β折叠中起作用,而白蛋白结合表位仅在3-α折叠中起作用。这些结果表明,两种单体折叠和两种不同功能可以仅由蛋白质中12%的氨基酸(56个中的7个)编码。这些蛋白质中有49个氨基酸与两种折叠都兼容,这一事实表明,决定一种折叠的基本信息可以高度集中在少数几个氨基酸中,并且蛋白质中非常有限的一部分相互作用就可以使平衡从一种单体折叠转向另一种单体折叠。这种微妙的平衡有助于解释为什么蛋白质结构预测如此具有挑战性。此外,由于少数突变可能导致新的构象和新的功能,由对替代功能的自然选择驱动的新折叠的进化可能比以前认为的更有可能。

相似文献

1
The design and characterization of two proteins with 88% sequence identity but different structure and function.
Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):11963-8. doi: 10.1073/pnas.0700922104. Epub 2007 Jul 3.
2
NMR structures of two designed proteins with high sequence identity but different fold and function.
Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14412-7. doi: 10.1073/pnas.0805857105. Epub 2008 Sep 16.
5
One-state downhill versus conventional protein folding.
J Mol Biol. 2004 Nov 19;344(2):295-301. doi: 10.1016/j.jmb.2004.09.069.
6
Current computer modeling cannot explain why two highly similar sequences fold into different structures.
Biochemistry. 2011 Dec 20;50(50):10965-73. doi: 10.1021/bi2015663. Epub 2011 Nov 23.
7
Role of the amino acid sequence in domain swapping of the B1 domain of protein G.
Proteins. 2008 Jul;72(1):88-104. doi: 10.1002/prot.21901.
9
Solution structure of the albumin-binding GA module: a versatile bacterial protein domain.
J Mol Biol. 1997 Mar 14;266(5):859-65. doi: 10.1006/jmbi.1996.0856.
10
Context-dependent secondary structure formation of a designed protein sequence.
Nature. 1996 Apr 25;380(6576):730-4. doi: 10.1038/380730a0.

引用本文的文献

1
Fold-switching proteins.
ArXiv. 2025 Jul 14:arXiv:2507.10839v1.
3
Aromatic-aromatic interactions drive fold switch of GA95 and GB95 with three residue difference.
Chem Sci. 2024 Dec 18;16(4):1885-1893. doi: 10.1039/d4sc04951a. eCollection 2025 Jan 22.
4
Amino-Acid Characteristics in Protein Native State Structures.
Biomolecules. 2024 Jul 7;14(7):805. doi: 10.3390/biom14070805.
5
Predicting horizontal gene transfers with perfect transfer networks.
Algorithms Mol Biol. 2024 Feb 6;19(1):6. doi: 10.1186/s13015-023-00242-2.
6
Predicting multiple conformations via sequence clustering and AlphaFold2.
Nature. 2024 Jan;625(7996):832-839. doi: 10.1038/s41586-023-06832-9. Epub 2023 Nov 13.
7
SSDraw: Software for generating comparative protein secondary structure diagrams.
Protein Sci. 2023 Dec;32(12):e4836. doi: 10.1002/pro.4836.
8
SSDraw: software for generating comparative protein secondary structure diagrams.
bioRxiv. 2023 Nov 10:2023.08.25.554905. doi: 10.1101/2023.08.25.554905.
9
Identification of a covert evolutionary pathway between two protein folds.
Nat Commun. 2023 Jun 1;14(1):3177. doi: 10.1038/s41467-023-38519-0.
10
Design and characterization of a protein fold switching network.
Nat Commun. 2023 Jan 26;14(1):431. doi: 10.1038/s41467-023-36065-3.

本文引用的文献

4
G148-GA3: a streptococcal virulence module with atypical thermodynamics of folding optimally binds human serum albumin at physiological temperatures.
Biochim Biophys Acta. 2005 Dec 1;1753(2):226-33. doi: 10.1016/j.bbapap.2005.10.005. Epub 2005 Oct 26.
5
ZiCo: a peptide designed to switch folded state upon binding zinc.
J Am Chem Soc. 2005 Nov 2;127(43):15008-9. doi: 10.1021/ja0543604.
9
Crystal structure and biological implications of a bacterial albumin binding module in complex with human serum albumin.
J Biol Chem. 2004 Oct 8;279(41):42924-8. doi: 10.1074/jbc.M406957200. Epub 2004 Jul 21.
10
Prediction and functional analysis of native disorder in proteins from the three kingdoms of life.
J Mol Biol. 2004 Mar 26;337(3):635-45. doi: 10.1016/j.jmb.2004.02.002.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验