1
|
Mahmud S, Morehead A, Cheng J. Accurate prediction of protein tertiary structural changes induced by single-site mutations with equivariant graph neural networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560758. [PMID: 37873289 PMCID: PMC10592624 DOI: 10.1101/2023.10.03.560758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Predicting the change of protein tertiary structure caused by singlesite mutations is important for studying protein structure, function, and interaction. Even though computational protein structure prediction methods such as AlphaFold can predict the overall tertiary structures of most proteins rather accurately, they are not sensitive enough to accurately predict the structural changes induced by single-site amino acid mutations on proteins. Specialized mutation prediction methods mostly focus on predicting the overall stability or function changes caused by mutations without attempting to predict the exact mutation-induced structural changes, limiting their use in protein mutation study. In this work, we develop the first deep learning method based on equivariant graph neural networks (EGNN) to directly predict the tertiary structural changes caused by single-site mutations and the tertiary structure of any protein mutant from the structure of its wild-type counterpart. The results show that it performs substantially better in predicting the tertiary structures of protein mutants than the widely used protein structure prediction method AlphaFold.
Collapse
|
2
|
Shimizu N, Hamada Y, Morozumi R, Yamamoto J, Iwai S, Sugiyama KI, Ide H, Tsuda M. Repair of topoisomerase 1-induced DNA damage by tyrosyl-DNA phosphodiesterase 2 (TDP2) is dependent on its magnesium binding. J Biol Chem 2023; 299:104988. [PMID: 37392847 PMCID: PMC10407441 DOI: 10.1016/j.jbc.2023.104988] [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: 01/15/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 07/03/2023] Open
Abstract
Topoisomerases are enzymes that relax DNA supercoiling during replication and transcription. Camptothecin, a topoisomerase 1 (TOP1) inhibitor, and its analogs trap TOP1 at the 3'-end of DNA as a DNA-bound intermediate, resulting in DNA damage that can kill cells. Drugs with this mechanism of action are widely used to treat cancers. It has previously been shown that tyrosyl-DNA phosphodiesterase 1 (TDP1) repairs TOP1-induced DNA damage generated by camptothecin. In addition, tyrosyl-DNA phosphodiesterase 2 (TDP2) plays critical roles in repairing topoisomerase 2 (TOP2)-induced DNA damage at the 5'-end of DNA and in promoting the repair of TOP1-induced DNA damage in the absence of TDP1. However, the catalytic mechanism by which TDP2 processes TOP1-induced DNA damage has not been elucidated. In this study, we found that a similar catalytic mechanism underlies the repair of TOP1- and TOP2-induced DNA damage by TDP2, with Mg2+-TDP2 binding playing a role in both repair mechanisms. We show chain-terminating nucleoside analogs are incorporated into DNA at the 3'-end and abort DNA replication to kill cells. Furthermore, we found that Mg2+-TDP2 binding also contributes to the repair of incorporated chain-terminating nucleoside analogs. Overall, these findings reveal the role played by Mg2+-TDP2 binding in the repair of both 3'- and 5'-blocking DNA damage.
Collapse
Affiliation(s)
- Naoto Shimizu
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yusaku Hamada
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Ryosuke Morozumi
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Kei-Ichi Sugiyama
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Hiroshi Ide
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.
| | - Masataka Tsuda
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan; Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan; Division of Genetics and Mutagenesis, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan.
| |
Collapse
|
3
|
Hou Y, Lu X, Xu Z, Qu J, Huang J. How a single mutation alters the protein structure: a simulation investigation on protein tyrosine phosphatase SHP2. RSC Adv 2023; 13:4263-4274. [PMID: 36760301 PMCID: PMC9891203 DOI: 10.1039/d2ra07472a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/23/2023] [Indexed: 02/04/2023] Open
Abstract
Protein tyrosine phosphatase SHP2 is a key regulator modulating several signaling pathways. The oncogenic mutation E76K in SHP2 releases the enzyme from an autoinhibited, closed conformation into an active, open conformation. Here, we investigated the conformational dynamics of SHP2 and the effect of the E76K mutation on its conformational ensemble via extensive molecular dynamics (MD) and metadynamics (MetaD) simulations. Our simulations provide atomistic details on how the E76K mutated SHP2 prefers the open state and also reveal that the transition between the closed and the open states is highly collective. Several intermediate metastable states during the conformational transition between the closed and the open states were also investigated. Understanding how the single E76K mutation induces the conformational change in SHP2 could facilitate the further design of SHP2 inhibitors.
Collapse
Affiliation(s)
- Yingnan Hou
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine 18 Shilongshan Road Hangzhou 310024 Zhejiang China .,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University 18 Shilongshan Road Hangzhou 310024 Zhejiang China
| | - Xiaoli Lu
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine 18 Shilongshan Road Hangzhou 310024 Zhejiang China .,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University 18 Shilongshan Road Hangzhou 310024 Zhejiang China
| | - Ziyao Xu
- BioMap2 Kexueyuan South RoadBeijing 100000China
| | - Jiarun Qu
- BioMap2 Kexueyuan South RoadBeijing 100000China
| | - Jing Huang
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine 18 Shilongshan Road Hangzhou 310024 Zhejiang China .,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University 18 Shilongshan Road Hangzhou 310024 Zhejiang China
| |
Collapse
|
4
|
Araujo-Arcos LE, Montaño S, Bello-Rios C, Garibay-Cerdenares OL, Leyva-Vázquez MA, Illades-Aguiar B. Molecular insights into the interaction of HPV-16 E6 variants against MAGI-1 PDZ1 domain. Sci Rep 2022; 12:1898. [PMID: 35115618 PMCID: PMC8814009 DOI: 10.1038/s41598-022-05995-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 01/19/2022] [Indexed: 11/21/2022] Open
Abstract
Oncogenic protein E6 from Human Papilloma Virus 16 (HPV-16) mediates the degradation of Membrane-associated guanylate kinase with inverted domain structure-1 (MAGI-1), throughout the interaction of its protein binding motif (PBM) with the Discs-large homologous regions 1 (PDZ1) domain of MAG1-1. Generic variation in the E6 gene that translates to changes in the protein’s amino acidic sequence modifies the interaction of E6 with the cellular protein MAGI-1. MAGI-1 is a scaffolding protein found at tight junctions of epithelial cells, where it interacts with a variety of proteins regulating signaling pathways. MAGI-1 is a multidomain protein containing two WW (rsp-domain-9), one guanylate kinase-like, and six PDZ domains. PDZ domains played an important role in the function of MAGI-1 and served as targets for several viral proteins including the HPV-16 E6. The aim of this work was to evaluate, with an in silico approach, employing molecular dynamics simulation and protein–protein docking, the interaction of the intragenic variants E-G350 (L83V), E-C188/G350 (E29Q/L83V), E-A176/G350 (D25N/L83V), E6-AAa (Q14H/H78Y/83V) y E6-AAc (Q14H/I27RH78Y/L83V) and E6-reference of HPV-16 with MAGI-1. We found that variants E-G350, E-C188/G350, E-A176/G350, AAa and AAc increase their affinity to our two models of MAGI-1 compared to E6-reference.
Collapse
Affiliation(s)
- Lilian Esmeralda Araujo-Arcos
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico-Biológicas, Universidad Autonóma de Guerrero, 39090, Chilpancingo, CP, México
| | - Sarita Montaño
- Laboratorio de Bioinformática y Simulación Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, 80030, Culiacán Sinaloa, CP, México.
| | - Ciresthel Bello-Rios
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico-Biológicas, Universidad Autonóma de Guerrero, 39090, Chilpancingo, CP, México
| | - Olga Lilia Garibay-Cerdenares
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico-Biológicas, Universidad Autonóma de Guerrero, 39090, Chilpancingo, CP, México.,CONACyT-Universidad Autónoma de Guerrero, 39087, Chilpancingo, CP, México
| | - Marco Antonio Leyva-Vázquez
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico-Biológicas, Universidad Autonóma de Guerrero, 39090, Chilpancingo, CP, México
| | - Berenice Illades-Aguiar
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico-Biológicas, Universidad Autonóma de Guerrero, 39090, Chilpancingo, CP, México.
| |
Collapse
|
5
|
Periwal N, Rathod SB, Pal R, Sharma P, Nebhnani L, Barnwal RP, Arora P, Srivastava KR, Sood V. In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. J Biomol Struct Dyn 2021; 40:8216-8231. [PMID: 33797336 PMCID: PMC8043164 DOI: 10.1080/07391102.2021.1908170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
SARS-CoV-2 has recently emerged as a pandemic that has caused more than 2.4 million deaths worldwide. Since the onset of infections, several full-length sequences of viral genome have been made available which have been used to gain insights into viral dynamics. We utilised a meta-data driven comparative analysis tool for sequences (Meta-CATS) algorithm to identify mutations in 829 SARS-CoV-2 genomes from around the world. The algorithm predicted sixty-one mutations among SARS-CoV-2 genomes. We observed that most of the mutations were concentrated around three protein coding genes viz nsp3 (non-structural protein 3), RdRp (RNA-directed RNA polymerase) and Nucleocapsid (N) proteins of SARS-CoV-2. We used various computational tools including normal mode analysis (NMA), C-α discrete molecular dynamics (DMD) and all-atom molecular dynamic simulations (MD) to study the effect of mutations on functionality, stability and flexibility of SARS-CoV-2 structural proteins including envelope (E), N and spike (S) proteins. PredictSNP predictor suggested that four mutations (L37H in E, R203K and P344S in N and D614G in S) out of seven were predicted to be neutral whilst the remaining ones (P13L, S197L and G204R in N) were predicted to be deleterious in nature thereby impacting protein functionality. NMA, C-α DMD and all-atom MD suggested some mutations to have stabilizing roles (P13L, S197L and R203K in N protein) where remaining ones were predicted to destabilize mutant protein. In summary, we identified significant mutations in SARS-CoV-2 genomes as well as used computational approaches to further characterize the possible effect of highly significant mutations on SARS-CoV-2 structural proteins. Communicated by Ramaswamy H. Sarma
Collapse
Affiliation(s)
- Neha Periwal
- Department of Biochemistry, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India
| | - Shravan B Rathod
- Department of Chemistry, Smt. S. M. Panchal Science College, Talod, India
| | - Ranjan Pal
- Biocatalysis and Enzyme Engineering Lab, Regional Centre for Biotechnology, Faridabad, India
| | - Priya Sharma
- Department of Biochemistry, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India
| | - Lata Nebhnani
- Department of Chemistry, Gujarat University, Ahmedabad, India
| | - Ravi P Barnwal
- Department of Biophysics, Panjab University, Chandigarh, India
| | - Pooja Arora
- Department of Zoology, Hansraj College, University of Delhi, New Delhi, India
| | - Kinshuk Raj Srivastava
- Biocatalysis and Enzyme Engineering Lab, Regional Centre for Biotechnology, Faridabad, India
| | - Vikas Sood
- Department of Biochemistry, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India
| |
Collapse
|
6
|
Prabantu VM, Naveenkumar N, Srinivasan N. Influence of Disease-Causing Mutations on Protein Structural Networks. Front Mol Biosci 2021; 7:620554. [PMID: 33778000 PMCID: PMC7987782 DOI: 10.3389/fmolb.2020.620554] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/17/2020] [Indexed: 01/18/2023] Open
Abstract
The interactions between residues in a protein tertiary structure can be studied effectively using the approach of protein structure network (PSN). A PSN is a node-edge representation of the structure with nodes representing residues and interactions between residues represented by edges. In this study, we have employed weighted PSNs to understand the influence of disease-causing mutations on proteins of known 3D structures. We have used manually curated information on disease mutations from UniProtKB/Swiss-Prot and their corresponding protein structures of wildtype and disease variant from the protein data bank. The PSNs of the wildtype and disease-causing mutant are compared to analyse variation of global and local dissimilarity in the overall network and at specific sites. We study how a mutation at a given site can affect the structural network at a distant site which may be involved in the function of the protein. We have discussed specific examples of the disease cases where the protein structure undergoes limited structural divergence in their backbone but have large dissimilarity in their all atom networks and vice versa, wherein large conformational alterations are observed while retaining overall network. We analyse the effect of variation of network parameters that characterize alteration of function or stability.
Collapse
Affiliation(s)
| | - Nagarajan Naveenkumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.,National Centre for Biological Sciences, TIFR, Bangalore, India.,Bharathidasan University, Tiruchirappalli, India
| | | |
Collapse
|
7
|
Nikam R, Kulandaisamy A, Harini K, Sharma D, Gromiha MM. ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years. Nucleic Acids Res 2021; 49:D420-D424. [PMID: 33196841 PMCID: PMC7778892 DOI: 10.1093/nar/gkaa1035] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/14/2020] [Accepted: 10/26/2020] [Indexed: 11/12/2022] Open
Abstract
ProThermDB is an updated version of the thermodynamic database for proteins and mutants (ProTherm), which has ∼31 500 data on protein stability, an increase of 84% from the previous version. It contains several thermodynamic parameters such as melting temperature, free energy obtained with thermal and denaturant denaturation, enthalpy change and heat capacity change along with experimental methods and conditions, sequence, structure and literature information. Besides, the current version of the database includes about 120 000 thermodynamic data obtained for different organisms and cell lines, which are determined by recent high throughput proteomics techniques using whole-cell approaches. In addition, we provided a graphical interface for visualization of mutations at sequence and structure levels. ProThermDB is cross-linked with other relevant databases, PDB, UniProt, PubMed etc. It is freely available at https://web.iitm.ac.in/bioinfo2/prothermdb/index.html without any login requirements. It is implemented in Python, HTML and JavaScript, and supports the latest versions of major browsers, such as Firefox, Chrome and Safari.
Collapse
Affiliation(s)
- Rahul Nikam
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India
| | - A Kulandaisamy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India
| | - K Harini
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India
| | - Divya Sharma
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India
| |
Collapse
|
8
|
Zhang T, Na JH, Li S, Chen Z, Zhang G, Pang S, Daniyan AF, Li Y, Shi L, Du YCN. Functional impact of cancer patient-associated Bcl-xL mutations. MedComm (Beijing) 2020; 1:328-337. [PMID: 34308416 PMCID: PMC8302207 DOI: 10.1002/mco2.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Bcl-xL, an antiapoptotic protein, is frequently overexpressed in cancer to promote survival of tumor cells. However, we have previously shown that Bcl-xL promotes migration, invasion, and metastasis independent of its antiapoptotic function in mitochondria. The pro-metastatic function of Bcl-xL may require its translocation into the nucleus. Besides overexpression, patient-associated mutations of Bcl-xL have been identified in large-scale cancer genomics projects. Understanding the functions of these mutations will guide the development of precision medicine. Here, we selected four patient-associated Bcl-xL mutations, R132W, N136K, R165W, and A201T, to investigate their impacts on antiapoptosis, migration, and nuclear translocation. We found that all four mutation proteins could be detected in both the nucleus and cytosol. Although all four mutations disrupted the antiapoptosis function, one of these mutants, N136K, significantly improved the ability to promote cell migration. These data suggest the importance of developing novel Bcl-xL inhibitors to ablate both antiapoptotic and pro-metastatic functions of Bcl-xL in cancer.
Collapse
Affiliation(s)
- Tiantian Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Joseph HyungJoon Na
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Samantha Li
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Zhengming Chen
- Division of Biostatistics and Epidemiology, Department of Population Health Sciences, Weill Cornell Medicine, New York, New York
| | - George Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Sharon Pang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Anthony F Daniyan
- Department of Medicine, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yi Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Yi-Chieh Nancy Du
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| |
Collapse
|
9
|
Vattepu R, Klausmeyer RA, Ayella A, Yadav R, Dille JT, Saiz SV, Beck MR. Conserved tryptophan mutation disrupts structure and function of immunoglobulin domain revealing unusual tyrosine fluorescence. Protein Sci 2020; 29:2062-2074. [PMID: 32797644 DOI: 10.1002/pro.3929] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 12/27/2022]
Abstract
Immunoglobulin (Ig) domains are the most prevalent protein domain structure and share a highly conserved folding pattern; however, this structural family of proteins is also the most diverse in terms of biological roles and tissue expression. Ig domains vary significantly in amino acid sequence but share a highly conserved tryptophan in the hydrophobic core of this beta-stranded protein. Palladin is an actin binding and bundling protein that has five Ig domains and plays an important role in normal cell adhesion and motility. Mutation of the core tryptophan in one Ig domain of palladin has been identified in a pancreatic cancer cell line, suggesting a crucial role for this sole tryptophan in palladin Ig domain structure, stability, and function. We found that actin binding and bundling was not completely abolished with removal of this tryptophan despite a partially unfolded structure and significantly reduced stability of the mutant Ig domain as shown by circular dichroism investigations. In addition, this mutant palladin domain displays a tryptophan-like fluorescence attributed to an anomalous tyrosine emission at 341 nm. Our results indicate that this emission originates from a tyrosinate that may be formed in the excited ground state by proton transfer to a nearby aspartic acid residue. Furthermore, this study emphasizes the importance of tryptophan in protein structural stability and illustrates how tyrosinate emission contributions may be overlooked during the interpretation of the fluorescence properties of proteins.
Collapse
Affiliation(s)
- Ravi Vattepu
- Chemistry Department, Wichita State University, Wichita, Kansas, USA
| | | | - Allan Ayella
- Chemistry Department, Wichita State University, Wichita, Kansas, USA.,Chemistry Department, Washburn University, Topeka, Kansas, USA
| | - Rahul Yadav
- Chemistry Department, Wichita State University, Wichita, Kansas, USA
| | - Joseph T Dille
- Chemistry Department, Wichita State University, Wichita, Kansas, USA
| | - Stan V Saiz
- Chemistry Department, Wichita State University, Wichita, Kansas, USA
| | - Moriah R Beck
- Chemistry Department, Wichita State University, Wichita, Kansas, USA
| |
Collapse
|
10
|
Zhou G, Chen M, Ju CJT, Wang Z, Jiang JY, Wang W. Mutation effect estimation on protein-protein interactions using deep contextualized representation learning. NAR Genom Bioinform 2020; 2:lqaa015. [PMID: 32166223 PMCID: PMC7059401 DOI: 10.1093/nargab/lqaa015] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 01/20/2020] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
The functional impact of protein mutations is reflected on the alteration of conformation and thermodynamics of protein–protein interactions (PPIs). Quantifying the changes of two interacting proteins upon mutations is commonly carried out by computational approaches. Hence, extensive research efforts have been put to the extraction of energetic or structural features on proteins, followed by statistical learning methods to estimate the effects of mutations on PPI properties. Nonetheless, such features require extensive human labors and expert knowledge to obtain, and have limited abilities to reflect point mutations. We present an end-to-end deep learning framework, MuPIPR (Mutation Effects in Protein–protein Interaction PRediction Using Contextualized Representations), to estimate the effects of mutations on PPIs. MuPIPR incorporates a contextualized representation mechanism of amino acids to propagate the effects of a point mutation to surrounding amino acid representations, therefore amplifying the subtle change in a long protein sequence. On top of that, MuPIPR leverages a Siamese residual recurrent convolutional neural encoder to encode a wild-type protein pair and its mutation pair. Multi-layer perceptron regressors are applied to the protein pair representations to predict the quantifiable changes of PPI properties upon mutations. Experimental evaluations show that, with only sequence information, MuPIPR outperforms various state-of-the-art systems on estimating the changes of binding affinity for SKEMPI v1, and offers comparable performance on SKEMPI v2. Meanwhile, MuPIPR also demonstrates state-of-the-art performance on estimating the changes of buried surface areas. The software implementation is available at https://github.com/guangyu-zhou/MuPIPR.
Collapse
Affiliation(s)
- Guangyu Zhou
- Department of Computer Science, University of California, Los Angeles, CA 90095, USA
| | - Muhao Chen
- Department of Computer Science, University of California, Los Angeles, CA 90095, USA.,Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chelsea J T Ju
- Department of Computer Science, University of California, Los Angeles, CA 90095, USA
| | - Zheng Wang
- Department of Computer Science, University of California, Los Angeles, CA 90095, USA
| | - Jyun-Yu Jiang
- Department of Computer Science, University of California, Los Angeles, CA 90095, USA
| | - Wei Wang
- Department of Computer Science, University of California, Los Angeles, CA 90095, USA
| |
Collapse
|
11
|
Sleiman S, Dragon F. Recent Advances on the Structure and Function of RNA Acetyltransferase Kre33/NAT10. Cells 2019; 8:cells8091035. [PMID: 31491951 PMCID: PMC6770127 DOI: 10.3390/cells8091035] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/23/2019] [Accepted: 08/25/2019] [Indexed: 02/07/2023] Open
Abstract
Ribosome biogenesis is one of the most energy demanding processes in the cell. In eukaryotes, the main steps of this process occur in the nucleolus and include pre-ribosomal RNA (pre-rRNA) processing, post-transcriptional modifications, and assembly of many non-ribosomal factors and ribosomal proteins in order to form mature and functional ribosomes. In yeast and humans, the nucleolar RNA acetyltransferase Kre33/NAT10 participates in different maturation events, such as acetylation and processing of 18S rRNA, and assembly of the 40S ribosomal subunit. Here, we review the structural and functional features of Kre33/NAT10 RNA acetyltransferase, and we underscore the importance of this enzyme in ribosome biogenesis, as well as in acetylation of non-ribosomal targets. We also report on the role of human NAT10 in Hutchinson-Gilford progeria syndrome.
Collapse
Affiliation(s)
- Sophie Sleiman
- Département des Sciences Biologiques and Centre d'Excellence en Recherche sur les Maladies Orphelines-Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H3C 3P8, Canada.
| | - Francois Dragon
- Département des Sciences Biologiques and Centre d'Excellence en Recherche sur les Maladies Orphelines-Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H3C 3P8, Canada.
| |
Collapse
|
12
|
P. Katare D, Malik S, J. Mani R, Ranjpour M, Jain SK. Novel mutations in transthyretin gene associated with hepatocellular carcinoma. Mol Carcinog 2017; 57:70-77. [DOI: 10.1002/mc.22732] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/08/2017] [Accepted: 09/05/2017] [Indexed: 02/04/2023]
Affiliation(s)
- Deepshikha P. Katare
- Proteomics and Translational Research Lab; Centre for Medical Biotechnology; Amity Institute of Biotechnology; Amity University; Noida Uttar Pradesh India
| | - Shabnam Malik
- Faculty of Chemical and Life Sciences; Department of Biotechnology; Hamdard Institute of Medical Sciences and Research; Hamdard University; New Delhi India
| | - Ruchi J. Mani
- Proteomics and Translational Research Lab; Centre for Medical Biotechnology; Amity Institute of Biotechnology; Amity University; Noida Uttar Pradesh India
| | - Maryam Ranjpour
- Faculty of Chemical and Life Sciences; Department of Biotechnology; Hamdard Institute of Medical Sciences and Research; Hamdard University; New Delhi India
| | - Swatantra K. Jain
- Faculty of Chemical and Life Sciences; Department of Biotechnology; Hamdard Institute of Medical Sciences and Research; Hamdard University; New Delhi India
- Department of Medical Biochemistry; Hamdard Institute of Medical Sciences and Research; Hamdard University; New Delhi India
| |
Collapse
|
13
|
Hsu HJ, Lee KH, Jian JW, Chang HJ, Yu CM, Lee YC, Chen IC, Peng HP, Wu CY, Huang YF, Shao CY, Chiu KP, Yang AS. Antibody variable domain interface and framework sequence requirements for stability and function by high-throughput experiments. Structure 2013; 22:22-34. [PMID: 24268647 DOI: 10.1016/j.str.2013.10.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/03/2013] [Accepted: 10/01/2013] [Indexed: 01/21/2023]
Abstract
Protein structural stability and biological functionality are dictated by the formation of intradomain cores and interdomain interfaces, but the intricate sequence-structure-function interrelationships in the packing of protein cores and interfaces remain difficult to elucidate due to the intractability of enumerating all packing possibilities and assessing the consequences of all the variations. In this work, groups of β strand residues of model antibody variable domains were randomized with saturated mutagenesis and the functional variants were selected for high-throughput sequencing and high-throughput thermal stability measurements. The results show that the sequence preferences of the intradomain hydrophobic core residues are strikingly flexible among hydrophobic residues, implying that these residues are coupled indirectly with antigen binding through energetic stabilization of the protein structures. By contrast, the interdomain interface residues are directly coupled with antigen binding. The interdomain interface should be treated as an integral part of the antigen-binding site.
Collapse
Affiliation(s)
- Hung-Ju Hsu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan; Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Kuo Hao Lee
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Jhih-Wei Jian
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Hung-Ju Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Science, National Taiwan University, Taipei 106, Taiwan; Chemical Biology and Molecular Biophysics program, Taiwan International Graduate Program at Academia Sinica, Taipei 115, Taiwan
| | - Chung-Ming Yu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Ching Lee
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ing-Chien Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hung-Pin Peng
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Chih Yuan Wu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Feng Huang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chih-Yun Shao
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Zoology, College of Life Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Kuo Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - An-Suei Yang
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan; Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.
| |
Collapse
|
14
|
Chang HJ, Jian JW, Hsu HJ, Lee YC, Chen HS, You JJ, Hou SC, Shao CY, Chen YJ, Chiu KP, Peng HP, Lee KH, Yang AS. Loop-sequence features and stability determinants in antibody variable domains by high-throughput experiments. Structure 2013; 22:9-21. [PMID: 24268648 DOI: 10.1016/j.str.2013.10.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 10/11/2013] [Accepted: 10/12/2013] [Indexed: 12/24/2022]
Abstract
Protein loops are frequently considered as critical determinants in protein structure and function. Recent advances in high-throughput methods for DNA sequencing and thermal stability measurement have enabled effective exploration of sequence-structure-function relationships in local protein regions. Using these data-intensive technologies, we investigated the sequence-structure-function relationships of six complementarity-determining regions (CDRs) and ten non-CDR loops in the variable domains of a model vascular endothelial growth factor (VEGF)-binding single-chain antibody variable fragment (scFv) whose sequence had been optimized via a consensus-sequence approach. The results show that only a handful of residues involving long-range tertiary interactions distant from the antigen-binding site are strongly coupled with antigen binding. This implies that the loops are passive regions in protein folding; the essential sequences of these regions are dictated by conserved tertiary interactions and the consensus local loop-sequence features contribute little to protein stability and function.
Collapse
Affiliation(s)
- Hung-Ju Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Jhih-Wei Jian
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Hung-Ju Hsu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Ching Lee
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hong-Sen Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Jhong-Jhe You
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Shin-Chen Hou
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chih-Yun Shao
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Zoology, College of Life Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Yen-Ju Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University, Taipei 106, Taiwan
| | - Kuo-Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hung-Pin Peng
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Kuo Hao Lee
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - An-Suei Yang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.
| |
Collapse
|
15
|
Nickson AA, Wensley BG, Clarke J. Take home lessons from studies of related proteins. Curr Opin Struct Biol 2012; 23:66-74. [PMID: 23265640 PMCID: PMC3578095 DOI: 10.1016/j.sbi.2012.11.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 11/26/2012] [Accepted: 11/27/2012] [Indexed: 11/30/2022]
Abstract
The 'Fold Approach' involves a detailed analysis of the folding of several topologically, structurally and/or evolutionarily related proteins. Such studies can reveal determinants of the folding mechanism beyond the gross topology, and can dissect the residues required for folding from those required for stability or function. While this approach has not yet matured to the point where we can predict the native conformation of any polypeptide chain in silico, it has been able to highlight, amongst others, the specific residues that are responsible for nucleation, pathway malleability, kinetic intermediates, chain knotting, internal friction and Paracelsus switches. Some of the most interesting discoveries have resulted from the attempt to explain differences between homologues.
Collapse
Affiliation(s)
- Adrian A Nickson
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW, UK.
| | | | | |
Collapse
|
16
|
Reva B, Antipin Y, Sander C. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res 2011; 39:e118. [PMID: 21727090 PMCID: PMC3177186 DOI: 10.1093/nar/gkr407] [Citation(s) in RCA: 1414] [Impact Index Per Article: 108.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
As large-scale re-sequencing of genomes reveals many protein mutations, especially in human cancer tissues, prediction of their likely functional impact becomes important practical goal. Here, we introduce a new functional impact score (FIS) for amino acid residue changes using evolutionary conservation patterns. The information in these patterns is derived from aligned families and sub-families of sequence homologs within and between species using combinatorial entropy formalism. The score performs well on a large set of human protein mutations in separating disease-associated variants (∼19 200), assumed to be strongly functional, from common polymorphisms (∼35 600), assumed to be weakly functional (area under the receiver operating characteristic curve of ∼0.86). In cancer, using recurrence, multiplicity and annotation for ∼10 000 mutations in the COSMIC database, the method does well in assigning higher scores to more likely functional mutations ('drivers'). To guide experimental prioritization, we report a list of about 1000 top human cancer genes frequently mutated in one or more cancer types ranked by likely functional impact; and, an additional 1000 candidate cancer genes with rare but likely functional mutations. In addition, we estimate that at least 5% of cancer-relevant mutations involve switch of function, rather than simply loss or gain of function.
Collapse
Affiliation(s)
- Boris Reva
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, NY 10065, USA
| | | | | |
Collapse
|
17
|
Targeting Protein–Protein Interactions and Fragment-Based Drug Discovery. Top Curr Chem (Cham) 2011; 317:145-79. [DOI: 10.1007/128_2011_265] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
18
|
What lessons can be learned from studying the folding of homologous proteins? Methods 2010; 52:38-50. [PMID: 20570731 PMCID: PMC2965948 DOI: 10.1016/j.ymeth.2010.06.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 05/25/2010] [Accepted: 06/01/2010] [Indexed: 01/30/2023] Open
Abstract
The studies of the folding of structurally related proteins have proved to be a very important tool for investigating protein folding. Here we review some of the insights that have been gained from such studies. Our highlighted studies show just how such an investigation should be designed and emphasise the importance of the synergy between experiment and theory. We also stress the importance of choosing the right system carefully, exploiting the excellent structural and sequence databases at our disposal.
Collapse
|
19
|
Steward A, McDowell GS, Clarke J. Topology is the principal determinant in the folding of a complex all-alpha Greek key death domain from human FADD. J Mol Biol 2009; 389:425-37. [PMID: 19362094 PMCID: PMC2724026 DOI: 10.1016/j.jmb.2009.04.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Revised: 03/26/2009] [Accepted: 04/01/2009] [Indexed: 11/24/2022]
Abstract
In order to elucidate the relative importance of secondary structure and topology in determining folding mechanism, we have carried out a phi-value analysis of the death domain (DD) from human FADD. FADD DD is a 100 amino acid domain consisting of six anti-parallel alpha helices arranged in a Greek key structure. We asked how does the folding of this domain compare with that of (a) other all-alpha-helical proteins and (b) other Greek key proteins? Is the folding pathway determined mainly by secondary structure or is topology the principal determinant? Our Φ-value analysis reveals a striking resemblance to the all-beta Greek key immunoglobulin-like domains. Both fold via diffuse transition states and, importantly, long-range interactions between the four central elements of secondary structure are established in the transition state. The elements of secondary structure that are less tightly associated with the central core are less well packed in both cases. Topology appears to be the dominant factor in determining the pathway of folding in all Greek key domains.
Collapse
Affiliation(s)
- Annette Steward
- University of Cambridge, Department of Chemistry, MRC Centre for Protein Engineering, Lensfield Road, Cambridge, CB2 1EW, UK
| | | | | |
Collapse
|
20
|
Mallam AL, Jackson SE. Use of protein engineering techniques to elucidate protein folding pathways. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2008; 84:57-113. [PMID: 19121700 DOI: 10.1016/s0079-6603(08)00403-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Anna L Mallam
- Department of Chemistry, Cambridge, CB2 1EW, United Kingdom
| | | |
Collapse
|
21
|
Billings KS, Best RB, Rutherford TJ, Clarke J. Crosstalk between the protein surface and hydrophobic core in a core-swapped fibronectin type III domain. J Mol Biol 2007; 375:560-71. [PMID: 18035373 PMCID: PMC2291452 DOI: 10.1016/j.jmb.2007.10.056] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Accepted: 10/10/2007] [Indexed: 11/11/2022]
Abstract
Two homologous fibronectin type III (fnIII) domains, FNfn10 (the
10th fnIII domain of human fibronectin) and TNfn3 (the third fnIII domain of
human tenascin), have essentially the same backbone structure, although they
share only ∼ 24% sequence identity. While they share a similar
folding mechanism with a common core of key residues in the folding transition
state, they differ in many other physical properties. We use a chimeric protein,
FNoTNc, to investigate the molecular basis for these differences. FNoTNc is a
core-swapped protein, containing the “outside” (surface and loops) of FNfn10 and
the hydrophobic core of TNfn3. Remarkably, FNoTNc retains the structure of the
parent proteins despite the extent of redesign, allowing us to gain insight into
which components of each parent protein are responsible for different aspects of
its behaviour. Naively, one would expect properties that appear to depend
principally on the core to be similar to TNfn3, for example, the response to
mutations, folding kinetics and side-chain dynamics, while properties apparently
determined by differences in the surface and loops, such as backbone dynamics,
would be more like FNfn10. While this is broadly true, it is clear that there
are also unexpected crosstalk effects between the core and the surface. For
example, the anomalous response of FNfn10 to mutation is not solely a property
of the core as we had previously suggested.
Collapse
Affiliation(s)
- Kate S Billings
- Cambridge University Chemical Laboratory, MRC Centre for Protein Engineering, Lensfield Road, Cambridge CB2 1EW, UK
| | | | | | | |
Collapse
|
22
|
Lappalainen I, Hurley MG, Clarke J. Plasticity within the obligatory folding nucleus of an immunoglobulin-like domain. J Mol Biol 2007; 375:547-59. [PMID: 18022190 PMCID: PMC2291451 DOI: 10.1016/j.jmb.2007.09.088] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Revised: 09/25/2007] [Accepted: 09/28/2007] [Indexed: 11/30/2022]
Abstract
A number of β-sandwich immunoglobulin-like domains have been shown
to fold using a set of structurally equivalent residues that form a folding
nucleus deep within the core of the protein. Formation of this nucleus is
sufficient to establish the complex Greek key topology of the native state.
These nucleating residues are highly conserved within the immunoglobulin
superfamily, but are less well conserved in the fibronectin type III (fnIII)
superfamily, where the requirement is simply to have four interacting
hydrophobic residues. However, there are rare examples where this nucleation
pattern is absent. In this study, we have investigated the folding of a novel
member of the fnIII superfamily whose nucleus appears to lack one of the four
buried hydrophobic residues. We show that the folding mechanism is unaltered,
but the folding nucleus has moved within the hydrophobic core.
Collapse
Affiliation(s)
- Ilkka Lappalainen
- University of Cambridge Department of Chemistry, MRC Centre for Protein Engineering, Lensfield Rd, Cambridge CB2 1EW, UK
| | | | | |
Collapse
|
23
|
Zarrine-Afsar A, Dahesh S, Davidson AR. Protein folding kinetics provides a context-independent assessment of beta-strand propensity in the Fyn SH3 domain. J Mol Biol 2007; 373:764-74. [PMID: 17850820 DOI: 10.1016/j.jmb.2007.07.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 07/13/2007] [Accepted: 07/26/2007] [Indexed: 11/16/2022]
Abstract
Structural database-derived propensities for amino acids to adopt particular local protein structures, such as alpha-helix and beta-strand, have long been recognized and effectively exploited for the prediction of protein secondary structure. However, the experimental verification of database-derived propensities using mutagenesis studies has been problematic, especially for beta-strand propensities, because local structural preferences are often confounded by non-local interactions arising from formation of the native tertiary structure. Thus, the overall thermodynamic stability of a protein is not always altered in a predictable manner by changes in local structural propensity at a single position. In this study, we have undertaken an investigation of the relationship between beta-strand propensity and protein folding kinetics. By characterizing the effects of a wide variety of amino acid substitutions at two different beta-strand positions in an SH3 domain, we have found that the observed changes in protein folding rates are very well correlated to beta-strand propensities for almost all of the substitutions examined. In contrast, there is little correlation between propensities and unfolding rates. These data indicate that beta-strand conformation is well formed in the structured portion of the SH3 domain transition state, and that local structure propensity strongly influences the stability of the transition state. Since the transition state is known to be packed more loosely than the native state and likely lacks many of the non-local stabilizing interactions seen in the native state, we suggest that folding kinetics studies may generally provide an effective means for the experimental validation of database-derived local structural propensities.
Collapse
Affiliation(s)
- Arash Zarrine-Afsar
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S-1A8
| | | | | |
Collapse
|
24
|
Han JH, Batey S, Nickson AA, Teichmann SA, Clarke J. The folding and evolution of multidomain proteins. Nat Rev Mol Cell Biol 2007; 8:319-30. [PMID: 17356578 DOI: 10.1038/nrm2144] [Citation(s) in RCA: 277] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Analyses of genomes show that more than 70% of eukaryotic proteins are composed of multiple domains. However, most studies of protein folding focus on individual domains and do not consider how interactions between domains might affect folding. Here, we address this by analysing the three-dimensional structures of multidomain proteins that have been characterized experimentally and observe that where the interface is small and loosely packed, or unstructured, the folding of the domains is independent. Furthermore, recent studies indicate that multidomain proteins have evolved mechanisms to minimize the problems of interdomain misfolding.
Collapse
Affiliation(s)
- Jung-Hoon Han
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
| | | | | | | | | |
Collapse
|
25
|
Nordlund A, Oliveberg M. Folding of Cu/Zn superoxide dismutase suggests structural hotspots for gain of neurotoxic function in ALS: parallels to precursors in amyloid disease. Proc Natl Acad Sci U S A 2006; 103:10218-10223. [PMID: 16798882 PMCID: PMC1502438 DOI: 10.1073/pnas.0601696103] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease linked to misfolding of the ubiquitous enzyme Cu/Zn superoxide dismutase (SOD). In contrast to other protein-misfolding disorders with similar neuropathogenesis, ALS is not always associated with the in vivo deposition of protein aggregates. Thus, under the assumption that all protein-misfolding disorders share at primary level a similar disease mechanism, ALS constitutes an interesting disease model for identifying the yet-mysterious precursor states from which the cytotoxic pathway emerges. In this study, we have mapped out the conformational repertoire of the apoSOD monomer through analysis of its folding behavior. The results allow us to target the regions of the SOD structure that are most susceptible to unfolding locally under physiological conditions, leading to the exposure of structurally promiscuous interfaces that are normally hidden in the protein's interior. The structure of this putative ALS precursor is strikingly similar to those implicated in amyloid disease.
Collapse
Affiliation(s)
- Anna Nordlund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, 10691 Stockholm, Sweden
| |
Collapse
|
26
|
Sato S, Religa TL, Fersht AR. Phi-analysis of the folding of the B domain of protein A using multiple optical probes. J Mol Biol 2006; 360:850-64. [PMID: 16782128 DOI: 10.1016/j.jmb.2006.05.051] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Revised: 03/23/2006] [Accepted: 05/19/2006] [Indexed: 10/24/2022]
Abstract
We examined the co-operativity of ultra-fast folding of a protein and whether the Phi-value analysis of its transition state depended on the location of the optical probe. We incorporated in turn a tryptophan residue into each of the three helices of the B domain of Protein A. Each Trp mutant of the three-helix bundle protein was used as a pseudo-wild-type parent for Phi-analysis in which the intrinsic Trp fluorescence probed the formation of each helix during the transition state. Apart from local effects in the immediate vicinity of the probe, the three separate sets of Phi-values were in excellent agreement, demonstrating the overall co-operativity of folding and the robustness of the Phi-analysis. The transition state of folding of Protein A contains the second helix being well formed with many stabilizing tertiary hydrophobic interactions. In contrast, the first and the third helices are more poorly structured in the transition state. The mechanism of folding thus involves the concurrent formation of secondary and tertiary interactions, and is towards the nucleation-condensation extreme in the nucleation-condensation-framework continuum of mechanism, with helix 2 being the nucleus. We provide an error analysis of Phi-values derived purely from the kinetics of two-state chevron plots.
Collapse
Affiliation(s)
- Satoshi Sato
- MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK
| | | | | |
Collapse
|
27
|
Sinha KK, Udgaonkar JB. Dependence of the size of the initially collapsed form during the refolding of barstar on denaturant concentration: evidence for a continuous transition. J Mol Biol 2006; 353:704-18. [PMID: 16188274 DOI: 10.1016/j.jmb.2005.08.056] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2005] [Revised: 08/15/2005] [Accepted: 08/23/2005] [Indexed: 11/20/2022]
Abstract
Two-site fluorescence resonance energy transfer (FRET) measurements have been made to determine how two intra-molecular distances contract in the sub-millisecond collapse reaction that occurs initially during the refolding of the small protein barstar. FRET measurements were made on two, single-Cys and single-Trp-containing mutant forms of barstar, Cys25 and Cys62, in each of which a thionitrobenzoate (TNB) adduct was attached to the cysteine thiol. In each protein, the core tryptophan, Trp53, acted as the FRET donor, and the TNB adduct, located either at C25 or at C62, acted as the FRET acceptor. The stabilities as well as observable folding kinetics of the Cys25 and Cys62 mutant proteins were found to be identical. The presence of the TNB adduct on the cysteine did not alter the stability or folding kinetics of either protein. Thus, the FRET-monitored changes in the two labeled mutant proteins, Cys25-TNB and Cys62-TNB, could be compared directly. Refolding was commenced from unfolded protein in 8M urea, and both the Trp53 to C25-TNB distance and the Trp53 to C62-TNB distance were found to contract upon dilution of urea. The extent of contraction of each distance, which was measured at a few milliseconds of refolding, was dependent continuously on the concentration of urea present during refolding, and was different for the two distances. For either FRET pair, the gradual contraction of distance with a decrease in the concentration of urea in which refolding occurs, was continuous with the contraction of the polypeptide chain that is seen with a decrease in the concentration of urea in the range in which the protein remains completely unfolded. It therefore appears that the products of the initial sub-millisecond refolding reaction of barstar are collapsed forms, whose dimensions do not change cooperatively in an all-or-none manner, but instead, change gradually with a change in concentration of urea. Thus, the sub-millisecond polypeptide chain collapse reaction of barstar upon denaturant dilution, appears to be a continuous structural transition.
Collapse
Affiliation(s)
- Kalyan K Sinha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
| | | |
Collapse
|
28
|
Xu Z, Fang S, Shi H, Li H, Deng Y, Liao Y, Wu JM, Zheng H, Zhu H, Chen HM, Tsang SY, Xue H. Topology characterization of a benzodiazepine-binding beta-rich domain of the GABAA receptor alpha1 subunit. Protein Sci 2005; 14:2622-37. [PMID: 16195550 PMCID: PMC2253290 DOI: 10.1110/ps.051555205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Structural investigation of GABAA receptors has been limited by difficulties imposed by its trans-membrane-complex nature. In the present study, the topology of a membrane-proximal beta-rich (MPB) domain in the C139-L269 segment of the receptor alpha1 subunit was probed by mapping the benzodiazepine (BZ)-binding and epitopic sites, as well as fluorescence resonance energy transfer (FRET) analysis. Ala-scanning and semiconservative substitutions within this segment revealed the contribution of the phenyl rings of Y160 and Y210, the hydroxy group of S186 and the positive charge on R187 to BZ-binding. FRET with the bound BZ ligand indicated the proximity of Y160, S186, R187, and S206 to the BZ-binding site. On the other hand, epitope-mapping using the monoclonal antibodies (mAbs) against the MPB domain established a clustering of T172, R173, E174, Q196, and T197. Based on the lack of FRET between Trp substitutionally placed at R173 or V198 and bound BZ, this epitope-mapped cluster is located on a separate end of the folded protein from the BZ-binding site. Mutations of the five conserved Cys and Trp residues in the MPB domain gave rise to synergistic and rescuing effects on protein secondary structures and unfolding stability that point to a CCWCW-pentad, reminiscent to the CWC-triad "pin" of immunoglobulin (Ig)-like domains, important for the structural maintenance. These findings, together with secondary structure and fold predictions suggest an anti-parallel beta-strand topology with resemblance to Ig-like fold, having the BZ-binding and the epitopic residues being clustered at two different ends of the fold.
Collapse
Affiliation(s)
- Zhiwen Xu
- Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
González-Díaz H, Uriarte E. Proteins QSAR with Markov average electrostatic potentials. Bioorg Med Chem Lett 2005; 15:5088-94. [PMID: 16169216 DOI: 10.1016/j.bmcl.2005.07.056] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2005] [Revised: 06/28/2005] [Accepted: 07/05/2005] [Indexed: 11/30/2022]
Abstract
Classic physicochemical and topological indices have been largely used in small molecules QSAR but less in proteins QSAR. In this study, a Markov model is used to calculate, for the first time, average electrostatic potentials xik for an indirect interaction between aminoacids placed at topologic distances k within a given protein backbone. The short-term average stochastic potential xi1 for 53 Arc repressor mutants was used to model the effect of Alanine scanning on thermal stability. The Arc repressor is a model protein of relevance for biochemical studies on bioorganics and medicinal chemistry. A linear discriminant analysis model developed correctly classified 43 out of 53, 81.1% of proteins according to their thermal stability. More specifically, the model classified 20/28, 71.4% of proteins with near wild-type stability and 23/25, 92.0% of proteins with reduced stability. Moreover, predictability in cross-validation procedures was of 81.0%. Expansion of the electrostatic potential in the series xi0, xi1, xi2, and xi3, justified the use of the abrupt truncation approach, being the overall accuracy >70.0% for xi0 but equal for xi1, xi2, and xi3. The xi1 model compared favorably with respect to others based on D-Fire potential, surface area, volume, partition coefficient, and molar refractivity, with less than 77.0% of accuracy [Ramos de Armas, R.; González-Díaz, H.; Molina, R.; Uriarte, E. Protein Struct. Func. Bioinf.2004, 56, 715]. The xi1 model also has more tractable interpretation than others based on Markovian negentropies and stochastic moments. Finally, the model is notably simpler than the two models based on quadratic and linear indices. Both models, reported by Marrero-Ponce et al., use four-to-five time more descriptors. Introduction of average stochastic potentials may be useful for QSAR applications; having xik amenable physical interpretation and being very effective.
Collapse
Affiliation(s)
- Humberto González-Díaz
- Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela 15782, Spain.
| | | |
Collapse
|
30
|
Jemth P, Day R, Gianni S, Khan F, Allen M, Daggett V, Fersht AR. The Structure of the Major Transition State for Folding of an FF Domain from Experiment and Simulation. J Mol Biol 2005; 350:363-78. [PMID: 15935381 DOI: 10.1016/j.jmb.2005.04.067] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2005] [Revised: 04/26/2005] [Accepted: 04/27/2005] [Indexed: 11/26/2022]
Abstract
We have analysed the transition state of folding of the four-helix FF domain from HYPA/FBP11 by high-resolution experiment and simulation as part of a continuing effort to understand the principles of folding and the refinement of predictive methods. The major transition state for folding was subjected to a Phi-value analysis utilising 50 mutants. The transition state contained a nucleus for folding centred around the end of helix 1 (H1) and the beginning of helix 2 (H2). Secondary structure in this region was fully formed (PhiF=0.9-1) and tertiary interactions were well developed. Interactions in the distal part of the native structure were weak (PhiF=0-0.2). The hydrophobic core and other parts of the protein displayed intermediate Phi-values, suggesting that interactions coalesce as the end of H1 and beginning of H2 are in the process of being formed. The distribution of Phi-values resembled that of barnase, which folds via an intermediate, rather than that of CI2 which folds by a concerted nucleation-condensation mechanism. The overall picture of the transition state structure identified in molecular dynamics simulations is in qualitative agreement, with the turn connecting H1 and H2 being formed, a loosened core, and H4 partially unfolded and detached from the core. There are some differences in the details and interpretation of specific Phi-values.
Collapse
Affiliation(s)
- Per Jemth
- MRC Centre for Protein Engineering, Hills Road, CB2 2QH Cambridge, UK
| | | | | | | | | | | | | |
Collapse
|
31
|
González-Díaz H, Uriarte E, Ramos de Armas R. Predicting stability of Arc repressor mutants with protein stochastic moments. Bioorg Med Chem 2005; 13:323-31. [PMID: 15598555 DOI: 10.1016/j.bmc.2004.10.024] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2004] [Revised: 10/08/2004] [Accepted: 10/09/2004] [Indexed: 11/18/2022]
Abstract
As more and more protein structures are determined and applied to drug manufacture, there is increasing interest in studying their stability. In this study, the stochastic moments ((SR)pi(k)) of 53 Arc repressor mutants were introduced as molecular descriptors modeling protein stability. The Linear Discriminant Analysis model developed correctly classified 43 out of 53, 81.13% of proteins according to their thermal stability. More specifically, the model classified 20/28 (71.4%) proteins with near wild-type stability and 23/25 (92%) proteins with reduced stability. Moreover, validation of the model was carried out by re-substitution procedures (81.0%). In addition, the stochastic moments based model compared favorably with respect to others based on physicochemical and geometric parameters such as D-Fire potential, surface area, volume, partition coefficient, and molar refractivity, which presented less than 77% of accuracy. This result illustrates the possibilities of the stochastic moments' method for the study of bioorganic and medicinal chemistry relevant proteins.
Collapse
Affiliation(s)
- Humberto González-Díaz
- Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela 15706, Spain.
| | | | | |
Collapse
|
32
|
Gromiha MM, Selvaraj S. Inter-residue interactions in protein folding and stability. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2004; 86:235-77. [PMID: 15288760 DOI: 10.1016/j.pbiomolbio.2003.09.003] [Citation(s) in RCA: 225] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
During the process of protein folding, the amino acid residues along the polypeptide chain interact with each other in a cooperative manner to form the stable native structure. The knowledge about inter-residue interactions in protein structures is very helpful to understand the mechanism of protein folding and stability. In this review, we introduce the classification of inter-residue interactions into short, medium and long range based on a simple geometric approach. The features of these interactions in different structural classes of globular and membrane proteins, and in various folds have been delineated. The development of contact potentials and the application of inter-residue contacts for predicting the structural class and secondary structures of globular proteins, solvent accessibility, fold recognition and ab initio tertiary structure prediction have been evaluated. Further, the relationship between inter-residue contacts and protein-folding rates has been highlighted. Moreover, the importance of inter-residue interactions in protein-folding kinetics and for understanding the stability of proteins has been discussed. In essence, the information gained from the studies on inter-residue interactions provides valuable insights for understanding protein folding and de novo protein design.
Collapse
Affiliation(s)
- M Michael Gromiha
- Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Aomi Frontier Building 17F, 2-43 Aomi, Koto-ku, Tokyo 135-0064, Japan.
| | | |
Collapse
|
33
|
Saeki K, Arai M, Yoda T, Nakao M, Kuwajima K. Localized nature of the transition-state structure in goat alpha-lactalbumin folding. J Mol Biol 2004; 341:589-604. [PMID: 15276846 DOI: 10.1016/j.jmb.2004.06.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2004] [Revised: 06/03/2004] [Accepted: 06/04/2004] [Indexed: 11/22/2022]
Abstract
To investigate whether the structure partially formed in the molten globule folding intermediate of goat alpha-lactalbumin is further organized in the transition state of folding, we constructed a number of mutant proteins and performed Phi-value analysis on them. For this purpose, we measured the equilibrium unfolding transitions and kinetic refolding and unfolding reactions of the mutants using equilibrium and stopped-flow kinetic circular dichroism techniques. The results show that the mutants with mutations located in the A-helix (V8A, L12A), the B-helix (V27A), the beta-domain (L52A, W60A), the C-helix (K93A, L96A), the C-D loop (Y103F), the D-helix (L105A, L110A), and the C-terminal 3(10)-helix (W118F), have low Phi-values, less than 0.2. On the other hand, D87N, which is located on the Ca(2+)-binding site, has a high Phi-value, 0.91, indicating that tight packing of the side-chain around Asp87 occurs in the transition state. One beta-domain mutant (I55V) and three C-helix mutants (I89V, V90A, and I95V) demonstrated intermediate Phi-values, between 0.4 and 0.7. These results indicate that the folding nucleus in the transition state of goat alpha-LA is not extensively distributed over the alpha-domain of the protein, but very localized in a region that contains the Ca(2+)-binding site and the interface between the C-helix and the beta-domain. This is apparently in contrast with the fact that the molten globule state of alpha-lactalbumin has a partially formed structure inside the alpha-domain. It is concluded that the specific docking of the alpha and beta-domains at a domain interface is necessary for this protein to organize its native structure from the molten globule intermediate.
Collapse
Affiliation(s)
- Kimiko Saeki
- Department of Physics, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | | | | | | |
Collapse
|
34
|
Cliff MJ, Higgins LD, Sessions RB, Waltho JP, Clarke AR. Beyond the EX1 limit: probing the structure of high-energy states in protein unfolding. J Mol Biol 2004; 336:497-508. [PMID: 14757061 DOI: 10.1016/j.jmb.2003.12.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Hydrogen exchange kinetics in native solvent conditions have been used to explore the conformational fluctuations of an immunoglobulin domain (CD2.domain1). The global folding/unfolding kinetics of the protein are unaltered between pH 4.5 and pH 9.5, allowing us to use the pH-dependence of amide hydrogen/deuterium exchange to characterise conformational states with energies up to 7.2kcal/mol higher than the folded ground state. The study was intended to search for discreet unfolding intermediates in this region of the energy spectrum, their presence being revealed by the concerted exchange behaviour of subsets of amide groups that become accessible at a given free energy, i.e. the spectrum would contain discreet groupings. Protection factors for 58 amide groups were measured across the pH range and the hydrogen-exchange energy profile is described. More interestingly, exchange behaviour could be grouped into three categories; the first two unremarkable, the third unexpected. (1) In 33 cases, amide exchange was dominated by rapid fluctuation, i.e. the free energy difference between the ground state and the rapidly accessed open state is sufficiently low that the contribution from crossing the unfolding barrier is negligible. (2) In 18 cases exchange is dominated by the global folding transition barrier across the whole pH range measured. The relationship between hydroxyl ion concentration and observed exchange rate is hyperbolic, with the limiting rate being that for global unfolding; the so-called EX1 limit. For these, the free energy difference between the folded ground state and any rapidly-accessed open state is too great for the proton to be exchanged through such fluctuations, even at the highest pH employed in this study. (3) For the third group, comprising five cases, we observe a behaviour that has not been described. In this group, as in category 2, the rate of exchange reaches a plateau; the EX1 limit. However, as the intrinsic exchange rate (k(int)) is increased, this limit is breached and the rate begins to rise again. This unintuitive behaviour does not result from pH instability, rather it is a consequence of amide groups experiencing two processes; rapid fluctuation of structure and crossing the global barrier for unfolding. The boundary at which the EX1 limit is overcome is determined by the equilibrium distribution of the fluctuating open and closed states (K(O/C)) and the rate constant for unfolding (k(u)). This critical boundary is reached when k(int)K(O/C)=k(u). Given that, in a simple transition state formalism: k(u)=K(#)k' (where K(#) describes the equilibrium distribution between the transition and ground state and k' describes the rate of a barrierless rearrangement), it follows that if the pH is raised to a level where k(int)=k', then the entire free energy spectrum from ground state to transition state could be sampled.
Collapse
Affiliation(s)
- Matthew J Cliff
- The Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, BS8 1TD, Bristol, UK.
| | | | | | | | | |
Collapse
|
35
|
Pometun MS, Chekmenev EY, Wittebort RJ. Quantitative Observation of Backbone Disorder in Native Elastin. J Biol Chem 2004; 279:7982-7. [PMID: 14625282 DOI: 10.1074/jbc.m310948200] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Elastin is a key protein in soft tissue function and pathology. Establishing a structural basis for understanding its reversible elasticity has proven to be difficult. Complementary to structure is the important aspect of flexibility and disorder in elastin. We have used solid-state NMR methods to examine polypeptide and hydrate ordering in both elastic (hydrated) and brittle (dry) elastin fibers and conclude (i) that tightly bound waters are absent in both dry and hydrated elastin and (ii) that the backbone in the hydrated protein is highly disordered with large amplitude motions. The hydrate was studied by (2)H and (17)O NMR, and the polypeptide by (13)C and (2)H NMR. Using a two-dimensional (13)C MAS method, an upper limit of S < 0.1 was determined for the backbone carbonyl group order parameter in hydrated elastin. For comparison, S approximately approximately 0.9 in most proteins. The former result is substantiated by two additional observations: the absence of the characteristic (2)H spectrum for stationary amides and "solution-like" (13)C magic angle spinning spectra at 75 degrees C, at which the material retains elasticity. Comparison of the observed shifts with accepted values for alpha-helices, beta-sheets, or random coils indicates a random coil structure at all carbons. These conclusions are discussed in the context of known thermodynamic properties of elastin and, more generally, protein folding. Because coacervation is an entropy-driven process, it is enhanced by the observed backbone disorder, which, we suggest, is the result of high proline content. This view is supported by recent studies of recombinant elastin polypeptides with systematic proline substitutions.
Collapse
Affiliation(s)
- Maxim S Pometun
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, USA
| | | | | |
Collapse
|
36
|
Best RB, Fowler SB, Herrera JLT, Steward A, Paci E, Clarke J. Mechanical unfolding of a titin Ig domain: structure of transition state revealed by combining atomic force microscopy, protein engineering and molecular dynamics simulations. J Mol Biol 2003; 330:867-77. [PMID: 12850153 DOI: 10.1016/s0022-2836(03)00618-1] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Titin I27 shows a high resistance to unfolding when subject to external force. To investigate the molecular basis of this mechanical stability, protein engineering Phi-value analysis has been combined with atomic force microscopy to investigate the structure of the barrier to forced unfolding. The results indicate that the transition state for forced unfolding is significantly structured, since highly destabilising mutations in the core do not affect the force required to unfold the protein. As has been shown before, mechanical strength lies in the region of the A' and G-strands but, contrary to previous suggestions, the results indicate clearly that side-chain interactions play a significant role in maintaining mechanical stability. Since Phi-values calculated from molecular dynamics simulations are the same as those determined experimentally, we can, with confidence, use the molecular dynamics simulations to analyse the structure of the transition state in detail, and are able to show loss of interactions between the A' and G-strands with associated A-B and E-F loops in the transition state. The key event is not a simple case of loss of hydrogen bonding interactions between the A' and G-strands alone. Comparison with Phi-values from traditional folding studies shows differences between the force and "no-force" transition states but, nevertheless, the region important for kinetic stability is the same in both cases. This explains the correspondence between hierarchy of kinetic stability (measured in stopped-flow denaturant studies) and mechanical strength in these titin domains.
Collapse
Affiliation(s)
- Robert B Best
- Department of Chemistry, University of Cambridge, MRC Centre for Protein Engineering, Lensfield Road, Cambridge CB2 1EW, UK
| | | | | | | | | | | |
Collapse
|
37
|
Zhou H, Zhou Y. Stability scale and atomic solvation parameters extracted from 1023 mutation experiments. Proteins 2002; 49:483-92. [PMID: 12402358 DOI: 10.1002/prot.10241] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The stability scale of 20 amino acid residues is derived from a database of 1023 mutation experiments on 35 proteins. The resulting scale of hydrophobic residues has an excellent correlation with the octanol-to-water transfer free energy corrected with an additional Flory-Huggins molar-volume term (correlation coefficient r = 0.95, slope = 1.05, and a near zero intercept). Thus, hydrophobic contribution to folding stability is characterized remarkably well by transfer experiments. However, no corresponding correlation is found for hydrophilic residues. Both the hydrophilic portion and the entire scale, however, correlate strongly with average burial accessible surface (r = 0.76 and 0.97, respectively). Such a strong correlation leads to a near uniform value of the atomic solvation parameters for atoms C, S, O/N, O(-0.5), and N(+0.5,1). All are in the range of 12-28 cal x mol(-1) A(-2), close to the original estimate of hydrophobic contribution of 25-30 cal x mol(-1) A(-2) to folding stability. Without any adjustable parameters, the new stability scale and new atomic solvation parameters yielded an accurate prediction of protein-protein binding free energy for a separate database of 21 protein-protein complexes (r = 0.80 and slope = 1.06, and r = 0.83 and slope = 0.93, respectively).
Collapse
Affiliation(s)
- Hongyi Zhou
- Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology & Biophysics, State University of New York at Buffalo, Buffalo, New York 14214, USA
| | | |
Collapse
|
38
|
Krantz BA, Mayne L, Rumbley J, Englander SW, Sosnick TR. Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding. J Mol Biol 2002; 324:359-71. [PMID: 12441113 DOI: 10.1016/s0022-2836(02)01029-x] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Do stable intermediates form very early in the protein folding process? New results and a quantity of literature that bear on this issue are examined here. Results available provide little support for early intermediate accumulation before an initial search-dependent nucleation barrier.
Collapse
Affiliation(s)
- Bryan A Krantz
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | | | | | | | | |
Collapse
|
39
|
Valerio-Lepiniec M, Nicaise M, Adjadj E, Minard P, Desmadril M. Key interactions in neocarzinostatin, a protein of the immunoglobulin fold family. Protein Eng Des Sel 2002; 15:861-9. [PMID: 12538905 DOI: 10.1093/protein/15.11.861] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Neocarzinostatin (NCS) is a seven-stranded beta-sandwich protein, the folding of which is similar to that of the variable domains of immunoglobulins (Ig). The investigation of the backbone dynamics of apo-NCS [Izadi-Pruneyre et al. (2001) Protein Sci., 10, 2228-2240] enabled us to identify the involvement of long side-chain residues in maintaining the rigidity of this beta-protein. In the perspective of using this protein for drug targeting, this raises the following question: do these residues also play a key role in the stabilization of the beta-sheet? To investigate this problem, various genetically engineered variants were constructed by mutating these residues to amino acids with shorter aliphatic side chains. These substitutions have no effects on the global fold. However, an important destabilization of the protein, higher than that expected for a simple 'large-to-small' substitution of buried hydrophobic residues, is observed for three mutants, V34A, V21A and V95A. Interestingly, the nature of the residues in these positions is highly conserved in the other Ig-like proteins. The absence of an evolutionary relationship between NCS and the other Ig-like proteins strongly suggests that this hydrophobic core is characteristic of the Ig-fold itself.
Collapse
Affiliation(s)
- Marielle Valerio-Lepiniec
- Laboratoire de Modélisation et d'Ingénierie des Protéines, UMR8619, Université de Paris-Sud, Bât 430, F-91405 Orsay Cedex, France
| | | | | | | | | |
Collapse
|
40
|
Borreguero JM, Dokholyan NV, Buldyrev SV, Shakhnovich EI, Stanley HE. Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics. J Mol Biol 2002; 318:863-76. [PMID: 12054829 DOI: 10.1016/s0022-2836(02)00136-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We perform a detailed analysis of the thermodynamics and folding kinetics of the SH3 domain fold with discrete molecular dynamic simulations. We propose a protein model that reproduces some of the experimentally observed thermodynamic and folding kinetic properties of proteins. Specifically, we use our model to study the transition state ensemble of the SH3 fold family of proteins, a set of unstable conformations that fold to the protein native state with probability 1/2. We analyze the participation of each secondary structure element formed at the transition state ensemble. We also identify the folding nucleus of the SH3 fold and test extensively its importance for folding kinetics. We predict that a set of amino acid contacts between the RT-loop and the distal hairpin are the critical folding nucleus of the SH3 fold and propose a hypothesis that explains this result.
Collapse
Affiliation(s)
- Jose M Borreguero
- Center for Polymer Studies and Department of Physics, Boston University, Boston, MA 02215, USA.
| | | | | | | | | |
Collapse
|
41
|
Klimov DK, Thirumalai D. Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains. J Mol Biol 2002; 317:721-37. [PMID: 11955020 DOI: 10.1006/jmbi.2002.5453] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Protein engineering experiments and Phi(F)-value analysis of SH3 domains reveal that their transition state ensemble (TSE) is conformationally restricted, i.e. the fluctuations in the transition state (TS) structures are small. In the TS of src SH3 and alpha-spectrin SH3 the distal loop and the associated hairpin are fully structured, while the rest of the protein is relatively disordered. If native structure predominantly determines the folding mechanism, the findings for SH3 folds raise the question: What are the features of the native topology that determine the nature of the TSE? We propose that the presence of stiff loops in the native state that connect local structural elements (such as the distal hairpin in SH3 domains) conformationally restricts TSE. We validate this hypothesis using the simulations of a "control" system (16 residue beta-hairpin forming C-terminal fragment of the GBl protein) and its variants. In these fragments the role of bending rigidity in determining the nature of the TSE can be directly examined without complications arising from interactions with the rest of the protein. The TSE structures in the beta-hairpins are determined computationally using cluster analysis and limited Phi(F)-value analysis. Both techniques prove that the conformational heterogeneity decreases as the bending rigidity of the loop increases. To extend this finding to SH3 domains a measure of bending rigidity based on loop curvature, which utilizes native structures in the Protein Data Bank (PDB), is introduced. Using this measure we show that, with few exceptions, the ordering of stiffness of the distal, n-src, and RT loops in the 29 PDB structures of SH3 domains is conserved. Combining the simulation results for beta-hairpins and the analysis of PDB structures for SH3 domains, we propose that the stiff distal loop restricts the conformational fluctuations in the TSE. We also predict that constraining the distal loop to be preformed in the denatured ensemble should not alter the nature of TSE. On the other hand, if the amino and carboxy terminals are cross-linked to form a circular polypeptide chain, the pathways and TSs are altered. These contrasting scenarios are illustrated using simulations of cross-linked WT beta-hairpin fragments. Computations of bending rigidities for immunoglobulin-like domain proteins reveal no clear separation in the stiffness of their loops. In the beta-sandwich proteins, which have large fractions of non-local native contacts, the nature of the TSE cannot be apparently determined using purely local structural characteristics. Nevertheless, the measure of loop stiffness still provides qualitative predictions of the ordered regions in the TSE of Ig27 and TenFn3.
Collapse
Affiliation(s)
- D K Klimov
- Department of Chemistry and Biochemistry and, Institute for Physical Science and Technology, College Park, MD 20742, USA
| | | |
Collapse
|
42
|
Larson SM, Ruczinski I, Davidson AR, Baker D, Plaxco KW. Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation. J Mol Biol 2002; 316:225-33. [PMID: 11851333 DOI: 10.1006/jmbi.2001.5344] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To what extent does natural selection act to optimize the details of protein folding kinetics? In an effort to address this question, the relationship between an amino acid's evolutionary conservation and its role in protein folding kinetics has been investigated intensively. Despite this effort, no consensus has been reached regarding the degree to which residues involved in native-like transition state structure (the folding nucleus) are conserved. Here we report the results of an exhaustive, systematic study of sequence conservation among residues known to participate in the experimentally (Phi-value) defined folding nuclei of all of the appropriately characterized proteins reported to date. We observe no significant evidence that these residues exhibit any anomalous sequence conservation. We do observe, however, a significant bias in the existing kinetic data: the mean sequence conservation of the residues that have been the subject of kinetic characterization is greater than the mean sequence conservation of all residues in 13 of 14 proteins studied. This systematic experimental bias gives rise to the previous observation that the median conservation of residues reported to participate in the folding nucleus is greater than the median conservation of all of the residues in a protein. When this bias is corrected (by comparing, for example, the conservation of residues known to participate in the folding nucleus with that of other, kinetically characterized residues) the previously reported preferential conservation is effectively eliminated. In contrast to well-established theoretical expectations, both poorly and highly conserved residues are apparently equally likely to participate in the protein-folding nucleus.
Collapse
Affiliation(s)
- Stefan M Larson
- Department of Chemistry and Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | | | | | | | | |
Collapse
|
43
|
Avbelj F, Baldwin RL. Role of backbone solvation in determining thermodynamic beta propensities of the amino acids. Proc Natl Acad Sci U S A 2002; 99:1309-13. [PMID: 11805303 PMCID: PMC122186 DOI: 10.1073/pnas.032665499] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2001] [Indexed: 11/18/2022] Open
Abstract
There is a paradox concerning the beta propensities of the amino acids: the amino acids with the highest beta propensities such as valine and isoleucine have the highest tendency to desolvate the peptide backbone, which should result in a loss of stability. Nevertheless, backbone solvation, calculated as electrostatic solvation free energy (ESF), is highly correlated with mutant stability in the zinc-finger system studied by Kim and Berg [Kim, C. A. & Berg, J. M. (1993) Nature (London) 362, 267-270], and valine and isoleucine are among the most stabilizing amino acids. This inverse correlation between stability and ESF can be explained, because the mutant ESF differences in the unfolded protein are larger than in the native protein. Consequently, mutations such as Ala to Val destabilize the unfolded form more than the native protein. By comparing mutant Delta ESF values in isolated beta-strands versus beta-sheets, we conclude that amino acids with high beta propensities should exert their stabilizing effects at early stages in folding. This deduction agrees with the studies by Clarke and coworkers [Lorch, M., Mason, J. M., Clarke, A. R. & Parker, M. J. (1999) Biochemistry 38, 1377-1385, and Lorch, M., Mason, J. M., Sessions, R. B. & Clarke, A. R. (2000) Biochemistry 39, 3480-3485] of the thermodynamics of folding of the beta-sheet protein CD2.d1.
Collapse
Affiliation(s)
- Franc Avbelj
- National Institute of Chemistry, Hajdrihova 19, Ljubljana SI 1115, Slovenia
| | | |
Collapse
|
44
|
Abstract
We propose a model that explains the hierarchical organization of proteins in fold families. The model, which is based on the evolutionary selection of proteins by their native state stability, reproduces patterns of amino acids conserved across protein families. Due to its dynamic nature, the model sheds light on the evolutionary time-scales. By studying the relaxation of the correlation function between consecutive mutations at a given position in proteins, we observe separation of the evolutionary time-scales: at short time intervals families of proteins with similar sequences and structures are formed, while at long time intervals the families of structurally similar proteins that have low sequence similarity are formed. We discuss the evolutionary implications of our model. We provide a "profile" solution to our model and find agreement between predicted patterns of conserved amino acids and those actually observed in nature.
Collapse
Affiliation(s)
- N V Dokholyan
- Department of Chemistry, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
| | | |
Collapse
|
45
|
Mirny L, Shakhnovich E. Protein folding theory: from lattice to all-atom models. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2001; 30:361-96. [PMID: 11340064 DOI: 10.1146/annurev.biophys.30.1.361] [Citation(s) in RCA: 232] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This review focuses on recent advances in understanding protein folding kinetics in the context of nucleation theory. We present basic concepts such as nucleation, folding nucleus, and transition state ensemble and then discuss recent advances and challenges in theoretical understanding of several key aspects of protein folding kinetics. We cover recent topology-based approaches as well as evolutionary studies and molecular dynamics approaches to determine protein folding nucleus and analyze other aspects of folding kinetics. Finally, we briefly discuss successful all-atom Monte-Carlo simulations of protein folding and conclude with a brief outlook for the future.
Collapse
Affiliation(s)
- L Mirny
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
| | | |
Collapse
|
46
|
Abstract
BACKGROUND Do proteins that have the same structure fold by the same pathway even when they are unrelated in sequence? To address this question, we are comparing the folding of a number of different immunoglobulin-like proteins. Here, we present a detailed protein engineering phi value analysis of the folding pathway of TI I27, an immunoglobulin domain from human cardiac titin. RESULTS TI I27 folds rapidly via a kinetic intermediate that is destabilized by most mutations. The transition state for folding is remarkably native-like in terms of solvent accessibility. We use phi value analysis to map this transition state and show that it is highly structured; only a few residues close to the N-terminal region of the protein remain completely unfolded. Interestingly, most mutations cause the transition state to become less native-like. This anti-Hammond behavior can be used as a novel means of obtaining additional structural information about the transition state. CONCLUSIONS The residues that are involved in nucleating the folding of TI I27 are structurally equivalent to the residues that form the folding nucleus in an evolutionary unrelated fibronectin type III protein. These residues form part of the common structural core of Ig-like domains. The data support the hypothesis that interactions essential for defining the structure of these beta sandwich proteins are also important in nucleation of folding.
Collapse
Affiliation(s)
- S B Fowler
- University of Cambridge, Centre for Protein Engineering, Department of Chemistry, CB2 1EW, Cambridge, United Kingdom
| | | |
Collapse
|
47
|
Gibbs N, Clarke AR, Sessions RB. Ab initio protein structure prediction using physicochemical potentials and a simplified off-lattice model. Proteins 2001; 43:186-202. [PMID: 11276088 DOI: 10.1002/1097-0134(20010501)43:2<186::aid-prot1030>3.0.co;2-l] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This study describes a computational method for ab inito protein structure prediction. Protein conformation has been modeled by using six optimized backbone torsion angles and fixed side chains approximating rotationally averaged real side chains. The approximations aim to keep complexity of the structure description to a minimum without seriously compromising the accuracy of the structural representation. An evolutionary Monte Carlo algorithm has been developed to search through this restricted conformational space to locate low-energy protein structures. A simple physicochemical force field has been developed to assess the energies of different conformations within this structural description. The corresponding residue interaction energies are based on hydrophobic, hydrophilic, steric, and hydrogen-bonding potentials. The search procedure has been used to locate native energy minima from primary sequence alone. The 3-D structures of polypeptides up to 38 residues with both beta and alpha secondary structural elements have been accurately predicted. The search procedure has been found to be highly efficient and follows an energetically and structurally plausible pathway to locate native populations. The simple force field described in the study has been compared with a more complex all-atom model and been found to be similarly effective in predicting the structures of proposed independent folding units. Proteins 2001;43:186-202.
Collapse
Affiliation(s)
- N Gibbs
- Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
| | | | | |
Collapse
|
48
|
Abstract
Here, we present statistical analysis of conservation profiles in families of homologous sequences for nine proteins whose folding nucleus was determined by protein engineering methods. We show that in all but one protein (AcP) folding nucleus residues are significantly more conserved than the rest of the protein. Two aspects of our study are especially important: (i) grouping of amino acid residues into classes according to their physical-chemical properties and (ii) proper normalization of amino acid probabilities that reflects the fact that evolutionary pressure to conserve some amino acid types may itself affect concentration of various amino acid types in protein families. Neglect of any of those two factors may make physical and biological "signals" from conservation profiles disappear.
Collapse
Affiliation(s)
- L Mirny
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | | |
Collapse
|
49
|
Ferguson N, Li W, Capaldi AP, Kleanthous C, Radford SE. Using chimeric immunity proteins to explore the energy landscape for alpha-helical protein folding. J Mol Biol 2001; 307:393-405. [PMID: 11243827 DOI: 10.1006/jmbi.2000.4492] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To address the role of sequence in the folding of homologous proteins, the folding and unfolding kinetics of the all-helical bacterial immunity proteins Im2 and Im9 were characterised, together with six chimeric derivatives of these proteins. We show that both Im2 and Im9 fold rapidly (k(UN)(H(2)O)) approximately 2000 s(-1) at pH 7.0, 25 degrees C) in apparent two-state transitions, through rate-limiting transition states that are highly compact (beta(TS)0.93 and 0.96, respectively). Whilst the folding and unfolding properties of three of the chimeras (Im2 (1-44)(Im9), Im2 (1-64)(Im9 )and Im2 (25-44)(Im9)) are similar to their parental counterparts, in other chimeric proteins the introduced sequence variation results in altered kinetic behaviour. At low urea concentrations, Im2 (1-29)(Im9) and Im2 (56-64)(Im9) fold in two-state transitions via transition states that are significantly less compact (beta(TS) approximately 0.7) than those characterised for the other immunity proteins presented here. At higher urea concentrations, however, the rate-limiting transition state for these two chimeras switches or moves to a more compact species (beta(TS) approximately 0.9). Surprisingly, Im2 (30-64)(Im9) populates a highly collapsed species (beta(I)=0.87) in the dead-time (2.5 ms) of stopped flow measurements. These data indicate that whilst topology may place significant constraints on the folding process, specific inter-residue interactions, revealed here through multiple sequence changes, can modulate the ruggedness of the folding energy landscape.
Collapse
Affiliation(s)
- N Ferguson
- School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | | | | | | | | |
Collapse
|
50
|
Carl P, Kwok CH, Manderson G, Speicher DW, Discher DE. Forced unfolding modulated by disulfide bonds in the Ig domains of a cell adhesion molecule. Proc Natl Acad Sci U S A 2001; 98:1565-70. [PMID: 11171991 PMCID: PMC29297 DOI: 10.1073/pnas.98.4.1565] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cell adhesion molecules (CAMs) mediate cell attachment and stress transfer through extracellular domains. Here we forcibly unfold the Ig domains of a prototypical Ig superfamily CAM that contains intradomain disulfide bonds. The Ig domains of all such CAMs have conformations homologous to cadherin extracellular domains, titin Ig-type domains, and fibronectin type-III (FNIII) domains. Atomic force microscopy has been used to extend the five Ig domains of Mel-CAM (melanoma CAM)--a protein that is overexpressed in metastatic melanomas--under conditions where the disulfide bonds were either left intact or disrupted through reduction. Under physiological conditions where intradomain disulfide bonds are intact, partial unfolding was observed at forces far smaller than those reported previously for either titin's Ig-type domains or tenascin's FNIII domains. This partial unfolding under low force may be an important mechanism for imparting elasticity to cell-cell contacts, as well as a regulatory mechanism for adhesive interactions. Under reducing conditions, Mel-CAM's Ig domains were found to fully unfold through a partially folded state and at slightly higher forces. The results suggest that, in divergent evolution of all such domains, stabilization imparted by disulfide bonds relaxes requirements for strong, noncovalent, folded-state interactions.
Collapse
Affiliation(s)
- P Carl
- Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104-6315, USA
| | | | | | | | | |
Collapse
|