1
|
Solution structure of Plasmodium falciparum Hsp90 indicates a high flexible dimer. Arch Biochem Biophys 2020; 690:108468. [PMID: 32679196 DOI: 10.1016/j.abb.2020.108468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/28/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023]
Abstract
Hsp90 is a ubiquitous, homodimer and modular molecular chaperone. Each Hsp90 protomer has three different domains, named the N-terminal domain (NTD), middle domain (MD) and C-terminal domain (CTD). The Hsp90 molecular cycle involves ATP binding and hydrolysis, which drive conformational changes. Hsp90 is critical for the viability of eukaryotic organisms, including the protozoan that causes the severe form of malaria, Plasmodium falciparum, the growth and differentiation of which are compromised when Hsp90 is inhibited. Here, we characterize the structure of a recombinant P. falciparum Hsp90 (PfHsp90) protein, as well as its MD (PfHsp90MD) and NTD plus MD (PfHsp90NMD) constructs. All the proteins were obtained with high purity and in the folded state. PfHsp90 and PfHsp90NMD interacted with adenosine nucleotides via the NTD, and Mg2+ was critical for strong binding. PfHsp90 behaved mostly as elongated and flexible dimers in solution, which dissociate with a sub-micromolar dissociation constant. The PfHsp90MD and PfHsp90NMD constructs behaved as globular and elongated monomers, respectively, confirming the importance of the CTD for dimerization. Small angle X-ray scattering data were obtained for all the constructs, and ab initio models were constructed, revealing PfHsp90 in an open conformation and as a greatly elongated and flexible protein.
Collapse
|
2
|
Dana H, Mahmoodi Chalbatani G, Gharagouzloo E, Miri SR, Memari F, Rasoolzadeh R, Zinatizadeh MR, Kheirandish Zarandi P, Marmari V. In silico Analysis, Molecular Docking, Molecular Dynamic, Cloning, Expression and Purification of Chimeric Protein in Colorectal Cancer Treatment. DRUG DESIGN DEVELOPMENT AND THERAPY 2020; 14:309-329. [PMID: 32158188 PMCID: PMC6986173 DOI: 10.2147/dddt.s231958] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 01/06/2020] [Indexed: 12/17/2022]
Abstract
Introduction Colorectal cancer (CRC) is a type of cancer in humans that leads to high mortality and morbidity. CD166 and CD326 are immunoglobulins that are associated with cell migration. These molecules are included in tumorigenesis of CRC and serve a great marker of CRC stem cells. In the present study, we devised a novel chimeric protein including the V1-domain of the CD166 and two epitopes of CD326 to use in diagnostic or therapeutic applications. Methods In silico techniques were launched to characterize the properties and structure of the protein. We have predicted physicochemical properties, structures, stability, MHC class I binding properties and ligand-receptor interaction of this chimeric protein by means of computational bioinformatics tools and servers. The sequence of chimeric gene was optimized for expression in prokaryotic host using online tools and cloned into pET-28a plasmid. The recombinant pET28a was transformed into the E. coli BL21DE3. Expression of recombinant protein was examined by SDS-PAGE and Western blotting. Results The designed chimeric protein retained high stability and the same immunogenicity as of the original proteins. Bioinformatics data indicated that the epitopes of the synthetic chimeric protein might induce B-cell- and T-cell-mediated immune responses. Furthermore, a gene was synthesized using the codon bias of a prokaryotic expression system. This synthetic gene expressed a bacterial expression system. The recombinant protein with molecular weights of 27kDa was expressed and confirmed by anti-his Western blot analysis. Conclusion The designed recombinant protein may be useful as a CRC diagnostic tool and for developing a protective vaccine against CRC.
Collapse
Affiliation(s)
- Hassan Dana
- Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Science, Tehran, Iran.,Department of Biology, Damghan Branch, Islamic Azad University, Damghan, Iran
| | | | - Elahe Gharagouzloo
- Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Science, Tehran, Iran
| | - Seyed Rouhollah Miri
- Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Science, Tehran, Iran
| | - Fereidoon Memari
- Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Science, Tehran, Iran
| | - Reza Rasoolzadeh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | | | - Vahid Marmari
- Department of Biology, Damghan Branch, Islamic Azad University, Damghan, Iran
| |
Collapse
|
3
|
Akouchekian M, Hakim Shooshtari M, Heidary H, Zahedi Abghari F, Moeinian P. The causative variants of amyloidosis in the autism. Int J Neurosci 2018; 129:10-15. [PMID: 30074416 DOI: 10.1080/00207454.2018.1503177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE Autism spectrum disorders (ASD) consist of a group of neurodevelopmental disorders that include autistic behavior, Asperger's syndrome and pervasive developmental disabilities. According to the increasing observations that patients with mitochondrial disorders have symptoms associated with ASD, we have aimed to analyze the role of mitochondrial DNA (mtDNA) variation in autistic patients. MATERIAL AND METHODS We selected children with autistic behaviors (15-60 CARS Score). The mitochondrial DNA extraction process was done by GeNet Bio DNA extraction kit. The regions of interest were amplified using independent PCR runs. After purification of PCR products, both strands were sequenced by Big Dye Termination system in a directly determined automated sequencing on an ABI 3700 capillary sequencer machine using both primers. All sequencing results were analyzed using bioinformatics' tools sequencher software 5. RESULTS In this study, 31 samples were examined, which 15 unique variants were detected in genes related to COXI-III. The most frequent variant (30.76%) were related to COX1 with amino acid change A → A. The only significant pathogenic variant was C8264G, except for C8264G, all variants seemed to be homoplasmic substitution. CONCLUSION In our study, among the variations we found, one variant what probably had an interesting association with possible amyloidosis, had been reported in patient with autism previously. It is hoped that with finding more definable genetic and biological markers, the autistic children diagnosis and treatment will be more effective.
Collapse
Affiliation(s)
- Mansoureh Akouchekian
- a Department of Medical Genetics and Molecular Biology, School of Medicine , Iran University of Medical Sciences , Tehran , Iran
| | - Mitra Hakim Shooshtari
- b Mental Health Research Center , Tehran Institute of Psychiatry- School of Medicine, Iran University of Medical Sciences , Tehran , Iran
| | - Hamed Heidary
- c Human Genetics Department, Ali Asghar Hospital , Iran University of Medical Sciences , Tehran , Iran
| | - Fateme Zahedi Abghari
- a Department of Medical Genetics and Molecular Biology, School of Medicine , Iran University of Medical Sciences , Tehran , Iran
| | - Parisa Moeinian
- a Department of Medical Genetics and Molecular Biology, School of Medicine , Iran University of Medical Sciences , Tehran , Iran
| |
Collapse
|
4
|
Fioramonte M, de Jesus HCR, Ferrari AJR, Lima DB, Drekener RL, Correia CRD, Oliveira LG, Neves-Ferreira AGDC, Carvalho PC, Gozzo FC. XPlex: An Effective, Multiplex Cross-Linking Chemistry for Acidic Residues. Anal Chem 2018; 90:6043-6050. [PMID: 29565564 DOI: 10.1021/acs.analchem.7b05135] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cross-linking/Mass spectrometry (XLMS) is a consolidated technique for structural characterization of proteins and protein complexes. Despite its success, the cross-linking chemistry currently used is mostly based on N-hydroxysuccinimide (NHS) esters, which react primarily with lysine residues. One way to expand the current applicability of XLMS into several new areas is to increase the number of cross-links obtainable for a target protein. We introduce a multiplex chemistry (denoted XPlex) that targets Asp, Glu, Lys, and Ser residues. XPlex can generate significantly more cross-links with reactions occurring at lower temperatures and enables targeting proteins that are not possible with NHS ester-based cross-linkers. We demonstrate the effectiveness of our approach in model proteins as well as a target Lys-poor protein, SalBIII. Identification of XPlex spectra requires a search engine capable of simultaneously considering multiple cross-linkers on the same run; to achieve this, we updated the SIM-XL search algorithm with a search mode tailored toward XPlex. In summary, we present a complete chemistry/computational solution for significantly increasing the number of possible distance constraints by mass spectrometry experiments, and thus, we are convinced that XPlex poses as a real complementary approach for structural proteomics studies.
Collapse
Affiliation(s)
- Mariana Fioramonte
- Institute of Chemistry , University of Campinas , CP 6154 , Campinas , Sao Paulo 13083-970 , Brazil
| | | | | | - Diogo Borges Lima
- Mass Spectrometry for Biology Unit, CNRS USR 2000 , Institut Pasteu , Paris , France
| | - Roberta Lopes Drekener
- Institute of Chemistry , University of Campinas , CP 6154 , Campinas , Sao Paulo 13083-970 , Brazil
| | | | - Luciana Gonzaga Oliveira
- Institute of Chemistry , University of Campinas , CP 6154 , Campinas , Sao Paulo 13083-970 , Brazil
| | | | - Paulo Costa Carvalho
- Laboratory for Proteomics and Protein Engineering , Carlos Chagas Institute , Fiocruz , Parana , Brazil
| | - Fabio Cesar Gozzo
- Institute of Chemistry , University of Campinas , CP 6154 , Campinas , Sao Paulo 13083-970 , Brazil
| |
Collapse
|
5
|
Adão R, Zanphorlin LM, Lima TB, Sriranganadane D, Dahlström KM, Pinheiro GMS, Gozzo FC, Barbosa LRS, Ramos CHI. Revealing the interaction mode of the highly flexible Sorghum bicolor Hsp70/Hsp90 organizing protein (Hop): A conserved carboxylate clamp confers high affinity binding to Hsp90. J Proteomics 2018; 191:191-201. [PMID: 29425735 DOI: 10.1016/j.jprot.2018.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 02/02/2018] [Accepted: 02/04/2018] [Indexed: 12/27/2022]
Abstract
Proteostasis is dependent on the Hsp70/Hsp90 system (the two chaperones and their co-chaperones). Of these, Hop (Hsp70/Hsp90 organizing protein), also known as Sti1, forms an important scaffold to simultaneously binding to both Hsp70 and Hsp90. Hop/Sti1 has been implicated in several disease states, for instance cancer and transmissible spongiform encephalopathies. Therefore, human and yeast homologous have been better studied and information on plant homologous is still limited, even though plants are continuously exposed to environmental stress. Particularly important is the study of crops that are relevant for agriculture, such as Sorghum bicolor, a C4 grass that is among the five most important cereals and is considered as a bioenergy feedstock. To increase the knowledge on plant chaperones, the hop putative gene for Sorghum bicolor was cloned and the biophysical and structural characterization of the protein was done by cross-linking coupled to mass spectroscopy, small angle X-ray scattering and structural modeling. Additionally, the binding to a peptide EEVD motif, which is present in both Hsp70 and Hsp90, was studied by isothermal titration calorimetry and hydrogen/deuterium exchange and the interaction pattern structurally modeled. The results indicate SbHop as a highly flexible, mainly alpha-helical monomer consisting of nine tetratricopeptide repeat domains, of which one confers high affinity binding to Hsp90 through a conserved carboxylate clamp. Moreover, the present insights into the conserved interactions formed between Hop and Hsp90 can help to design strategies for potential therapeutic approaches for the diseases in which Hop has been implicated.
Collapse
Affiliation(s)
- Regina Adão
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Letícia M Zanphorlin
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Tatiani B Lima
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Dev Sriranganadane
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Käthe M Dahlström
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Glaucia M S Pinheiro
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Fabio C Gozzo
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | | | - Carlos H I Ramos
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil.
| |
Collapse
|
6
|
Zhang X, Wang JH, Tan D, Li Q, Li M, Gong Z, Tang C, Liu Z, Dong MQ, Lei X. Carboxylate-Selective Chemical Cross-Linkers for Mass Spectrometric Analysis of Protein Structures. Anal Chem 2018; 90:1195-1201. [DOI: 10.1021/acs.analchem.7b03789] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Xiaoyun Zhang
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
Synthetic and Functional Biomolecules Center, and Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jian-Hua Wang
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
| | - Dan Tan
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
| | - Qiang Li
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
Synthetic and Functional Biomolecules Center, and Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
| | - Maodong Li
- Center
for Quantitative Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhou Gong
- CAS
Key Laboratory of Magnetic Resonance in Biological Systems, State
Key Laboratory of Magnetic Resonance and Atomic Molecular Physics,
National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Chun Tang
- CAS
Key Laboratory of Magnetic Resonance in Biological Systems, State
Key Laboratory of Magnetic Resonance and Atomic Molecular Physics,
National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Zhirong Liu
- Center
for Quantitative Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Meng-Qiu Dong
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
| | - Xiaoguang Lei
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
Synthetic and Functional Biomolecules Center, and Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
7
|
Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry. Proc Natl Acad Sci U S A 2017; 114:1732-1737. [PMID: 28130547 PMCID: PMC5321032 DOI: 10.1073/pnas.1617220114] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial protein interactions and complexes facilitate mitochondrial function. These complexes range from simple dimers to the respirasome supercomplex consisting of oxidative phosphorylation complexes I, III, and IV. To improve understanding of mitochondrial function, we used chemical cross-linking mass spectrometry to identify 2,427 cross-linked peptide pairs from 327 mitochondrial proteins in whole, respiring murine mitochondria. In situ interactions were observed in proteins throughout the electron transport chain membrane complexes, ATP synthase, and the mitochondrial contact site and cristae organizing system (MICOS) complex. Cross-linked sites showed excellent agreement with empirical protein structures and delivered complementary constraints for in silico protein docking. These data established direct physical evidence of the assembly of the complex I-III respirasome and enabled prediction of in situ interfacial regions of the complexes. Finally, we established a database and tools to harness the cross-linked interactions we observed as molecular probes, allowing quantification of conformation-dependent protein interfaces and dynamic protein complex assembly.
Collapse
|
8
|
Ding YH, Fan SB, Li S, Feng BY, Gao N, Ye K, He SM, Dong MQ. Increasing the Depth of Mass-Spectrometry-Based Structural Analysis of Protein Complexes through the Use of Multiple Cross-Linkers. Anal Chem 2016; 88:4461-9. [DOI: 10.1021/acs.analchem.6b00281] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yue-He Ding
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
- Graduate Program
in Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Sheng-Bo Fan
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology of CAS, University of CAS, Beijing 100049, China
| | - Shuang Li
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Bo-Ya Feng
- Ministry
of Education Protein Science Laboratory, Center for Structural Biology,
School of Life Sciences, and Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ning Gao
- Ministry
of Education Protein Science Laboratory, Center for Structural Biology,
School of Life Sciences, and Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Keqiong Ye
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Si-Min He
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology of CAS, University of CAS, Beijing 100049, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
- Graduate Program
in Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| |
Collapse
|
9
|
Pereira MBM, Santos AM, Gonçalves DC, Cardoso AC, Consonni SR, Gozzo FC, Oliveira PS, Pereira AHM, Figueiredo AR, Tiroli-Cepeda AO, Ramos CHI, de Thomaz AA, Cesar CL, Franchini KG. αB-crystallin interacts with and prevents stress-activated proteolysis of focal adhesion kinase by calpain in cardiomyocytes. Nat Commun 2014; 5:5159. [PMID: 25319025 DOI: 10.1038/ncomms6159] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 09/05/2014] [Indexed: 12/14/2022] Open
Abstract
Focal adhesion kinase (FAK) contributes to cellular homeostasis under stress conditions. Here we show that αB-crystallin interacts with and confers protection to FAK against calpain-mediated proteolysis in cardiomyocytes. A hydrophobic patch mapped between helices 1 and 4 of the FAK FAT domain was found to bind to the β4-β8 groove of αB-crystallin. Such an interaction requires FAK tyrosine 925 and is enhanced following its phosphorylation by Src, which occurs upon FAK stimulation. αB-crystallin silencing results in calpain-dependent FAK depletion and in the increased apoptosis of cardiomyocytes in response to mechanical stress. FAK overexpression protects cardiomyocytes depleted of αB-crystallin against the stretch-induced apoptosis. Consistently, load-induced apoptosis is blunted in the hearts from cardiac-specific FAK transgenic mice transiently depleted of αB-crystallin by RNA interference. These studies define a role for αB-crystallin in controlling FAK function and cardiomyocyte survival through the prevention of calpain-mediated degradation of FAK.
Collapse
Affiliation(s)
- Michelle B M Pereira
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Aline M Santos
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Danieli C Gonçalves
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Alisson C Cardoso
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Sílvio R Consonni
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Fabio C Gozzo
- Chemistry Institute, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Paulo S Oliveira
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Ana Helena M Pereira
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Alana R Figueiredo
- Chemistry Institute, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Ana O Tiroli-Cepeda
- Chemistry Institute, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Carlos H I Ramos
- Chemistry Institute, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - André A de Thomaz
- Gleb Wataghin Physics Institute, University of Campinas, Campinas, São Paulo 13083-859, Brazil
| | - Carlos L Cesar
- Gleb Wataghin Physics Institute, University of Campinas, Campinas, São Paulo 13083-859, Brazil
| | - Kleber G Franchini
- 1] Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil [2] Department of Internal Medicine, School of Medicine, University of Campinas, Campinas, São Paulo 13081-970, Brazil
| |
Collapse
|
10
|
Tinnefeld V, Sickmann A, Ahrends R. Catch me if you can: challenges and applications of cross-linking approaches. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2014; 20:99-116. [PMID: 24881459 DOI: 10.1255/ejms.1259] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Biomolecular complexes are the groundwork of life and the basis for cell signaling, energy transfer, motion, stability and cellular metabolism. Understanding the underlying complex interactions on the molecular level is an essential step to obtain a comprehensive insight into cellular and systems biology. For the investigation of molecular interactions, various methods, including Förster resonance energy transfer, nuclear magnetic resonance spectroscopy, X-ray crystallography and yeast two-hybrid screening, can be utilized. Nevertheless, the most reliable approach for structural proteomics and the identification of novel protein-binding partners is chemical cross-linking. The rationale is that upon forming a covalent bond between a protein and its interaction partner (protein, lipid, RNA/DNA, carbohydrate) the native complex state is "frozen" and accessible for detailed mass spectrometric analysis. In this review we provide a synopsis on crosslinker design, chemistry, pitfalls, limitations and novel applications in the field, and feature an overview of current software applications.
Collapse
|
11
|
Mass spectrometry coupled experiments and protein structure modeling methods. Int J Mol Sci 2013; 14:20635-57. [PMID: 24132151 PMCID: PMC3821635 DOI: 10.3390/ijms141020635] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/17/2013] [Accepted: 09/19/2013] [Indexed: 01/02/2023] Open
Abstract
With the accumulation of next generation sequencing data, there is increasing interest in the study of intra-species difference in molecular biology, especially in relation to disease analysis. Furthermore, the dynamics of the protein is being identified as a critical factor in its function. Although accuracy of protein structure prediction methods is high, provided there are structural templates, most methods are still insensitive to amino-acid differences at critical points that may change the overall structure. Also, predicted structures are inherently static and do not provide information about structural change over time. It is challenging to address the sensitivity and the dynamics by computational structure predictions alone. However, with the fast development of diverse mass spectrometry coupled experiments, low-resolution but fast and sensitive structural information can be obtained. This information can then be integrated into the structure prediction process to further improve the sensitivity and address the dynamics of the protein structures. For this purpose, this article focuses on reviewing two aspects: the types of mass spectrometry coupled experiments and structural data that are obtainable through those experiments; and the structure prediction methods that can utilize these data as constraints. Also, short review of current efforts in integrating experimental data in the structural modeling is provided.
Collapse
|