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Arshad F, Eaton-Rye JJ. Indirect interactions involving the PsbM or PsbT subunits and the PsbO, PsbU and PsbV proteins stabilize assembly and activity of Photosystem II in Synechocystis sp. PCC 6803. Photosynth Res 2024:10.1007/s11120-024-01091-9. [PMID: 38488942 DOI: 10.1007/s11120-024-01091-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/05/2024] [Indexed: 03/17/2024]
Abstract
The low-molecular-weight PsbM and PsbT proteins of Photosystem II (PS II) are both located at the monomer-monomer interface of the mature PS II dimer. Since the extrinsic proteins are associated with the final step of assembly of an active PS II monomer and, in the case of PsbO, are known to impact the stability of the PS II dimer, we have investigated the potential cooperativity between the PsbM and PsbT subunits and the PsbO, PsbU and PsbV extrinsic proteins. Blue-native polyacrylamide electrophoresis and western blotting detected stable PS II monomers in the ∆PsbM:∆PsbO and ∆PsbT:∆PsbO mutants that retained sufficient oxygen-evolving activity to support reduced photoautotrophic growth. In contrast, the ∆PsbM:∆PsbU and ∆PsbT:∆PsbU mutants assembled dimeric PS II at levels comparable to wild type and supported photoautotrophic growth at rates similar to those obtained with the corresponding ∆PsbM and ∆PsbT cells. Removal of PsbV was more detrimental than removal of PsbO. Only limited levels of dimeric PS II were observed in the ∆PsbM:∆PsbV mutant and the overall reduced level of assembled PS II in this mutant resulted in diminished rates of photoautotrophic growth and PS II activity below those obtained in the ∆PsbM:∆PsbO and ∆PsbT:∆PsbO strains. In addition, the ∆PsbT:∆PsbV mutant did not assemble active PS II centers although inactive monomers could be detected. The inability of the ∆PsbT:∆PsbV mutant to grow photoautotrophically, or to evolve oxygen, suggested a stable oxygen-evolving complex could not assemble in this mutant.
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Affiliation(s)
- Faiza Arshad
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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Liu J, Bao X, Huang J, Chen R, Tan Y, Zhang Z, Xiao B, Kong F, Gu C, Du J, Wang H, Qi J, Tan J, Ma D, Shi C, Xu G. TMEM135 maintains the equilibrium of osteogenesis and adipogenesis by regulating mitochondrial dynamics. Metabolism 2024; 152:155767. [PMID: 38154611 DOI: 10.1016/j.metabol.2023.155767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/10/2023] [Accepted: 12/20/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND Disturbance in the differentiation process of bone marrow mesenchymal stem cells (BMSCs) leads to osteoporosis. Mitochondrial dynamics plays a pivotal role in the metabolism and differentiation of BMSCs. However, the mechanisms underlying mitochondrial dynamics and their impact on the differentiation equilibrium of BMSCs remain unclear. METHODS We investigated the mitochondrial morphology and markers related to mitochondrial dynamics during BMSCs osteogenic and adipogenic differentiation. Bioinformatics was used to screen potential genes regulating BMSCs differentiation through mitochondrial dynamics. Subsequently, we evaluated the impact of Transmembrane protein 135 (TMEM135) deficiency on bone homeostasis by comparing Tmem135 knockout mice with their littermates. The mechanism of TMEM135 in mitochondrial dynamics and BMSCs differentiation was also investigated in vivo and in vitro. RESULTS Distinct changes in mitochondrial morphology were observed between osteogenic and adipogenic differentiation of BMSCs, manifesting as fission in the late stage of osteogenesis and fusion in adipogenesis. Additionally, we revealed that TMEM135, a modulator of mitochondrial dynamics, played a functional role in regulating the equilibrium between adipogenesis and osteogenesis. The TMEM135 deficiency impaired mitochondrial fission and disrupted crucial mitochondrial energy metabolism during osteogenesis. Tmem135 knockout mice showed osteoporotic phenotype, characterized by reduced osteogenesis and increased adipogenesis. Mechanistically, TMEM135 maintained intracellular calcium ion homeostasis and facilitated the dephosphorylation of dynamic-related protein 1 at Serine 637 in BMSCs. CONCLUSIONS Our findings underscore the significant role of TMEM135 as a modulator in orchestrating the differentiation trajectory of BMSCs and promoting a shift in mitochondrial dynamics toward fission. This ultimately contributes to the osteogenesis process. This work has provided promising biological targets for the treatment of osteoporosis.
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Affiliation(s)
- Jia Liu
- Department of Orthopedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai 200003, PR China
| | - Xiaogang Bao
- Department of Orthopedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai 200003, PR China
| | - Jian Huang
- Department of Orthopedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai 200003, PR China
| | - Rukun Chen
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Yixuan Tan
- Department of Orthopedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai 200003, PR China
| | - Zheng Zhang
- Department of Orthopedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai 200003, PR China
| | - Bing Xiao
- Department of Orthopedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai 200003, PR China
| | - Fanqi Kong
- Department of Orthopedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai 200003, PR China
| | - Changjiang Gu
- Department of Orthopedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai 200003, PR China
| | - Jianhang Du
- Department of Orthopedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai 200003, PR China
| | - Haotian Wang
- Department of Orthopedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai 200003, PR China
| | - Junqiang Qi
- Department of Orthopedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai 200003, PR China
| | - Junming Tan
- Department of Orthopedics, The 72nd Army Hospital of the People's Liberation Army, Huzhou 313099, PR China
| | - Duan Ma
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Changgui Shi
- Department of Orthopedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai 200003, PR China.
| | - Guohua Xu
- Department of Orthopedic Surgery, Changzheng Hospital, Naval Medical University, Shanghai 200003, PR China.
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Lei H, Fang F, Yang C, Chen X, Li Q, Shen X. Lifting the veils on transmembrane proteins: Potential anticancer targets. Eur J Pharmacol 2024; 963:176225. [PMID: 38040080 DOI: 10.1016/j.ejphar.2023.176225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/08/2023] [Accepted: 11/24/2023] [Indexed: 12/03/2023]
Abstract
Cancer, as a prevalent cause of mortality, poses a substantial global health burden and hinders efforts to enhance life expectancy. Nevertheless, the prognosis of patients with malignant tumors remains discouraging, owing to the lack of specific diagnostic and therapeutic targets. Therefore, the development of early diagnostic indicators and novel therapeutic drugs for the prevention and treatment of cancer is essential. Transmembrane proteins (TMEMs) are a class of proteins that can span the phospholipid bilayer and are stably anchored. They are associated with fibrotic diseases, neurodegenerative diseases, autoimmune diseases, developmental disorders, and cancer. It has been found that the expression levels of TMEMs were elevated or reduced in cancer cells, exerting pro/anticancer effects. These aberrant expression levels have also been linked to the prognostic and clinicopathological features of diverse tumors. In this review, the structures, functions, and roles of TMEMs in cancer were discussed, and the scientific perspectives were described. This review also explored the potential of TMEMs as tumor drug candidates from the perspective of targeted therapies, and the challenges that need to be overcome in a wide range of preclinical and clinical anticancer research were summarized.
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Affiliation(s)
- Huan Lei
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China; Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Fujin Fang
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Chuanli Yang
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Xiaowei Chen
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Qiong Li
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Xiaobing Shen
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China; Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China.
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Tilahun L, Asrat A, Wessel GM, Simachew A. Ancestors in the Extreme: A Genomics View of Microbial Diversity in Hypersaline Aquatic Environments. Results Probl Cell Differ 2024; 71:185-212. [PMID: 37996679 DOI: 10.1007/978-3-031-37936-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
The origin of eukaryotic cells, and especially naturally occurring syncytial cells, remains debatable. While a majority of our biomedical research focuses on the eukaryotic result of evolution, our data remain limiting on the prokaryotic precursors of these cells. This is particularly evident when considering extremophile biology, especially in how the genomes of organisms in extreme environments must have evolved and adapted to unique habitats. Might these rapidly diversifying organisms have created new genetic tools eventually used to enhance the evolution of the eukaryotic single nuclear or syncytial cells? Many organisms are capable of surviving, or even thriving, in conditions of extreme temperature, acidity, organic composition, and then rapidly adapt to yet new conditions. This study identified organisms found in extremes of salinity. A lake and a nearby pond in the Ethiopian Rift Valley were interrogated for life by sequencing the DNA of populations of organism collected from the water in these sites. Remarkably, a vast diversity of microbes were identified, and even though the two sites were nearby each other, the populations of organisms were distinctly different. Since these microbes are capable of living in what for humans would be inhospitable conditions, the DNA sequences identified should inform the next step in these investigations; what new gene families, or modifications to common genes, do these organisms employ to survive in these extreme conditions. The relationship between organisms and their environment can be revealed by decoding genomes of organisms living in extreme environments. These genomes disclose new biological mechanisms that enable life outside moderate environmental conditions, new gene functions for application in biotechnology, and may even result in identification of new species. In this study, we have collected samples from two hypersaline sites in the Danakil depression, the shorelines of Lake As'ale and an actively mixing salt pond called Muda'ara (MUP), to identify the microbial community by metagenomics. Shotgun sequencing was applied to high density sampling, and the relative abundance of Operational Taxonomic Units (OTUs) was calculated. Despite the broad taxonomic similarities among the salt-saturated metagenomes analyzed, MUP stood out from Lake As'ale samples. In each sample site, Archaea accounted for 95% of the total OTUs, largely to the class Halobacteria. The remaining 5% of organisms were eubacteria, with an unclassified strain of Salinibacter ruber as the dominant OTU in both the Lake and the Pond. More than 40 different genes coding for stress proteins were identified in the three sample sites of Lake As'ale, and more than 50% of the predicted stress-related genes were associated with oxidative stress response proteins. Chaperone proteins (DnaK, DnaJ, GrpE, and ClpB) were predicted, with percentage of query coverage and similarities ranging between 9.5% and 99.2%. Long reads for ClpB homologous protein from Lake As'ale metagenome datasets were modeled, and compact 3D structures were generated. Considering the extreme environmental conditions of the Danakil depression, this metagenomics dataset can add and complement other studies on unique gene functions on stress response mechanisms of thriving bio-communities that could have contributed to cellular changes leading to single and/or multinucleated eukaryotic cells.
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Affiliation(s)
- Lulit Tilahun
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Asfawossen Asrat
- Department of Mining and Geological Engineering, Botswana International University of Science and Technology, Palapye, Botswana
- School of Earth Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gary M Wessel
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI, USA.
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
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Abstract
Many computational methods are available for predicting protein sorting in bacteria. When comparing them, it is important to know that they can be grouped into three fundamentally different approaches: signal-based, global property-based, and homology-based prediction. In this chapter, the strengths and drawbacks of each of these approaches are described through many examples of methods that predict secretion, integration into membranes, or subcellular locations in general. The aim of this chapter is to provide a user-level introduction to the field with a minimum of computational theory.
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Affiliation(s)
- Henrik Nielsen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark.
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Sawhney A, Li J, Liao L. Improving AlphaFold predicted contacts in alpha-helical transmembrane proteins structures using structural features. Res Sq 2023:rs.3.rs-3475769. [PMID: 37961476 PMCID: PMC10635369 DOI: 10.21203/rs.3.rs-3475769/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background Residue contacts maps offer a 2-d reduced representation of 3-d protein structures and constitute a structural constraint and scaffold in structural modeling. In addition, contact maps are also an effective tool in identifying interhelical binding sites and drawing insights about protein function. While most works predict contact maps using features derived from sequences, we believe information from known structures can be leveraged for a prediction improvement in unknown structures where decent approximate structures such as ones predicted by AlphaFold2 are available. Results Alphafold2's predicted structures are found to be quite accurate at inter-helical residue contact prediction task, achieving 83% average precision. We adopt an unconventional approach, using features extracted from atomic structures in the neighborhood of a residue pair and use them to predicting residue contact. We trained on features derived from experimentally determined structures and predicted on features derived from AlphaFold2's predicted structures. Our results demonstrate a remarkable improvement over AlphaFold2 achieving over 91.9% average precision for held-out and over 89.5% average precision in cross validation experiments. Conclusion Training on features generated from experimentally determined structures, we were able to leverage knowledge from known structures to significantly improve the contacts predicted using AlphaFold2 structures. We demonstrated that using coordinates directly (instead of the proposed features) does not lead to an improvement in contact prediction performance.
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Affiliation(s)
- Aman Sawhney
- Department of Computer and Information Sciences, University of
Delaware, Smith Hall, 18 Amstel Avenue, Newark, DE, 19716,United States
| | - Jiefu Li
- School of Optical-Electrical and Computer Engineering, University
of Shanghai for Science and Technology, 516 Jun Gong Road, Shanghai 200093, P. R.
China
| | - Li Liao
- Department of Computer and Information Sciences, University of
Delaware, Smith Hall, 18 Amstel Avenue, Newark, DE, 19716,United States
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Kawamala BK, Abrol R. Three-stage model of helical membrane protein folding: Role of membrane-water interface as the intermediate stage vestibule for TM helices during their in membrano assembly. Biochem Biophys Res Commun 2022; 624:1-7. [PMID: 35926384 PMCID: PMC10587497 DOI: 10.1016/j.bbrc.2022.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 07/02/2022] [Indexed: 11/22/2022]
Abstract
Integral membrane proteins (MPs) are dominated by transmembrane α-helical (TMH) proteins playing critical roles in cellular signaling processes. These proteins display a wide range of sizes from one TMH domain to at least 26 TMH domains and diverse structural folds. A common feature of most of these folds is the TM orientation of the helical domains and the approximately parallel packing of these domains into helical bundles of varying stability, however, it has been challenging to study the folding of these proteins experimentally. The contribution of helix stabilization in membrane and interface to the folding energy landscape are investigated here for the full range of TMH protein sizes containing 1 TM domain (1-TMH protein) to 24 TM domains (24-TMH protein) for all TMH proteins with available structures using structural bioinformatics based hydropathy analysis. The TM helix insertion stabilization energies from Water to membrane-water Interface (WAT→INT energies) are on average half of those insertion energies from water to transmembrane orientation (WAT→TM energies) for the whole polytopic helical membrane proteome (1-TMH to 24-TMH proteins). This suggests a potentially dominant role of the membrane-water interface as a viable holding vestibule for the TM helices during their release from the translocon. This provides proteome-level evidence for the broadly applicable four-step thermodynamic framework by White and co-workers as well as a natural extension of Popot and Engelman's original two-stage model of helical MP folding to a three-stage model, where, in the new intermediate stage, the membrane-water interface acts as a holding vestibule for the translated TM helices, reconciling the interface's critical role in MP folding seen in many previous studies. Support for this model is provided by showing the stability of hydrophobic TM helices at the membrane-water interface through several microsecond long molecular dynamics simulations of five hydrophobic helical domains and a helical hairpin pre-folded from the ribosomal exit vestibule.
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Affiliation(s)
- Bridget-K Kawamala
- Department of Chemistry and Biochemistry, California State University, Northridge, CA, USA
| | - Ravinder Abrol
- Department of Chemistry and Biochemistry, California State University, Northridge, CA, USA.
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8
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Danazumi AU, Iliyasu Gital S, Idris S, BS Dibba L, Balogun EO, Górna MW. Immunoinformatic design of a putative multi-epitope vaccine candidate against Trypanosoma brucei gambiense. Comput Struct Biotechnol J 2022; 20:5574-5585. [PMID: 36284708 PMCID: PMC9576565 DOI: 10.1016/j.csbj.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/13/2022] [Accepted: 10/02/2022] [Indexed: 11/28/2022] Open
Abstract
Human African trypanosomiasis (HAT) is a neglected tropical disease that is caused by flagellated parasites of the genus Trypanosoma. HAT imposes a significant socio-economic burden on many countries in sub-Saharan Africa and its control is hampered by several drawbacks ranging from the ineffectiveness of drugs, complex dosing regimens, drug resistance, and lack of a vaccine. Despite more than a century of research and investigations, the development of a vaccine to tackle HAT is still challenging due to the complex biology of the pathogens. Advancements in computational modeling coupled with the availability of an unprecedented amount of omics data from different organisms have allowed the design of new generation vaccines that offer better antigenicity and safety profile. One of such new generation approaches is a multi-epitope vaccine (MEV) designed from a collection of antigenic peptides. A MEV can stimulate both cellular and humoral immune responses as well as avoiding possible allergenic reactions. Herein, we take advantage of this approach to design a MEV from conserved hypothetical plasma membrane proteins of Trypanosoma brucei gambiense, the trypanosome subspecies that is responsible for the west and central African forms of HAT. The designed MEV is 402 amino acids long (41.5 kDa). It is predicted to be antigenic, non-toxic, to assume a stable 3D conformation, and to interact with a key immune receptor. In addition, immune simulation foresaw adequate immune stimulation by the putative antigen and a lasting memory. Therefore, the designed chimeric vaccine represents a potential candidate that could be used to target HAT.
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Affiliation(s)
- Ammar Usman Danazumi
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland,Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland,Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands,Corresponding authors at: Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland (A.U. Danazumi, M. W. Górna).
| | | | - Salisu Idris
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria,Department of Medical Laboratory Science, Kazaure School of Health Technology, Jigawa, Nigeria
| | - Lamin BS Dibba
- Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria,Department of Physical and Natural Sciences, School of Arts and Sciences, University of the Gambia, Brikama Campus. P.O Box 3530, Serrekunda, the Gambia
| | - Emmanuel Oluwadare Balogun
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria,Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria,Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Maria Wiktoria Górna
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland,Corresponding authors at: Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland (A.U. Danazumi, M. W. Górna).
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Hegedűs T, Geisler M, Lukács GL, Farkas B. Ins and outs of AlphaFold2 transmembrane protein structure predictions. Cell Mol Life Sci 2022; 79:73. [PMID: 35034173 PMCID: PMC8761152 DOI: 10.1007/s00018-021-04112-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/25/2021] [Accepted: 12/20/2021] [Indexed: 12/20/2022]
Abstract
Transmembrane (TM) proteins are major drug targets, but their structure determination, a prerequisite for rational drug design, remains challenging. Recently, the DeepMind's AlphaFold2 machine learning method greatly expanded the structural coverage of sequences with high accuracy. Since the employed algorithm did not take specific properties of TM proteins into account, the reliability of the generated TM structures should be assessed. Therefore, we quantitatively investigated the quality of structures at genome scales, at the level of ABC protein superfamily folds and for specific membrane proteins (e.g. dimer modeling and stability in molecular dynamics simulations). We tested template-free structure prediction with a challenging TM CASP14 target and several TM protein structures published after AlphaFold2 training. Our results suggest that AlphaFold2 performs well in the case of TM proteins and its neural network is not overfitted. We conclude that cautious applications of AlphaFold2 structural models will advance TM protein-associated studies at an unexpected level.
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Affiliation(s)
- Tamás Hegedűs
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
- TKI, Eötvös Loránd Research Network, Budapest, Hungary.
| | - Markus Geisler
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Bianka Farkas
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
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10
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Jernigan RL, Khade P, Kumar A, Kloczkowski A. Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites: Application to the Interactions of E-cadherins. Methods Mol Biol 2022; 2340:41-50. [PMID: 35167069 PMCID: PMC9131873 DOI: 10.1007/978-1-0716-1546-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Studying the interactions within protein structures can inform about the details of how proteins of various types interact and aggregate. Empirical contact potentials have proven to be extremely important in the evaluation of individual modeled protein structures, but have found few applications to protein-protein interactions. In part, this is caused by a lack of properly formulated potentials with a proper reference state. Since the comparisons are made between different bound structures, the proper reference state should take into account other contacts. Therefore, a preferred reference state should be defined with respect to a given residue type interacting with an average residue instead of interacting with solvent as typically is used in derivation of statistical contact potentials. Here, a two-stage procedure for generating and evaluating interacting protein pairs is described, and an example of E-cadherin interactions is shown.
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Affiliation(s)
- Robert L Jernigan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA.
| | - Pranav Khade
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Ambuj Kumar
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Andrzej Kloczkowski
- Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
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11
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Sales AD, Duarte ABG, Rocha RMP, Brito IR, Locatelli Y, Alves BG, Alves KA, Figueiredo JR, Rodrigues APR. Transcriptional downregulation of ABC transporters is related to follicular degeneration after vitrification and in vitro culture of ovine ovarian tissue. Theriogenology 2022; 177:127-32. [PMID: 34700069 DOI: 10.1016/j.theriogenology.2021.10.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 08/22/2021] [Accepted: 10/16/2021] [Indexed: 12/19/2022]
Abstract
ATP-binding cassette (ABC) transporters perform multiple functions in reproductive tissues. During ovarian tissue vitrification, the plasma membrane has important functions in the influx or efflux of water, and substances such as cryoprotectants and channel proteins that are required in this process. Thus, the present study aimed to verify the relative abundance of mRNA transcript of ABC transporters ABCB1, ABCG2, and MRP2 after vitrification and in vitro culture (IVC) of ovine ovarian tissue. For this study, the ovarian cortex fragments were proportioned into four groups as fresh control, vitrified control, fresh culture, and vitrified culture groups. After vitrification and in vitro culture, the ovarian tissue was evaluated using morphological procedures. Further, relative abundance of ABCB1, ABCG2, and MRP2 transporter mRNA transcripts in the ovarian cortex subjected to aforementioned treatment conditions were evaluated using qPCR. Our results showed a negative association between degenerated follicles and mRNA transcript abundances of ABCB1 and ABCG2. In addition, the percentage of growing follicles in the ovine ovarian cortex after vitrification was similar to that of the fresh control tissue without in vitro culture. The in vitro culture of fresh and vitrified tissue however, showed a significant decrease in the percentage of growing follicles. To the best of our knowledge, we believe that our data for the first time has studied the relative abundances of ABCB1 and ABCG2 mRNA transcripts in the ovine ovarian cortex. In addition, alterations of these protein channels may be indicative of a deleterious effect of osmotic stress on follicular survival during vitrification. Furthermore, these effects were detectable only after the IVC of the ovarian tissues. Nonetheless, further studies are required to investigate the functions of ABC transporters in ovine folliculogenesis, especially after in vitro culture of ovarian tissue.
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12
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Lujan P, Campelo F. Should I stay or should I go? Golgi membrane spatial organization for protein sorting and retention. Arch Biochem Biophys 2021; 707:108921. [PMID: 34038703 DOI: 10.1016/j.abb.2021.108921] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/12/2021] [Accepted: 05/03/2021] [Indexed: 12/23/2022]
Abstract
The Golgi complex is the membrane-bound organelle that lies at the center of the secretory pathway. Its main functions are to maintain cellular lipid homeostasis, to orchestrate protein processing and maturation, and to mediate protein sorting and export. These functions are not independent of one another, and they all require that the membranes of the Golgi complex have a well-defined biochemical composition. Importantly, a finely-regulated spatiotemporal organization of the Golgi membrane components is essential for the correct performance of the organelle. In here, we review our current mechanistic and molecular understanding of how Golgi membranes are spatially organized in the lateral and axial directions to fulfill their functions. In particular, we highlight the current evidence and proposed models of intra-Golgi transport, as well as the known mechanisms for the retention of Golgi residents and for the sorting and export of transmembrane cargo proteins. Despite the controversies, conflicting evidence, clashes between models, and technical limitations, the field has moved forward and we have gained extensive knowledge in this fascinating topic. However, there are still many important questions that remain to be completely answered. We hope that this review will help boost future investigations on these issues.
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Affiliation(s)
- Pablo Lujan
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860, Barcelona, Spain.
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860, Barcelona, Spain.
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13
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Ye J. Regulated Alternative Translocation: A Mechanism Regulating Transmembrane Proteins Through Topological Inversion. Adv Exp Med Biol 2021; 21:183-190. [PMID: 32986129 DOI: 10.1007/5584_2020_585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2023]
Abstract
Transmembrane proteins must adopt a proper topology to execute their functions. In mammalian cells, a transmembrane protein is believed to adopt a fixed topology. This assumption has been challenged by recent reports that ceramide or related sphingolipids regulate some transmembrane proteins by inverting their topology. Ceramide inverts the topology of certain newly synthesized polytopic transmembrane proteins by altering the direction through which their first transmembrane helices are translocated across membranes. Thus, this regulatory mechanism has been designated as Regulated Alternative Translocation (RAT). The physiological importance of this topological regulation has been demonstrated by the finding that ceramide-induced RAT of TM4SF20 (Transmembrane 4 L6 family member 20) is crucial for the effectiveness of doxorubicin-based chemotherapy, and that dihydroceramide-induced RAT of CCR5 (C-C chemokine receptor type 5), a G protein-coupled receptor, is required for lipopolysaccharide (LPS) to inhibit chemotaxis of macrophages. These observations suggest that topological inversion through RAT could be an emerging mechanism to regulate transmembrane proteins.
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Affiliation(s)
- Jin Ye
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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14
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Jiang R, Li Y, Wang H, Kong D, Wu X, Xu J. A study on the degradation efficiency of fluoranthene and the transmembrane protein mechanism of Rhodococcus sp. BAP-1 based on iTRAQ. Sci Total Environ 2020; 737:140208. [PMID: 32783839 DOI: 10.1016/j.scitotenv.2020.140208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/20/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Based on previous studies that examined the whole proteome of Rhodococcus sp. BAP-1 during the degradation of polycyclic aromatic hydrocarbons (PAHs), transmembrane proteins have a large role in the degradation of fluoranthene. To further study the specific functions and mechanisms of transmembrane proteins from Rhodococcus sp. BAP-1 involved in the degradation process of fluoranthene, the degradation of PAHs and the membrane permeability were determined. In addition, the isobaric tags for relative and absolute quantization (iTRAQ) method were used to conduct a proteomics analysis of Rhodococcus sp. BAP-1 after exposure to fluoranthene for 1 d, 3 d, and 6 d. The results showed that the degradation rate was the highest on the first and sixth days, and the membrane permeability was also the highest on the sixth day. The iTRAQ analysis results showed 18, 29, and 48 upregulated proteins and 111, 97, and 21 downregulated proteins in the 1 d group vs control group, 3 d group vs control group, and 6 d group vs control group samples respectively. According to a Clusters of Orthologous Groups of proteins (COG) analysis, amino acid transport and metabolism are the most important functions. According to functional analysis from the gene ontology (GO) database, the oxidation-reduction process is the most important biological process; transporter activity is the main molecular function; and transmembrane proteins are the most important in the cell composition. This study combined the degradation rate, membrane permeability and transmembrane protein functions to analyze the functions and mechanisms of transmembrane proteins from Rhodococcus sp. BAP-1, which are involved in the degradation of fluoranthene at the protein level, and this study provides a solid foundation for further research on the metabolic processes of bacteria.
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Affiliation(s)
- Ruhan Jiang
- College of Water Sciences, Beijing Normal University, 100875 Beijing, China
| | - Yi Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China, Guangxi Normal University, 541004 Guilin, Guangxi, China; College of Environment and Resources, Guangxi Normal University, 541004 Guilin, Guangxi, China.
| | - Hongqi Wang
- College of Water Sciences, Beijing Normal University, 100875 Beijing, China.
| | - Dekang Kong
- College of Water Sciences, Beijing Normal University, 100875 Beijing, China
| | - Xiaoxiong Wu
- College of Water Sciences, Beijing Normal University, 100875 Beijing, China
| | - Jie Xu
- Shunyi District Ecological Protection Bureau, 101300 Beijing, China
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15
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Hönigschmid P, Breimann S, Weigl M, Frishman D. AllesTM: predicting multiple structural features of transmembrane proteins. BMC Bioinformatics 2020; 21:242. [PMID: 32532211 PMCID: PMC7291640 DOI: 10.1186/s12859-020-03581-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 06/03/2020] [Indexed: 12/04/2022] Open
Abstract
Background This study is motivated by the following three considerations: a) the physico-chemical properties of transmembrane (TM) proteins are distinctly different from those of globular proteins, necessitating the development of specialized structure prediction techniques, b) for many structural features no specialized predictors for TM proteins are available at all, and c) deep learning algorithms allow to automate the feature engineering process and thus facilitate the development of multi-target methods for predicting several protein properties at once. Results We present AllesTM, an integrated tool to predict almost all structural features of transmembrane proteins that can be extracted from atomic coordinate data. It blends several machine learning algorithms: random forests and gradient boosting machines, convolutional neural networks in their original form as well as those enhanced by dilated convolutions and residual connections, and, finally, long short-term memory architectures. AllesTM outperforms other available methods in predicting residue depth in the membrane, flexibility, topology, relative solvent accessibility in its bound state, while in torsion angles, secondary structure and monomer relative solvent accessibility prediction it lags only slightly behind the currently leading technique SPOT-1D. High accuracy on a multitude of prediction targets and easy installation make AllesTM a one-stop shop for many typical problems in the structural bioinformatics of transmembrane proteins. Conclusions In addition to presenting a highly accurate prediction method and eliminating the need to install and maintain many different software tools, we also provide a comprehensive overview of the impact of different machine learning algorithms and parameter choices on the prediction performance. AllesTM is freely available at https://github.com/phngs/allestm.
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Affiliation(s)
- Peter Hönigschmid
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354, Freising, Germany
| | - Stephan Breimann
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354, Freising, Germany
| | - Martina Weigl
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354, Freising, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354, Freising, Germany.
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16
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Ngo AM, Wang R, Puschnik AS. Dual Fluorescence Cytometry Assay to Assess Cellular Protein Levels. Bio Protoc 2020; 10:e3597. [PMID: 33659563 DOI: 10.21769/bioprotoc.3597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/27/2020] [Accepted: 03/17/2020] [Indexed: 11/02/2022] Open
Abstract
Expression levels of cellular proteins can be affected by various perturbations, such as genetic knockout of interactors, drug treatments or cell stress. To specifically measure the effects on protein levels post-synthesis under different experimental conditions, it is important to compensate for transcriptional and other upstream changes. Here, we provide a protocol for a dual-fluorescence flowcytometry-based assay to determine protein levels. The protein of interest is genetically linked to enhanced GFP (eGFP) followed by a viral 2A self-cleaving peptide sequence and mCherry. As a result, translation of the reporter construct leads to two fluorescent protein products from the same mRNA template, which enables unambiguous protein expression analysis with normalization across samples.
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Affiliation(s)
- Ashley M Ngo
- Chan Zuckerberg Biohub, San Francisco, United States
| | - Ruofan Wang
- Chan Zuckerberg Biohub, San Francisco, United States
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17
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Abstract
While X-ray crystallography remains the most popular and productive technique for protein structure determination, it very often produces incomplete models, either due to truncations introduced by the scientists or locally weak experimental data. This problem is even more common for transmembrane proteins, owing to the difficulties inherent in their crystallization. By the virtue of operating in solution, SAXS bypasses the problems with crystallization and allows for easier work with full-length constructs and, thus, can potentially be used to fill the missing (and often crucial) details. Here, we describe a complete procedure to build a complete model of a transmembrane protein based on a truncated crystallographic model and experimental SEC-SAXS data using refractometry and UV absorption for internal validation of the measurements.
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Affiliation(s)
| | - Javier Pérez
- Synchrotron SOLEIL, Gif sur Yvette Cedex, France.
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18
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Sharma M, Anirudh CR. In silico characterization of residues essential for substrate binding of human cystine transporter, xCT. J Mol Model 2019; 25:336. [PMID: 31705320 DOI: 10.1007/s00894-019-4233-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/14/2019] [Indexed: 02/06/2023]
Abstract
xCT is a sodium-independent amino acid antiporter that imports L-cystine and exports L-glutamate in a 1:1 ratio. It is a component of heterodimeric amino acid transporter system Xc- working at the cross-roads of maintaining neurological processes and regulating antioxidant defense. The transporter has 12 transmembrane domains with intracellular N- and C-termini, and like other transporter proteins can undergo various conformational changes while switching the ligand accessibilities from intracellular to extracellular site. In the present study, we generated two homology models of human xCT in two distinct conformations: inward-facing occluded state and outward-facing open state. Our results indicated the substrate translocation channel composed of transmembrane helices TMs 1, 3, 6, 8, and 10. We docked anionic L-cystine and L-glutamate within the cavities to assess the two distinct binding scenarios for xCT as antiporter. We also assessed the interactions between the ligands and transporter and observed that ligands bind to similar residues within the channel. Using MM-PBSA/MM-GBSA approach, we computed the binding energies of these ligands to different conformational states. Cystine and glutamate bind xCT with favorable binding energies, with more favorable binding observed in inward occluded state than in outward open state. We further computed the residue-wise decomposition of these binding energies and identified the residues as essential for substrate binding/permeation. Filtering the residues that form favorable energetic contributions to the ligand binding in both the states, our studies suggest T56, A60, R135, A138, V141, Y244, A247, F250, S330, L392, and R396 as critical residues for ligand binding as well as ligand transport for any conformational state adopted by xCT during its transport cycle. .Graphical Abstract.
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Affiliation(s)
- Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Sector 81, Knowledge City, SAS, Nagar, Punjab, India.
| | - C R Anirudh
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Sector 81, Knowledge City, SAS, Nagar, Punjab, India
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19
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Walseng E, Roche PA. Monitoring Protein Endocytosis and Recycling Using FACS-Based Assays. Methods Mol Biol 2019; 1988:279-88. [PMID: 31147947 DOI: 10.1007/978-1-4939-9450-2_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Cell surface MHC class II (MHC-II) is known to internalize and can recycle back to the plasma membrane from endosomes in antigen presenting cells. We now describe a simple protocol that allows one to follow the internalization kinetics of proteins from the surface of cells. Furthermore, a simple adaptation of this assay allows one to monitor the rate of appearance of internalized proteins back to the plasma membrane. This assay allows for quantitation of trafficking of proteins on even rare subsets of cells, something that is not possible with traditional biochemical assays.
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20
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Huang J, Li X, Shi X, Zhu M, Wang J, Huang S, Huang X, Wang H, Li L, Deng H, Zhou Y, Mao J, Long Z, Ma Z, Ye W, Pan J, Xi X, Jin J. Platelet integrin αIIbβ3: signal transduction, regulation, and its therapeutic targeting. J Hematol Oncol 2019; 12:26. [PMID: 30845955 PMCID: PMC6407232 DOI: 10.1186/s13045-019-0709-6] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 02/21/2019] [Indexed: 12/18/2022] Open
Abstract
Integrins are a family of transmembrane glycoprotein signaling receptors that can transmit bioinformation bidirectionally across the plasma membrane. Integrin αIIbβ3 is expressed at a high level in platelets and their progenitors, where it plays a central role in platelet functions, hemostasis, and arterial thrombosis. Integrin αIIbβ3 also participates in cancer progression, such as tumor cell proliferation and metastasis. In resting platelets, integrin αIIbβ3 adopts an inactive conformation. Upon agonist stimulation, the transduction of inside-out signals leads integrin αIIbβ3 to switch from a low- to high-affinity state for fibrinogen and other ligands. Ligand binding causes integrin clustering and subsequently promotes outside-in signaling, which initiates and amplifies a range of cellular events to drive essential platelet functions such as spreading, aggregation, clot retraction, and thrombus consolidation. Regulation of the bidirectional signaling of integrin αIIbβ3 requires the involvement of numerous interacting proteins, which associate with the cytoplasmic tails of αIIbβ3 in particular. Integrin αIIbβ3 and its signaling pathways are considered promising targets for antithrombotic therapy. This review describes the bidirectional signal transduction of integrin αIIbβ3 in platelets, as well as the proteins responsible for its regulation and therapeutic agents that target integrin αIIbβ3 and its signaling pathways.
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Affiliation(s)
- Jiansong Huang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xia Li
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaofeng Shi
- Department of Hematology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Mark Zhu
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jinghan Wang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shujuan Huang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xin Huang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Huafeng Wang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Ling Li
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Huan Deng
- Department of Pathology, The Fourth Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yulan Zhou
- Department of Hematology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jianhua Mao
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Sino-French Research Centre for Life Sciences and Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhangbiao Long
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhixin Ma
- Clinical Prenatal Diagnosis Center, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wenle Ye
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jiajia Pan
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaodong Xi
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Sino-French Research Centre for Life Sciences and Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jie Jin
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China. .,Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Hangzhou, Zhejiang, China. .,Institute of Hematology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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21
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Leal-Gutiérrez JD, Elzo MA, Johnson DD, Hamblen H, Mateescu RG. Genome wide association and gene enrichment analysis reveal membrane anchoring and structural proteins associated with meat quality in beef. BMC Genomics 2019; 20:151. [PMID: 30791866 PMCID: PMC6385435 DOI: 10.1186/s12864-019-5518-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 02/07/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Meat quality related phenotypes are difficult and expensive to measure and predict but are ideal candidates for genomic selection if genetic markers that account for a worthwhile proportion of the phenotypic variation can be identified. The objectives of this study were: 1) to perform genome wide association analyses for Warner-Bratzler Shear Force (WBSF), marbling, cooking loss, tenderness, juiciness, connective tissue and flavor; 2) to determine enriched pathways present in each genome wide association analysis; and 3) to identify potential candidate genes with multiple quantitative trait loci (QTL) associated with meat quality. RESULTS The WBSF, marbling and cooking loss traits were measured in longissimus dorsi muscle from 672 steers. Out of these, 495 animals were used to measure tenderness, juiciness, connective tissue and flavor by a sensory panel. All animals were genotyped for 221,077 markers and included in a genome wide association analysis. A total number of 68 genomic regions covering 52 genes were identified using the whole genome association approach; 48% of these genes encode transmembrane proteins or membrane associated molecules. Two enrichment analysis were performed: a tissue restricted gene enrichment applying a correlation analysis between raw associated single nucleotide polymorphisms (SNPs) by trait, and a functional classification analysis performed using the DAVID Bioinformatic Resources 6.8 server. The tissue restricted gene enrichment approach identified eleven pathways including "Endoplasmic reticulum membrane" that influenced multiple traits simultaneously. The DAVID functional classification analysis uncovered eleven clusters related to transmembrane or structural proteins. A gene network was constructed where the number of raw associated uncorrelated SNPs for each gene across all traits was used as a weight. A multiple SNP association analysis was performed for the top five most connected genes in the gene-trait network. The gene network identified the EVC2, ANXA10 and PKHD1 genes as potentially harboring multiple QTLs. Polymorphisms identified in structural proteins can modulate two different processes with direct effect on meat quality: in vivo myocyte cytoskeletal organization and postmortem proteolysis. CONCLUSION The main result from the present analysis is the uncovering of several candidate genes associated with meat quality that have structural function in the skeletal muscle.
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Affiliation(s)
| | - Mauricio A. Elzo
- Department of Animal Sciences, University of Florida, Gainesville, FL USA
| | - D. Dwain Johnson
- Department of Animal Sciences, University of Florida, Gainesville, FL USA
| | - Heather Hamblen
- Department of Animal Sciences, University of Florida, Gainesville, FL USA
| | - Raluca G. Mateescu
- Department of Animal Sciences, University of Florida, Gainesville, FL USA
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22
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Abstract
Protein-protein interactions (PPIs) are responsible for a number of key physiological processes in the living cells and underlie the pathomechanism of many diseases. Nowadays, along with the concept of so-called "hot spots" in protein-protein interactions, which are well-defined interface regions responsible for most of the binding energy, these interfaces can be targeted with modulators. In order to apply structure-based design techniques to design PPIs modulators, a three-dimensional structure of protein complex has to be available. In this context in silico approaches, in particular protein-protein docking, are a valuable complement to experimental methods for elucidating 3D structure of protein complexes. Protein-protein docking is easy to use and does not require significant computer resources and time (in contrast to molecular dynamics) and it results in 3D structure of a protein complex (in contrast to sequence-based methods of predicting binding interfaces). However, protein-protein docking cannot address all the aspects of protein dynamics, in particular the global conformational changes during protein complex formation. In spite of this fact, protein-protein docking is widely used to model complexes of water-soluble proteins and less commonly to predict structures of transmembrane protein assemblies, including dimers and oligomers of G protein-coupled receptors (GPCRs). In this chapter we review the principles of protein-protein docking, available algorithms and software and discuss the recent examples, benefits, and drawbacks of protein-protein docking application to water-soluble proteins, membrane anchoring and transmembrane proteins, including GPCRs.
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Affiliation(s)
- Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, Lublin, Poland. .,School of Pharmacy, University of Eastern Finland, Kuopio, Finland.
| | - Damian Bartuzi
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, Lublin, Poland
| | - Tomasz Maciej Stępniewski
- GPCR Drug Discovery Group, Research Programme on Biomedical Informatics (GRIB), Universitat Pompeu Fabra (UPF)-Hospital del Mar Medical Research Institute (IMIM), Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain
| | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, Lublin, Poland
| | - Jana Selent
- GPCR Drug Discovery Group, Research Programme on Biomedical Informatics (GRIB), Universitat Pompeu Fabra (UPF)-Hospital del Mar Medical Research Institute (IMIM), Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain
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23
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Bremmer F. [Identification of diagnostic tumour markers and therapeutic targets in testicular tumours]. Pathologe 2018; 39:215-20. [PMID: 30206653 DOI: 10.1007/s00292-018-0493-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Today, tumour classification has been expanded due to immunohistochemical and molecular-pathological analyses due to corresponding patterns/profiles of protein and gene expression. The latter analyses often include growth factors and their ligands, intracellular signalling pathways, DNA-binding proteins, and oncogenes and suppressor genes, thus functionally including primarily the regulation of growth including angiogenesis and apoptosis as well as the induction of metastases to adhesion and migration disorders. Based on observations that testicular tumours often show microcalcifications, possibly due to impaired calcium metabolism, we focused on calcium-dependent transmembrane proteins, particularly cadherins, in the search for new tumour markers and therapeutic targets. N‑cadherin is expressed differently in the various subtypes of germ cell tumours and is useful in N‑cadherin-positive germ cell tumours as a novel therapeutic targeting structure, particularly in cisplatin resistance, due to functional analysis. In the tumours of the sex cord stroma beta-catenin and the transcription factor SOX-9 give a clear classification of these tumours. Thus, morphological investigations prove to be pilot experiments to purposefully narrow the spectrum of functionally important proteins and thus to establish promising new differential diagnostic markers or target structures.
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24
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Abstract
Many computational methods are available for predicting protein sorting in bacteria. When comparing them, it is important to know that they can be grouped into three fundamentally different approaches: signal-based, global-property-based and homology-based prediction. In this chapter, the strengths and drawbacks of each of these approaches is described through many examples of methods that predict secretion, integration into membranes, or subcellular locations in general. The aim of this chapter is to provide a user-level introduction to the field with a minimum of computational theory.
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Affiliation(s)
- Henrik Nielsen
- Technical University of Denmark, Kemitorvet, Building 208, DK-2800, Kgs. Lyngby, Denmark.
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25
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Abstract
The concept of protein intrinsic disorder persistently penetrates into all areas of modern protein science. It cannot be ignored anymore, and cannot be shrugged off, as it represents a vital feature (or, more correctly, a broad spectrum of important features), which, when added to and mixed with features arising from the well established protein structure-function paradigm, complete the picture of a functioning protein. The field of protein intrinsic disorder is very dynamic and fast developing. This Multi-Author Review represents a snapshot of this field by introducing some recent advances. Articles assembled in this Multi-Author Review introduce some of the new aspects of intrinsic disorder, outline some fascinating ideas related to the intrinsically disordered proteins, their structure, and functionality, and show challenges related to the analysis of proteins carrying intrinsic disorder.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL, 33612, USA. .,Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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26
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Abstract
Protein-protein interactions (PPIs) play an essential role in all biological processes. In vivo, PPIs occur dynamically and depend on extracellular cues. To discover novel protein-protein interactions in mammalian cells, we developed a high-throughput automated technology called LUMIER (LUminescence-based Mammalian IntERactome). In this approach, we co-express a Luciferase (LUC)-tagged fusion protein along with a Flag-tagged protein in an efficiently transfectable cell line such as HEK-293T cells. The interaction between the two proteins is determined by co-immunoprecipitation using an anti-Flag antibody, and the presence of the LUC-tagged interactor in the complex is subsequently detected via its luciferase activity. LUMIER can easily detect transmembrane protein partners, interactions that are signaling- or splice isoform-dependent, as well as those that may occur only in the presence of posttranslational modifications. Using various collections of Flag-tagged proteins, we have generated protein interaction networks for several TGF-β family receptors, Wnt pathway members, and have systematically analyzed the effect of neural-specific alternative splicing on protein interaction networks. The results have provided important insights into the physiological and functional relevance of some of the novel interactions found. LUMIER is highly scalable and can be used for both low- and high-throughput strategies. LUMIER is thus a valuable tool for the identification and characterization of dynamically regulated PPIs in mammalian systems. Here, we describe a manual version of LUMIER in a 96-well format that can be easily implemented in any laboratory.
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Affiliation(s)
- Miriam Barrios-Rodiles
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, Canada, M5G 1X5.
| | - Jonathan D Ellis
- Donnelly Centre, University of Toronto, Toronto, ON, Canada, M5S 3E1
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON, Canada, M5S 3E1
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jeffrey L Wrana
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, Canada, M5G 1X5
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Breast Cancer Research, Mary Janigan Chair in Molecular Cancer Therapeutics, Toronto, ON, Canada
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Qudrat A, Truong K. Modular assembly of synthetic proteins that span the plasma membrane in mammalian cells. BMC Biotechnol 2016; 16:88. [PMID: 27938351 PMCID: PMC5148844 DOI: 10.1186/s12896-016-0320-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 12/07/2016] [Indexed: 11/26/2022] Open
Abstract
Background To achieve synthetic control over how a cell responds to other cells or the extracellular environment, it is important to reliably engineer proteins that can traffic and span the plasma membrane. Using a modular approach to assemble proteins, we identified the minimum necessary components required to engineer such membrane-spanning proteins with predictable orientation in mammalian cells. Results While a transmembrane domain (TM) fused to the N-terminus of a protein is sufficient to traffic it to the endoplasmic reticulum (ER), an additional signal peptidase cleavage site downstream of this TM enhanced sorting out of the ER. Next, a second TM in the synthetic protein helped anchor and accumulate the membrane-spanning protein on the plasma membrane. The orientation of the components of the synthetic protein were determined through measuring intracellular Ca2+ signaling using the R-GECO biosensor and through measuring extracellular quenching of yellow fluorescent protein variants by saturating acidic and salt conditions. Conclusions This work forms the basis of engineering novel proteins that span the plasma membrane to potentially control intracellular responses to extracellular conditions. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0320-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anam Qudrat
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street Room 407, Rosebrugh Building, Toronto, ON, M5S 3G9, Canada
| | - Kevin Truong
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street Room 407, Rosebrugh Building, Toronto, ON, M5S 3G9, Canada. .,Edward S. Rogers, Sr. Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Circle, Toronto, ON, M5S 3G4, Canada.
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Kandemir-Cavas C, Cavas L, Alyuruk H. The Topology Prediction of Membrane Proteins: A Web-Based Tutorial. Interdiscip Sci 2018; 10:291-6. [PMID: 27718149 DOI: 10.1007/s12539-016-0190-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 09/19/2016] [Accepted: 09/22/2016] [Indexed: 01/15/2023]
Abstract
There is a great need for development of educational materials on the transfer of current bioinformatics knowledge to undergraduate students in bioscience departments. In this study, it is aimed to prepare an example in silico laboratory tutorial on the topology prediction of membrane proteins by bioinformatics tools. This laboratory tutorial is prepared for biochemistry lessons at bioscience departments (biology, chemistry, biochemistry, molecular biology and genetics, and faculty of medicine). The tutorial is intended for students who have not taken a bioinformatics course yet or already have taken a course as an introduction to bioinformatics. The tutorial is based on step-by-step explanations with illustrations. It can be applied under supervision of an instructor in the lessons, or it can be used as a self-study guide by students. In the tutorial, membrane-spanning regions and α-helices of membrane proteins were predicted by internet-based bioinformatics tools. According to the results achieved from internet-based bioinformatics tools, the algorithms and parameters used were effective on the accuracy of prediction. The importance of this laboratory tutorial lies on the facts that it provides an introduction to the bioinformatics and that it also demonstrates an in silico laboratory application to the students at natural sciences. The presented example education material is applicable easily at all departments that have internet connection. This study presents an alternative education material to the students in biochemistry laboratories in addition to classical laboratory experiments.
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Ilango P, Mahalingam A, Parthasarathy H, Katamreddy V, Subbareddy V. Evaluation of TLR2 and 4 in Chronic Periodontitis. J Clin Diagn Res 2016; 10:ZC86-9. [PMID: 27504418 DOI: 10.7860/jcdr/2016/18353.8027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/01/2016] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Periodontal disease is the major cause of adult tooth loss and is commonly characterized by a chronic inflammation caused by infection due to oral bacteria. Members of Toll-Like Receptor (TLR) family recognize conserved microbial structures, such as bacterial lipopolysaccharides and activate signalling pathways that result in immune responses against microbial infections. AIM The aim of the present study was to assess the mRNA expression of Toll-Like Receptor 2 and 4 in tissues with or without chronic periodontitis. MATERIALS AND METHODS Gingival tissue samples were collected from controls (30 subjects with healthy periodontal tissues) and experimental group (30 subjects with chronic periodontitis). Total RNA was extracted and RT-PCR was done for evaluation of TLR-2 and TLR-4. Mann Whitney U-test, Pearson Chi-square Test was used for statistics. RESULTS The results showed that there is a significant (p-value= 0.004) association between TLR-4 and the experimental group comprising of chronic periodontitis patients in comparison to the insignificant (p-value= 0.085) TLR-2 expression. CONCLUSION This study concludes that TLR-2 and TLR-4 expressed in the gingival tissues recognize different bacterial cell wall components thus helping us to associate its potential in diagnosing periodontal disease. Hence, in the future, these scientific findings can pave the way in using TLR as a diagnostic biomarker for periodontal disease.
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Affiliation(s)
- Paavai Ilango
- Reader, Department of Periodontology, Priyadarshini Dental College and Hospital , Pandur, Tamil Nadu, India
| | - Arulpari Mahalingam
- Reader, Department of Pedodontics, Thai Moogambigai Dental College and Hospital , Chennai, Tamil Nadu, India
| | - Harinath Parthasarathy
- Professor, Department of Periodontology, SRM Dental College and Hospital , Chennai, Tamil Nadu, India
| | - Vineela Katamreddy
- Reader, Department of Periodontology, Indira Gandhi Institute of Dental Sciences , Pondicherry, Tamil Nadu, India
| | - Venkat Subbareddy
- Reader, Department of Periodontology, CKS Teja Dental College and Hospital , Tirupathi, Andhra Pradesh, India
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Hanukoglu I, Hanukoglu A. Epithelial sodium channel (ENaC) family: Phylogeny, structure-function, tissue distribution, and associated inherited diseases. Gene 2016; 579:95-132. [PMID: 26772908 PMCID: PMC4756657 DOI: 10.1016/j.gene.2015.12.061] [Citation(s) in RCA: 238] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/20/2015] [Accepted: 12/22/2015] [Indexed: 01/24/2023]
Abstract
The epithelial sodium channel (ENaC) is composed of three homologous subunits and allows the flow of Na(+) ions across high resistance epithelia, maintaining body salt and water homeostasis. ENaC dependent reabsorption of Na(+) in the kidney tubules regulates extracellular fluid (ECF) volume and blood pressure by modulating osmolarity. In multi-ciliated cells, ENaC is located in cilia and plays an essential role in the regulation of epithelial surface liquid volume necessary for cilial transport of mucus and gametes in the respiratory and reproductive tracts respectively. The subunits that form ENaC (named as alpha, beta, gamma and delta, encoded by genes SCNN1A, SCNN1B, SCNN1G, and SCNN1D) are members of the ENaC/Degenerin superfamily. The earliest appearance of ENaC orthologs is in the genomes of the most ancient vertebrate taxon, Cyclostomata (jawless vertebrates) including lampreys, followed by earliest representatives of Gnathostomata (jawed vertebrates) including cartilaginous sharks. Among Euteleostomi (bony vertebrates), Actinopterygii (ray finned-fishes) branch has lost ENaC genes. Yet, most animals in the Sarcopterygii (lobe-finned fish) branch including Tetrapoda, amphibians and amniotes (lizards, crocodiles, birds, and mammals), have four ENaC paralogs. We compared the sequences of ENaC orthologs from 20 species and established criteria for the identification of ENaC orthologs and paralogs, and their distinction from other members of the ENaC/Degenerin superfamily, especially ASIC family. Differences between ENaCs and ASICs are summarized in view of their physiological functions and tissue distributions. Structural motifs that are conserved throughout vertebrate ENaCs are highlighted. We also present a comparative overview of the genotype-phenotype relationships in inherited diseases associated with ENaC mutations, including multisystem pseudohypoaldosteronism (PHA1B), Liddle syndrome, cystic fibrosis-like disease and essential hypertension.
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Affiliation(s)
- Israel Hanukoglu
- Laboratory of Cell Biology, Faculty of Natural Sciences, Ariel University, Ariel, Israel.
| | - Aaron Hanukoglu
- Division of Pediatric Endocrinology, E. Wolfson Medical Center, Holon, Israel; Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
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Abstract
Toll-like receptors are type I membrane proteins and bind other membrane proteins often via a specific interaction between transmembrane domains. The co-immunoprecipitation assay is a widely used biochemical technique for assessing interactions among proteins in cell lysates or tissue extracts. By isolating a native protein complex with a specific antibody against a protein of interest, followed by western blotting with an antibody for a binding partner, the co-immunoprecipitation assay can be used to confirm a putative interaction between two proteins. The co-immunoprecipitation assay can also be combined with a proteomics approach such as protein mass spectrometry to build an interactome of a target protein. Despite its usefulness and popularity to probe protein interactions within complex biological samples, the co-immunoprecipitation assay of membrane proteins is rather tricky, often resulting in false data. Here, we describe a co-immunoprecipitation method for analyzing interactions between toll-like receptors and other membrane proteins, using the interaction between TLR9 and UNC93B1 as an example. Especially, we describe an optimal cell lysis and sample preparation method to preserve protein interactions mediated by transmembrane domains.
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Affiliation(s)
- Yu-Ran Lee
- Division of Integrative Biosciences and Biotechnologies, Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Republic of Korea
| | - Wondae Kang
- Division of Integrative Biosciences and Biotechnologies, Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Republic of Korea
| | - You-Me Kim
- Division of Integrative Biosciences and Biotechnologies, Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Republic of Korea.
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Sanmartí-Espinal M, Galve R, Iavicoli P, Persuy MA, Pajot-Augy E, Marco MP, Samitier J. Immunochemical strategy for quantification of G-coupled olfactory receptor proteins on natural nanovesicles. Colloids Surf B Biointerfaces 2015; 139:269-76. [PMID: 26724468 DOI: 10.1016/j.colsurfb.2015.11.062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 10/06/2015] [Accepted: 11/23/2015] [Indexed: 02/01/2023]
Abstract
Cell membrane proteins are involved in a variety of biochemical pathways and therefore constitute important targets for therapy and development of new drugs. Bioanalytical platforms and binding assays using these membrane protein receptors for drug screening or diagnostic require the construction of well-characterized liposome and lipid bilayer arrays that act as support to prevent protein denaturation during biochip processing. Quantification of the protein receptors in the lipid membrane arrays is a key issue in order to produce reproducible and well-characterized chips. Herein, we report a novel immunochemical analytical approach for the quantification of membrane proteins (i.e., G-protein-coupled receptor, GPCR) in nanovesicles (NVs). The procedure allows direct determination of tagged receptors (i.e., c-myc tag) without any previous protein purification or extraction steps. The immunochemical method is based on a microplate ELISA format and quantifies this tag on proteins embedded in NVs with detectability in the picomolar range, using protein bioconjugates as reference standards. The applicability of the method is demonstrated through the quantification of the c-myc-olfactory receptor (OR, c-myc-OR1740) in the cell membrane NVs. The reported method opens the possibility to develop well-characterized drug-screening platforms based on G-coupled proteins embedded on membranes.
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Affiliation(s)
- Marta Sanmartí-Espinal
- IBEC-Institute for Bioengineering of Catalonia, Nanobioengineering Group, C/Baldiri Reixac, 15-21, 08028 Barcelona, Spain; Department of Electronics, University of Barcelona, C/Martí i Franquès 1, 08028 Barcelona, Spain.
| | - Roger Galve
- Nb4D-Nanobiotechnology for Diagnostics, IQAC-CSIC, C/Jordi Girona, 18-26, 08034 Barcelona, Spain; Centro de Investigación Biomédica en Red en Bioingeniería Biomateriales y Nanomedicina (CIBER-BBN), C/María de Luna 11, Edificio CEEI, 50018 Zaragoza, Spain
| | - Patrizia Iavicoli
- IBEC-Institute for Bioengineering of Catalonia, Nanobioengineering Group, C/Baldiri Reixac, 15-21, 08028 Barcelona, Spain
| | | | | | - M-Pilar Marco
- Nb4D-Nanobiotechnology for Diagnostics, IQAC-CSIC, C/Jordi Girona, 18-26, 08034 Barcelona, Spain; Centro de Investigación Biomédica en Red en Bioingeniería Biomateriales y Nanomedicina (CIBER-BBN), C/María de Luna 11, Edificio CEEI, 50018 Zaragoza, Spain
| | - Josep Samitier
- IBEC-Institute for Bioengineering of Catalonia, Nanobioengineering Group, C/Baldiri Reixac, 15-21, 08028 Barcelona, Spain; Department of Electronics, University of Barcelona, C/Martí i Franquès 1, 08028 Barcelona, Spain; Centro de Investigación Biomédica en Red en Bioingeniería Biomateriales y Nanomedicina (CIBER-BBN), C/María de Luna 11, Edificio CEEI, 50018 Zaragoza, Spain.
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Goparaju G, Fry BA, Chobot SE, Wiedman G, Moser CC, Leslie Dutton P, Discher BM. First principles design of a core bioenergetic transmembrane electron-transfer protein. Biochim Biophys Acta 2016; 1857:503-12. [PMID: 26672896 DOI: 10.1016/j.bbabio.2015.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 11/14/2015] [Accepted: 12/01/2015] [Indexed: 12/26/2022]
Abstract
Here we describe the design, Escherichia coli expression and characterization of a simplified, adaptable and functionally transparent single chain 4-α-helix transmembrane protein frame that binds multiple heme and light activatable porphyrins. Such man-made cofactor-binding oxidoreductases, designed from first principles with minimal reference to natural protein sequences, are known as maquettes. This design is an adaptable frame aiming to uncover core engineering principles governing bioenergetic transmembrane electron-transfer function and recapitulate protein archetypes proposed to represent the origins of photosynthesis. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Richards SA, Stutzer C, Bosman AM, Maritz-Olivier C. Transmembrane proteins--Mining the cattle tick transcriptome. Ticks Tick Borne Dis 2015; 6:695-710. [PMID: 26096851 DOI: 10.1016/j.ttbdis.2015.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/12/2015] [Accepted: 06/08/2015] [Indexed: 11/28/2022]
Abstract
Managing the spread and load of pathogen-transmitting ticks is an important task worldwide. The cattle tick, Rhipicephalus microplus, not only impacts the economy through losses in dairy and meat production, but also raises concerns for human health in regards to the potential of certain transmitted pathogens becoming zoonotic. However, novel strategies to control R. microplus are hindered by lack of understanding tick biology and the discovery of suitable vaccine or acaricide targets. The importance of transmembrane proteins as vaccine targets are well known, as is the case in tick vaccines with Bm86 as antigen. In this study, we describe the localization and functional annotation of 878 putative transmembrane proteins. Thirty proteins could be confirmed in the R. microplus gut using LC-MS/MS analysis and their roles in tick biology are discussed. To the best of our knowledge, 19 targets have not been reported before in any proteomics study in various tick species and the possibility of using the identified proteins as targets for tick control are discussed. Although tissue expression of identified putative proteins through expansive proteomics is necessary, this study demonstrates the possibility of using bioinformatics for the identification of targets for further evaluation in tick control strategies.
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Affiliation(s)
- Sabine A Richards
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of Pretoria, South Africa
| | - Christian Stutzer
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of Pretoria, South Africa
| | - Anna-Mari Bosman
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, South Africa
| | - Christine Maritz-Olivier
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of Pretoria, South Africa.
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Hagemeijer MC, Monastyrska I, Griffith J, van der Sluijs P, Voortman J, van Bergen en Henegouwen PM, Vonk AM, Rottier PJM, Reggiori F, de Haan CAM. Membrane rearrangements mediated by coronavirus nonstructural proteins 3 and 4. Virology 2014; 458-459:125-35. [PMID: 24928045 PMCID: PMC7111329 DOI: 10.1016/j.virol.2014.04.027] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 02/26/2014] [Accepted: 04/22/2014] [Indexed: 01/20/2023]
Abstract
Coronaviruses replicate their genomes in association with rearranged cellular membranes. The coronavirus nonstructural integral membrane proteins (nsps) 3, 4 and 6, are key players in the formation of the rearranged membranes. Previously, we demonstrated that nsp3 and nsp4 interact and that their co-expression results in the relocalization of these proteins from the endoplasmic reticulum (ER) into discrete perinuclear foci. We now show that these foci correspond to areas of rearranged ER-derived membranes, which display increased membrane curvature. These structures, which were able to recruit other nsps, were only detected when nsp3 and nsp4 were derived from the same coronavirus species. We propose, based on the analysis of a large number of nsp3 and nsp4 mutants, that interaction between the large luminal loops of these proteins drives the formation of membrane rearrangements, onto which the coronavirus replication-transcription complexes assemble in infected cells.
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Affiliation(s)
- Marne C Hagemeijer
- Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Iryna Monastyrska
- Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Janice Griffith
- Department of Cell Biology and Institute of Biomembranes, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Peter van der Sluijs
- Department of Cell Biology and Institute of Biomembranes, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Jarno Voortman
- Division of Cell Biology, Department of Biology, Science Faculty, Utrecht University, Utrecht, The Netherlands
| | | | - Annelotte M Vonk
- Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Peter J M Rottier
- Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Fulvio Reggiori
- Department of Cell Biology and Institute of Biomembranes, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Cornelis A M de Haan
- Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands.
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Paavilainen S, Grandy D, Karelehto E, Chang E, Susi P, Erdjument-Bromage H, Nikolov D, Himanen J. High-level expression of a full-length Eph receptor. Protein Expr Purif 2013; 92:112-8. [PMID: 24036371 DOI: 10.1016/j.pep.2013.08.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 08/21/2013] [Accepted: 08/23/2013] [Indexed: 01/04/2023]
Abstract
Eph receptors are the largest family of Receptor Tyrosine Kinases containing a single membrane-spanning segment. They are involved in a various developmental and cell-cell communication events. Although there is extensive structural information available on both the extra- and intracellular regions of Eph's in isolation, no structures are available for the entire receptor. To facilitate structural studies on functionally relevant Eph/ephrin complexes, we have developed an expression system for producing the full-length human EphA2 receptor. We successfully expressed milligram amounts of the receptor using baculovirus-based vector and insect cells. We were also able to extract the protein from the cell membranes and purify it to near homogeneity in two simple steps. The purified receptor was shown to retain its biological activity in terms of both binding to its functional ligands and being able to auto-phosphorylate the key tyrosine residues of the cytoplasmic kinase domain.
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Affiliation(s)
- Sari Paavilainen
- Joint Biotechnology Lab, University of Turku, BioCity 6A, 20520 Turku, Finland
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Kaczor AA, Selent J, Sanz F, Pastor M. Modeling Complexes of Transmembrane Proteins: Systematic Analysis of ProteinProtein Docking Tools. Mol Inform 2013; 32:717-33. [PMID: 27480064 DOI: 10.1002/minf.201200150] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 05/16/2013] [Indexed: 01/25/2023]
Abstract
Proteinprotein docking methodology is frequently used to model complexes of transmembrane proteins, in particular oligomers of G protein-coupled receptors (GPCRs), even if its applicability for these systems has never been fully validated. The aim of this work is to perform a systematic study on the suitability of some widely-used proteinprotein docking software for modeling complexes of transmembrane proteins. In this study we tested the programs ZDOCK, ClusPro, HEX, GRAMM-X, PatchDock, SymmDock, and HADDOCK, using a set of membrane protein oligomers for which the 3D structure has been obtained experimentally, including opsin dimer, the recently published chemokine CXCR4 and kappa opioid receptor dimers. The results show that the docking success depends on the applied docking algorithm and scoring functions, but also on inherent structural features of the transmembrane proteins. Thus, proteins with large interface surfaces, rich in surface cavities, high-order symmetry, and small conformational change upon complex formation are well predicted more often than proteins without these features. The results of this systematic analysis provide guidelines that can be used for obtaining reliable models of transmembrane proteins, including GPCRs. Therefore they can be useful for the application of structure-based methods in drug discovery projects involving these targets.
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Affiliation(s)
- Agnieszka A Kaczor
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute). Dr. Aiguader 88, Barcelona, Spain phone: +48 815357365, fax: +48 815357355; phone: +34 933160515, fax: +34 93 316 0550. .,Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Faculty of Pharmacy with Division for Medical Analytics, Medical University of Lublin 4A Chodźki St., PL-20059 Lublin, Poland.
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute). Dr. Aiguader 88, Barcelona, Spain phone: +48 815357365, fax: +48 815357355; phone: +34 933160515, fax: +34 93 316 0550.
| | - Ferran Sanz
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute). Dr. Aiguader 88, Barcelona, Spain phone: +48 815357365, fax: +48 815357355; phone: +34 933160515, fax: +34 93 316 0550
| | - Manuel Pastor
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute). Dr. Aiguader 88, Barcelona, Spain phone: +48 815357365, fax: +48 815357355; phone: +34 933160515, fax: +34 93 316 0550
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Abstract
The E5 proteins are short transmembrane proteins encoded by many animal and human papillomaviruses. These proteins display transforming activity in cultured cells and animals, and they presumably also play a role in the productive virus life cycle. The E5 proteins are thought to act by modulating the activity of cellular proteins. Here, we describe the biological activities of the best-studied E5 proteins and discuss the evidence implicating specific protein targets and pathways in mediating these activities. The primary target of the 44-amino acid BPV1 E5 protein is the PDGF β receptor, whereas the EGF receptor appears to be an important target of the 83-amino acid HPV16 E5 protein. Both E5 proteins also bind to the vacuolar ATPase and affect MHC class I expression and cell-cell communication. Continued studies of the E5 proteins will elucidate important aspects of transmembrane protein-protein interactions, cellular signal transduction, cell biology, virus replication, and tumorigenesis.
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Affiliation(s)
- Daniel DiMaio
- Department of Genetics, Yale School of Medicine, USA; Department of Therapeutic Radiology, Yale School of Medicine, USA; Department of Molecular Biophysics & Biochemistry, Yale University, USA; Yale Cancer Center, USA.
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