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Yang G, Zhang L, Xie S, Wu J, Khan M, Zhang Y, Liu L, Li J. Protonation State-Induced Unfolding of Protein Secondary Structure in the Gas Phase. J Phys Chem Lett 2024:9374-9379. [PMID: 39240543 DOI: 10.1021/acs.jpclett.4c02103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024]
Abstract
The combination of infrared spectroscopy (IR) and ion mobility mass spectrometry (IM-MS) has revealed that protein secondary structures are retained upon transformation from aqueous solution to the gas phase under gentle conditions. Yet the details about where and how these structural elements are embedded in the gas phase remain elusive. In this study, we employ long time scale molecular dynamics (MD) simulations to examine the extent to which proteins retain their solution structures and the impact of protonation state on the stability of secondary structures in the gas phase. Our investigation focuses on two well-studied proteins, myoglobin and β-lactoglobulin, representing typical helical and β-sheet proteins, respectively. Our simulations accurately reproduce the experimental collision cross section (CCS) data measured by IM-MS. Based on accurately reproducing previous experimental collision cross section data and dominant secondary structural species obtained from IM-MS and IR, we confirm that both proteins largely retain their native secondary structural components upon passing from aqueous solution to the gas phase. However, we observe significant reductions in secondary structure contents (19.2 ± 1.2% for myoglobin and 7.3 ± 0.6% for β-lactoglobulin) in specific regions predominantly composed of ionizable residues. Further mechanistic analysis suggests that alterations in protonation states of these residues after phase transition induce changes in their local interaction networks and backbone dihedral angles, which potentially promote the unfolding of secondary structures in the gas phase. We anticipate that similar protonation state induced unfolding may be observed in other proteins possessing distinct secondary structures. Further studies on a broader array of proteins will be essential to refine our understanding of protein structural behavior during the transition to the gas phase.
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Affiliation(s)
- Guiqian Yang
- College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Lanbi Zhang
- College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Song Xie
- College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Juhong Wu
- College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Majid Khan
- College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Yongqi Zhang
- College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Lin Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, People's Republic of China
| | - Jinyu Li
- College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
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Persson LJ, Sahin C, Landreh M, Marklund EG. High-Performance Molecular Dynamics Simulations for Native Mass Spectrometry of Large Protein Complexes with the Fast Multipole Method. Anal Chem 2024. [PMID: 39231152 DOI: 10.1021/acs.analchem.4c03272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Native mass spectrometry (MS) is widely employed to study the structures and assemblies of proteins ranging from small monomers to megadalton complexes. Molecular dynamics (MD) simulation is a useful complement as it provides the spatial detail that native MS cannot offer. However, MD simulations performed in the gas phase have suffered from rapidly increasing computational costs with the system size. The primary bottleneck is the calculation of electrostatic forces, which are effective over long distances and must be explicitly computed for each atom pair, precluding efficient use of methods traditionally used to accelerate condensed-phase simulations. As a result, MD simulations have been unable to match the capacity of MS in probing large multimeric protein complexes. Here, we apply the fast multipole method (FMM) for computing the electrostatic forces, recently implemented by Kohnke et al. (J. Chem. Theory Comput., 2020, 16, 6938-6949), showing that it significantly enhances the performance of gas-phase simulations of large proteins. We assess how to achieve adequate accuracy and optimal performance with FMM, finding that it expands the accessible size range and time scales dramatically. Additionally, we simulate a 460 kDa ferritin complex over microsecond time scales, alongside complementary ion mobility (IM)-MS experiments, uncovering conformational changes that are not apparent from the IM-MS data alone.
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Affiliation(s)
- Louise J Persson
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Cagla Sahin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-17165 Solna, Sweden
- Department of Biology, Structural Biology and NMR Laboratory and the Linderstro̷m-Lang Centre for Protein Science, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-17165 Solna, Sweden
- Department of Cell and Molecular Biology, Uppsala University, SE-75124 Uppsala, Sweden
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
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Identification and Tetramer Structure of Hemin-Binding Protein SPD_0310 Linked to Iron Homeostasis and Virulence of Streptococcus pneumoniae. mSystems 2022; 7:e0022122. [PMID: 35414267 PMCID: PMC9238395 DOI: 10.1128/msystems.00221-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Iron and iron-containing compounds are essential for bacterial virulence and host infection. Hemin is an important supplement compound for bacterial survival in an iron-deficient environment. Despite strong interest in hemin metabolism, the detailed mechanism of hemin transportation in Gram-positive bacteria is yet to be reported. The results of our study revealed that the homologous proteins of SPD_0310 were significantly conservative in Gram-positive bacteria (P < 0.001), and these proteins were identified as belonging to an uncharacterized protein family (UPF0371). The results of thermodynamic and kinetic studies have shown that SPD_0310 has a high hemin-binding affinity. Interestingly, we found that the crystal structure of SPD_0310 presented a homotetramer conformation, which is required for hemin binding. SPD_0310 can interact with many hemin-binding proteins (SPD_0090, SPD_1609, and GAPDH) located on the cell surface, which contributes to hemin transfer to the cytoplasm. It also has a high affinity with other iron transporters in the cytoplasm (SPD_0226 and SPD_0227), which facilitates iron redistribution in cells. More importantly, the knockout of the spd_0310 gene (Δspd_0310) resulted in a decrease in the iron content and protein expression levels of many bacterial adhesion factors. Moreover, the animal model showed that the Δspd_0310 strain has a lower virulence than the wild type. Based on the crystallographic and biochemical studies, we inferred that SPD_0310 is a hemin intermediate transporter which contributes to iron homeostasis and further affects the virulence of Streptococcus pneumoniae in the host. Our study provides not only an important theoretical basis for the in-depth elucidation of the hemin transport mechanism in bacteria but also an important candidate target for the development of novel antimicrobial agents based on metal transport systems. IMPORTANCE Iron is an essential element for bacterial virulence and infection of the host. The detailed hemin metabolism in Gram-positive bacteria has rarely been studied. SPD_0310 belongs to the UPF0371 family of proteins, and results of homology analysis and evolutionary tree analysis suggested that it was widely distributed and highly conserved in Gram-positive bacteria. However, the function of the UPF0371 family remains unknown. We successfully determined the crystal structure of apo-SPD_0310, which is a homotetramer. We found that cytoplasmic protein SPD_0310 with a special tetramer structure has a strong hemin-binding ability and interacts with many iron transporters, which facilitates hemin transfer from the extracellular space to the cytoplasm. The results of detailed functional analyses indicated that SPD_0310 may function as a hemin transporter similar to hemoglobin in animals and contributes to bacterial iron homeostasis and virulence. This study provides a novel target for the development of antimicrobial drugs against pathogenic Gram-positive bacteria.
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Ji ZS, Gao GB, Ma YM, Luo JX, Zhang GW, Yang H, Li N, He QY, Lin HS. Highly bioactive iridium metal-complex alleviates spinal cord injury via ROS scavenging and inflammation reduction. Biomaterials 2022; 284:121481. [DOI: 10.1016/j.biomaterials.2022.121481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/15/2022] [Accepted: 03/20/2022] [Indexed: 11/28/2022]
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5
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Koy C, Opuni KFM, Danquah BD, Neamtu A, Glocker MO. Mass Spectrometric and Bio-Computational Binding Strength Analysis of Multiply Charged RNAse S Gas-Phase Complexes Obtained by Electrospray Ionization from Varying In-Solution Equilibrium Conditions. Int J Mol Sci 2021; 22:ijms221910183. [PMID: 34638522 PMCID: PMC8508491 DOI: 10.3390/ijms221910183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 11/18/2022] Open
Abstract
We investigated the influence of a solvent’s composition on the stability of desorbed and multiply charged RNAse S ions by analyzing the non-covalent complex’s gas-phase dissociation processes. RNAse S was dissolved in electrospray ionization-compatible buffers with either increasing organic co-solvent content or different pHs. The direct transition of all the ions and the evaporation of the solvent from all the in-solution components of RNAse S under the respective in-solution conditions by electrospray ionization was followed by a collision-induced dissociation of the surviving non-covalent RNAse S complex ions. Both types of changes of solvent conditions yielded in mass spectrometrically observable differences of the in-solution complexation equilibria. Through quantitative analysis of the dissociation products, i.e., from normalized ion abundances of RNAse S, S-protein, and S-peptide, the apparent kinetic and apparent thermodynamic gas-phase complex properties were deduced. From the experimental data, it is concluded that the stability of RNAse S in the gas phase is independent of its in-solution equilibrium but is sensitive to the complexes’ gas-phase charge states. Bio-computational in-silico studies showed that after desolvation and ionization by electrospray, the remaining binding forces kept the S-peptide and S-protein together in the gas phase predominantly by polar interactions, which indirectly stabilized the in-bulk solution predominating non-polar intermolecular interactions. As polar interactions are sensitive to in-solution protonation, bio-computational results provide an explanation of quantitative experimental data with single amino acid residue resolution.
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Affiliation(s)
- Cornelia Koy
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18057 Rostock, Germany; (C.K.); (K.F.M.O.); (B.D.D.)
| | - Kwabena F. M. Opuni
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18057 Rostock, Germany; (C.K.); (K.F.M.O.); (B.D.D.)
- Department of Pharmaceutical Chemistry, School of Pharmacy, College of Health Science, University of Ghana, P.O. Box LG43, Legon, Ghana
| | - Bright D. Danquah
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18057 Rostock, Germany; (C.K.); (K.F.M.O.); (B.D.D.)
| | - Andrei Neamtu
- Department of Physiology, Grigore T. Popa University of Medicine and Pharmacy of Iasi, Str. Universitatii nr. 16, 700051 Iasi, Romania;
| | - Michael O. Glocker
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18057 Rostock, Germany; (C.K.); (K.F.M.O.); (B.D.D.)
- Correspondence: ; Tel.: +49-381-494-4930; Fax: +49-381-494-4932
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Ji ZS, Liu QL, Zhang JF, Yang YH, Li J, Zhang GW, Tan MH, Lin HS, Guo GQ. SUMOylation of spastin promotes the internalization of GluA1 and regulates dendritic spine morphology by targeting microtubule dynamics. Neurobiol Dis 2020; 146:105133. [PMID: 33049318 DOI: 10.1016/j.nbd.2020.105133] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/24/2020] [Accepted: 10/06/2020] [Indexed: 10/23/2022] Open
Abstract
Dendritic spines are specialized structures involved in neuronal processes on which excitatory synaptic contact occurs. The microtubule cytoskeleton is vital for maintaining spine morphology and mature synapses. Spastin is related to microtubule-severing proteases and is involved in synaptic bouton formation. However, it is not yet known if spastin can be modified by Small Ubiquitin-like Modifier (SUMO) or how this modification regulates dendritic spines. Spastin was shown to be SUMOylated at K427, and its deSUMOylation promoted microtubule stability. In addition, SUMOylation of spastin was shown to affect signalling pathways associated with long term synaptic depression. SUMOylated spastin promoted the development of dendrites and dendritic spines. Moreover, SUMOylated spastin regulated endocytosis and affected the transport of the AMPA receptor, GluA1. Our findings suggest that SUMOylation of spastin promotes GluA1 internalization and regulates dendritic spine morphology through targeting of microtubule dynamics.
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Affiliation(s)
- Zhi-Sheng Ji
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, No.601 West Huangpu Avenue, Tianhe, Guangzhou 510630, China
| | - Qiu-Ling Liu
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, No.601 West Huangpu Avenue, Tianhe, Guangzhou 510630, China
| | - Ji-Feng Zhang
- Department of Anatomy, Neuroscience Laboratory for Cognitive and Developmental Disorders, Medical College of Jinan University, No.601 West Huangpu Avenue, Tianhe, Guangzhou 510630, China
| | - Yu-Hao Yang
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, No.601 West Huangpu Avenue, Tianhe, Guangzhou 510630, China
| | - Jiong Li
- Department of Anatomy, Neuroscience Laboratory for Cognitive and Developmental Disorders, Medical College of Jinan University, No.601 West Huangpu Avenue, Tianhe, Guangzhou 510630, China
| | - Guo-Wei Zhang
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, No.601 West Huangpu Avenue, Tianhe, Guangzhou 510630, China
| | - Ming-Hui Tan
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, No.601 West Huangpu Avenue, Tianhe, Guangzhou 510630, China.
| | - Hong-Sheng Lin
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, No.601 West Huangpu Avenue, Tianhe, Guangzhou 510630, China.
| | - Guo-Qing Guo
- Department of Anatomy, Neuroscience Laboratory for Cognitive and Developmental Disorders, Medical College of Jinan University, No.601 West Huangpu Avenue, Tianhe, Guangzhou 510630, China.
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Alvarez-Martin A, Cleland TP, Kavich GM, Janssens K, Newsome GA. Rapid Evaluation of the Debromination Mechanism of Eosin in Oil Paint by Direct Analysis in Real Time and Direct Infusion-Electrospray Ionization Mass Spectrometry. Anal Chem 2019; 91:10856-10863. [DOI: 10.1021/acs.analchem.9b02568] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Alba Alvarez-Martin
- Smithsonian Institution Museum Conservation Institute, 4210 Silver Hill Road, Suitland, Maryland, United States of America
- AXES, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Timothy P. Cleland
- Smithsonian Institution Museum Conservation Institute, 4210 Silver Hill Road, Suitland, Maryland, United States of America
| | - Gwénaëlle M. Kavich
- Smithsonian Institution Museum Conservation Institute, 4210 Silver Hill Road, Suitland, Maryland, United States of America
| | - Koen Janssens
- AXES, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - G. Asher Newsome
- Smithsonian Institution Museum Conservation Institute, 4210 Silver Hill Road, Suitland, Maryland, United States of America
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Liu L, Dong X, Liu Y, Österlund N, Gräslund A, Carloni P, Li J. Role of hydrophobic residues for the gaseous formation of helical motifs. Chem Commun (Camb) 2019; 55:5147-5150. [PMID: 30977489 DOI: 10.1039/c9cc01898k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The secondary structure content of proteins and their complexes may change significantly on passing from aqueous solution to the gas phase (as in mass spectrometry experiments). In this work, we investigate the impact of hydrophobic residues on the formation of the secondary structure of a real protein complex in the gas phase. We focus on a well-studied protein complex, the amyloid-β (1-40) dimer (2Aβ). Molecular dynamics simulations reproduce the results of ion mobility-mass spectrometry experiments. In addition, a helix (not present in the solution) is identified involving 19FFAED23, consistent with infrared spectroscopy data on an Aβ segment. Our simulations further point to the role of hydrophobic residues in the formation of helical motifs - hydrophobic sidechains "shield" helices from being approached by residues that carry hydrogen bond sites. In particular, two hydrophobic phenylalanine residues, F19 and F20, play an important role for the helix, which is induced in the gas phase in spite of the presence of two carboxyl-containing residues.
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Affiliation(s)
- Lin Liu
- College of Chemistry, Fuzhou University, 350002 Fuzhou, China.
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9
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Cao K, Li N, Wang H, Cao X, He J, Zhang B, He QY, Zhang G, Sun X. Two zinc-binding domains in the transporter AdcA from Streptococcus pyogenes facilitate high-affinity binding and fast transport of zinc. J Biol Chem 2018; 293:6075-6089. [PMID: 29491141 DOI: 10.1074/jbc.m117.818997] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 02/25/2018] [Indexed: 11/06/2022] Open
Abstract
Zinc is an essential metal in bacteria. One important bacterial zinc transporter is AdcA, and most bacteria possess AdcA homologs that are single-domain small proteins due to better efficiency of protein biogenesis. However, a double-domain AdcA with two zinc-binding sites is significantly overrepresented in Streptococcus species, many of which are major human pathogens. Using molecular simulation and experimental validations of AdcA from Streptococcus pyogenes, we found here that the two AdcA domains sequentially stabilize the structure upon zinc binding, indicating an organization required for both increased zinc affinity and transfer speed. This structural organization appears to endow Streptococcus species with distinct advantages in zinc-depleted environments, which would not be achieved by each single AdcA domain alone. This enhanced zinc transport mechanism sheds light on the significance of the evolution of the AdcA domain fusion, provides new insights into double-domain transporter proteins with two binding sites for the same ion, and indicates a potential target of antimicrobial drugs against pathogenic Streptococcus species.
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Affiliation(s)
- Kun Cao
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Nan Li
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Hongcui Wang
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Xin Cao
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Jiaojiao He
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Bing Zhang
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Qing-Yu He
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Gong Zhang
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Xuesong Sun
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
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Li J, Lyu W, Rossetti G, Konijnenberg A, Natalello A, Ippoliti E, Orozco M, Sobott F, Grandori R, Carloni P. Proton Dynamics in Protein Mass Spectrometry. J Phys Chem Lett 2017; 8:1105-1112. [PMID: 28207277 DOI: 10.1021/acs.jpclett.7b00127] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Native electrospray ionization/ion mobility-mass spectrometry (ESI/IM-MS) allows an accurate determination of low-resolution structural features of proteins. Yet, the presence of proton dynamics, observed already by us for DNA in the gas phase, and its impact on protein structural determinants, have not been investigated so far. Here, we address this issue by a multistep simulation strategy on a pharmacologically relevant peptide, the N-terminal residues of amyloid-β peptide (Aβ(1-16)). Our calculations reproduce the experimental maximum charge state from ESI-MS and are also in fair agreement with collision cross section (CCS) data measured here by ESI/IM-MS. Although the main structural features are preserved, subtle conformational changes do take place in the first ∼0.1 ms of dynamics. In addition, intramolecular proton dynamics processes occur on the picosecond-time scale in the gas phase as emerging from quantum mechanics/molecular mechanics (QM/MM) simulations at the B3LYP level of theory. We conclude that proton transfer phenomena do occur frequently during fly time in ESI-MS experiments (typically on the millisecond time scale). However, the structural changes associated with the process do not significantly affect the structural determinants.
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Affiliation(s)
- Jinyu Li
- College of Chemistry, Fuzhou University , 350002 Fuzhou, China
| | - Wenping Lyu
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH-Aachen University , 52056 Aachen, Germany
- Computation-Based Science and Technology Research Center, Cyprus Institute , 2121 Aglantzia, Nicosia, Cyprus
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University , 52062 Aachen, Germany
- Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich , D-52425 Jülich, Germany
| | - Albert Konijnenberg
- Biomolecular & Analytical Mass Spectrometry group, Department of Chemistry, University of Antwerp , 2000 Antwerpen, Belgium
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Emiliano Ippoliti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
| | - Modesto Orozco
- Joint BSC-IRB Program on Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac 10, Barcelona 08028, Spain
- Departament de Bioquímica i Biomedicina, Facultat de Biologia, Universitat de Barcelona , Avgda Diagonal 647, Barcelona 08028, Spain
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry group, Department of Chemistry, University of Antwerp , 2000 Antwerpen, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds LS2 9JT, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds , Leeds LS2 9JT, United Kingdom
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
- JARA-HPC, 52425 Jülich, Germany
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11
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In silico designing, cloning, and heterologous expression of novel chimeric human B lymphocyte CD20 extra loop. Tumour Biol 2016; 37:12547-12553. [DOI: 10.1007/s13277-016-5105-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 06/09/2016] [Indexed: 01/10/2023] Open
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12
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Li J, Santambrogio C, Brocca S, Rossetti G, Carloni P, Grandori R. Conformational effects in protein electrospray-ionization mass spectrometry. MASS SPECTROMETRY REVIEWS 2016; 35:111-22. [PMID: 25952139 DOI: 10.1002/mas.21465] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/14/2015] [Indexed: 05/11/2023]
Abstract
Electrospray-ionization mass spectrometry (ESI-MS) is a key tool of structural biology, complementing the information delivered by conventional biochemical and biophysical methods. Yet, the mechanism behind the conformational effects in protein ESI-MS is an object of debate. Two parameters-solvent-accessible surface area (As) and apparent gas-phase basicity (GBapp)-are thought to play a role in controlling the extent of protein ionization during ESI-MS experiments. This review focuses on recent experimental and theoretical investigations concerning the influence of these parameters on ESI-MS results and the structural information that can be derived. The available evidence supports a unified model for the ionization mechanism of folded and unfolded proteins. These data indicate that charge-state distribution (CSD) analysis can provide valuable structural information on normally folded, as well as disordered structures.
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Affiliation(s)
- Jinyu Li
- Computational Biophysics, German Research School for Simulation Sciences, and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, 52057 Aachen, Germany
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Giulia Rossetti
- Computational Biophysics, German Research School for Simulation Sciences, and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany
- Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Paolo Carloni
- Computational Biophysics, German Research School for Simulation Sciences, and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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Politis A, Borysik AJ. Assembling the pieces of macromolecular complexes: Hybrid structural biology approaches. Proteomics 2015; 15:2792-803. [DOI: 10.1002/pmic.201400507] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/26/2015] [Accepted: 02/24/2015] [Indexed: 01/14/2023]
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Atomistic insights into the lung cancer-associated L755P mutation in HER2 resistance to lapatinib: a molecular dynamics study. J Mol Model 2015; 21:24. [DOI: 10.1007/s00894-015-2580-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 01/07/2015] [Indexed: 10/24/2022]
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