1
|
Coarse-grained modeling of the calcium, sodium, magnesium and potassium cations interacting with proteins. J Mol Model 2022; 28:201. [PMID: 35748949 DOI: 10.1007/s00894-022-05154-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/12/2022] [Indexed: 10/17/2022]
Abstract
Metal ions play important biological roles, e.g., activation or deactivation of enzymatic reactions and signal transduction. Moreover, they can stabilize protein structure, or even be actively involved in the protein folding process. Therefore, accurate treatment of the ions is crucial to model and investigate biological phenomena properly. In this work the coarse-grained UNRES (UNited RESidue) force field was extended to include the interactions between proteins and four alkali or alkaline earth metal cations of biological significance, i.e., calcium, magnesium, sodium and potassium. Additionally, chloride anions were introduced as counter-ions. Parameters were derived from all-atom simulations and incorporate water in an implicit manner. The new force field was tested on the set of the proteins and was able to reproduce the ion-binding preferences.
Collapse
|
2
|
Marakasova E, Olivares P, Karnaukhova E, Chun H, Hernandez NE, Kurasawa JH, Hassink GU, Shestopal SA, Strickland DK, Sarafanov AG. Molecular chaperone RAP interacts with LRP1 in a dynamic bivalent mode and enhances folding of ligand-binding regions of other LDLR family receptors. J Biol Chem 2021; 297:100842. [PMID: 34058195 PMCID: PMC8239462 DOI: 10.1016/j.jbc.2021.100842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 05/20/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
The low-density lipoprotein receptor (LDLR) family of receptors are cell-surface receptors that internalize numerous ligands and play crucial role in various processes, such as lipoprotein metabolism, hemostasis, fetal development, etc. Previously, receptor-associated protein (RAP) was described as a molecular chaperone for LDLR-related protein 1 (LRP1), a prominent member of the LDLR family. We aimed to verify this role of RAP for LRP1 and two other LDLR family receptors, LDLR and vLDLR, and to investigate the mechanisms of respective interactions using a cell culture model system, purified system, and in silico modelling. Upon coexpression of RAP with clusters of the ligand-binding complement repeats (CRs) of the receptors in secreted form in insect cells culture, the isolated proteins had increased yield, enhanced folding, and improved binding properties compared with proteins expressed without RAP, as determined by circular dichroism and surface plasmon resonance. Within LRP1 CR-clusters II and IV, we identified multiple sites comprised of adjacent CR doublets, which provide alternative bivalent binding combinations with specific pairs of lysines on RAP. Mutational analysis of these lysines within each of isolated RAP D1/D2 and D3 domains having high affinity to LRP1 and of conserved tryptophans on selected CR-doublets of LRP1, as well as in silico docking of a model LRP1 CR-triplet with RAP, indicated a universal role for these residues in interaction of RAP and LRP1. Consequently, we propose a new model of RAP interaction with LDLR family receptors based on switching of the bivalent contacts between molecules over time in a dynamic mode.
Collapse
Affiliation(s)
- Ekaterina Marakasova
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Philip Olivares
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Elena Karnaukhova
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Haarin Chun
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Nancy E Hernandez
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - James H Kurasawa
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Gabriela U Hassink
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Svetlana A Shestopal
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Dudley K Strickland
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Andrey G Sarafanov
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA.
| |
Collapse
|
3
|
Bao X, Yuan X, Feng G, Zhang M, Ma S. Structural characterization of calcium-binding sunflower seed and peanut peptides and enhanced calcium transport by calcium complexes in Caco-2 cells. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:794-804. [PMID: 32898305 DOI: 10.1002/jsfa.10800] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/15/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Peptide-Ca complexes can promote Ca absorption. The present study aimed to determine the transport mechanism and structural characteristics of sunflower seed and peanut peptides with high Ca binding capacity with respect to developing third-generation Ca supplements and functional food ingredients. RESULTS High Ca-binding fractions of 1-3 kDa sunflower seed peptide (SSP4 ) and ≥ 10 kDa peanut peptide (PP1 ) had higher amount of Ca transported than CaCl2 and two hydrolyzed proteins in Caco-2 cells. SSP4 and PP1 were separated by Ca ion metal chelate affinity chromatography, and high Ca-binding fractions were observed for SSP4 -P2 and PP1 -P2 . The amino acid sequences of SSP4 -P2 and PP1 -P2 were characterized by high-performance liquid chromatography-electrospray ionization-time of flight mass spectrometry. Seven and eight peptides were identified from SSP4 -P2 and PP1 -P2 , respectively. These peptides had molecular weights ranging from 1500 Da to 2500 Da and a large number of characteristic amino acid sequences, such as EEEQQQ, EQ-QQQ-QQ, QQ-QQQQQ, E-EEE, EE-EEQ, RR, Q-QQ-QQQ, EE-EQ-EE-Q, QQ-QQQQ, and Q-QQQQ, where 'E' is glutamic acid and 'Q' is glutamine. CONCLUSION SSP4 and PP1 can promote Ca transport in Caco-2 cells without affecting cell permeability. The amino acid sequences of SSP4 -P2 and PP1 -P2 with high Ca-binding abilities contain characteristic sequences, such as continuous glutamic acid and glutamine, and have low molecular weights. © 2020 Society of Chemical Industry.
Collapse
Affiliation(s)
- Xiaolan Bao
- Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Xingyu Yuan
- Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Guoxue Feng
- Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Meili Zhang
- Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Sarina Ma
- Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| |
Collapse
|
4
|
Klein F, Cáceres D, Carrasco MA, Tapia JC, Caballero J, Alzate-Morales J, Pantano S. Coarse-Grained Parameters for Divalent Cations within the SIRAH Force Field. J Chem Inf Model 2020; 60:3935-3943. [DOI: 10.1021/acs.jcim.0c00160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Florencia Klein
- Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
| | - Daniela Cáceres
- Escuela de Medicina, Universidad de Talca, 1 Poniente 1141, Talca 3460000, Chile
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingenierı́a, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Talca 3460000, Chile
| | - Mónica A. Carrasco
- Escuela de Medicina, Universidad de Talca, 1 Poniente 1141, Talca 3460000, Chile
| | - Juan Carlos Tapia
- Escuela de Medicina, Universidad de Talca, 1 Poniente 1141, Talca 3460000, Chile
| | - Julio Caballero
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingenierı́a, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Talca 3460000, Chile
| | - Jans Alzate-Morales
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingenierı́a, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Talca 3460000, Chile
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| |
Collapse
|
5
|
Cui P, Lin S, Han W, Jiang P, Zhu B, Sun N. Calcium Delivery System Assembled by a Nanostructured Peptide Derived from the Sea Cucumber Ovum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:12283-12292. [PMID: 31610118 DOI: 10.1021/acs.jafc.9b04522] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this study, the binding mechanism, morphological, and conformational analysis of the complex of a sea cucumber ovum derived octapeptide (EDLAALEK) with Ca2+ as well as its calcium delivery behavior via the gastrointestinal (GI) tract were investigated. The Ca2+ specifically bound to two carboxyl oxygen atoms of C-terminal Glu and Asp on the EDLAALEK peptide at a stoichiometric ratio of 1:1. Calcium coordination induced the self-assembly of the EDLAALEK peptide, resulting in the formation of a nanocomposite with a crystal structure. Furthermore, the formed nanocomposite went through dissociation and self-assembly during in vitro GI digestion, accompanied by the release and rechelation of Ca2+, which was related to changes in their secondary structure. Nevertheless, the GI digests of the EDLAALEK-calcium complex could significantly enhance Ca2+ absorption across Caco-2 cell monolayers. The findings suggest that the sea cucumber ovum derived peptide has the potential as an efficient nanocarrier to transport calcium through the GI system.
Collapse
Affiliation(s)
- Pengbo Cui
- National Engineering Research Center of Seafood, School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , P. R. China
| | - Songyi Lin
- National Engineering Research Center of Seafood, School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , P. R. China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science , Jilin University , Changchun 130012 , P. R. China
| | - Pengfei Jiang
- National Engineering Research Center of Seafood, School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , P. R. China
| | - Beiwei Zhu
- National Engineering Research Center of Seafood, School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , P. R. China
| | - Na Sun
- National Engineering Research Center of Seafood, School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , P. R. China
| |
Collapse
|
6
|
Sieradzan AK, Bogunia M, Mech P, Ganzynkowicz R, Giełdoń A, Liwo A, Makowski M. Introduction of Phosphorylated Residues into the UNRES Coarse-Grained Model: Toward Modeling of Signaling Processes. J Phys Chem B 2019; 123:5721-5729. [PMID: 31194908 DOI: 10.1021/acs.jpcb.9b03799] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Phosphorylated proteins take part in many signaling pathways and play a key role in homeostasis regulation. The all-atom force fields enable us to study the systems containing phosphorylated proteins, but they are limited to short time scales. In this paper, we report the extension of the physics-based coarse-grained UNRES force field to treat systems with phosphorylated amino-acid residues. To derive the respective potentials, appropriate physics-based analytical expressions were fitted to the potentials of mean force of systems modeling phosphorylated amino-acid residues computed in our previous work and implemented in UNRES. The extended UNRES performed well in ab initio simulations of two miniproteins containing phosphorylated residues, strongly suggesting that realistic large-scale simulations of processes involving phosphorylated proteins, especially signaling processes, are now possible.
Collapse
Affiliation(s)
- Adam K Sieradzan
- Faculty of Chemistry , University of Gdańsk , ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Małgorzata Bogunia
- Faculty of Chemistry , University of Gdańsk , ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Paulina Mech
- Faculty of Chemistry , University of Gdańsk , ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Robert Ganzynkowicz
- Faculty of Chemistry , University of Gdańsk , ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Artur Giełdoń
- Faculty of Chemistry , University of Gdańsk , ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Adam Liwo
- Faculty of Chemistry , University of Gdańsk , ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Mariusz Makowski
- Faculty of Chemistry , University of Gdańsk , ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
| |
Collapse
|
7
|
Cui P, Lin S, Han W, Jiang P, Zhu B, Sun N. The formation mechanism of a sea cucumber ovum derived heptapeptide–calcium nanocomposite and its digestion/absorption behavior. Food Funct 2019; 10:8240-8249. [DOI: 10.1039/c9fo01335k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Calcium coordination induced the self-assembly of the sea cucumber ovum derived heptapeptide (NDEELNK), resulting in the formation of the nanocomposite with potential function to transport calcium through the gastrointestinal system.
Collapse
Affiliation(s)
- Pengbo Cui
- National Engineering Research Center of Seafood
- School of Food Science and Technology
- Dalian Polytechnic University
- Dalian 116034
- P. R. China
| | - Songyi Lin
- National Engineering Research Center of Seafood
- School of Food Science and Technology
- Dalian Polytechnic University
- Dalian 116034
- P. R. China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
- School of Life Science
- Jilin University
- Changchun 130012
- P. R. China
| | - Pengfei Jiang
- National Engineering Research Center of Seafood
- School of Food Science and Technology
- Dalian Polytechnic University
- Dalian 116034
- P. R. China
| | - Beiwei Zhu
- National Engineering Research Center of Seafood
- School of Food Science and Technology
- Dalian Polytechnic University
- Dalian 116034
- P. R. China
| | - Na Sun
- National Engineering Research Center of Seafood
- School of Food Science and Technology
- Dalian Polytechnic University
- Dalian 116034
- P. R. China
| |
Collapse
|
8
|
A novel calcium-binding peptide from Antarctic krill protein hydrolysates and identification of binding sites of calcium-peptide complex. Food Chem 2017; 243:389-395. [PMID: 29146354 DOI: 10.1016/j.foodchem.2017.09.152] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/27/2017] [Accepted: 09/29/2017] [Indexed: 11/22/2022]
Abstract
Trypsin was used for preparing peptides with high calcium-binding capacity from Antarctic krill. Hydroxyapatite chromatography (HAC), size-exclusion chromatography (SEC), and reversed phase high performance liquid chromatography (RP-HPLC) were used to capture and purify calcium-binding peptides. The peptide sequence was determined to be VLGYIQIR (N- to C-terminal, MW = 960.58 Da), using LTQ Orbitrap XL. According to the results of FTIR and mass spectrometry, chelating site of calcium ions may possibly involve the carbonal or amino groups of Gln, Ile and Arg residues. Molecular dynamic simulation showed the conformation of peptide was markedly varied, and the distance between calcium ion and Gln and Ile residues was changing all the time. However, the distance between calcium ion and carboxyl oxygen of arginine residues was not changed significantly from 2 ns to 100 ns. Identified peptide can be used as a novel calcium supplement.
Collapse
|
9
|
Gong Z, Sun H. A Coarse-Grained Force Field Parameterized for MgCl2 and CaCl2 Aqueous Solutions. J Chem Inf Model 2017; 57:1599-1608. [DOI: 10.1021/acs.jcim.7b00206] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Zheng Gong
- School of Chemistry and Chemical
Engineering and Ministry of Education Key Laboratory of Scientific
and Engineering Computing, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Huai Sun
- School of Chemistry and Chemical
Engineering and Ministry of Education Key Laboratory of Scientific
and Engineering Computing, Shanghai Jiao Tong University, Shanghai, 200240, China
| |
Collapse
|
10
|
Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
Collapse
Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
| |
Collapse
|
11
|
Vanommeslaeghe K, Guvench O, MacKerell AD. Molecular mechanics. Curr Pharm Des 2014; 20:3281-92. [PMID: 23947650 PMCID: PMC4026342 DOI: 10.2174/13816128113199990600] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/07/2013] [Indexed: 11/22/2022]
Abstract
Molecular Mechanics (MM) force fields are the methods of choice for protein simulations, which are essential in the study of conformational flexibility. Given the importance of protein flexibility in drug binding, MM is involved in most if not all Computational Structure-Based Drug Discovery (CSBDD) projects. This paper introduces the reader to the fundamentals of MM, with a special emphasis on how the target data used in the parametrization of force fields determine their strengths and weaknesses. Variations and recent developments such as polarizable force fields are discussed. The paper ends with a brief overview of common force fields in CSBDD.
Collapse
Affiliation(s)
- Kenno Vanommeslaeghe
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St, HSF-II Rm 633, Baltimore, MD 21201; tel: 410-706-7442; fax: 410-706-5017
| | - Olgun Guvench
- Department of Pharmaceutical Sciences, University of New England College of Pharmacy, 716 Stevens Ave, Portland, ME 04103
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St, HSF-II Rm 633, Baltimore, MD 21201; tel: 410-706-7442; fax: 410-706-5017
| |
Collapse
|
12
|
Improvement on the modified Lowry method against interference of divalent cations in soluble protein measurement. Appl Microbiol Biotechnol 2013; 97:4167-78. [PMID: 23474613 DOI: 10.1007/s00253-013-4783-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Revised: 02/14/2013] [Accepted: 02/15/2013] [Indexed: 10/27/2022]
Abstract
This paper systematically investigated the interference of calcium and magnesium in protein measurement with a modified Lowry method first proposed by Frølund et al. (Appl Microbiol Biotechnol 43:755-761, 1995). This interference has in the past been largely ignored resulting in variable and unreliable results when applied to natural water matrices. We discovered significant formation of calcium and magnesium precipitates that lead to a decline in light absorbance at 750 nm during protein determination. Underestimation of protein concentration (sometimes even yielding negative concentrations) and low experiment reproducibility were demonstrated at high concentrations of divalent cations (e.g., [Ca(2+)] over 1 mmol L(-1)). To eliminate interference from calcium and magnesium, two pretreatment strategies were established based on cation exchange and dialysis. These pretreatments were convenient and were found to be highly effective in removing calcium and magnesium in protein samples. By using the modified Lowry method with these pretreatments, proteins in standard solutions and in wastewater samples were successfully quantified with good reliability and reproducibility. In addition, we demonstrated that simultaneous quantification of humic substances with the modified Lowry method was not affected by the two pretreatments. These approaches are expected to be applicable to protein and humic substance determination in different research fields, in cases where the modified Lowry method is sensitive to divalent cation concentrations.
Collapse
|
13
|
Grahnen JA, Kubelka J, Liberles DA. Fast Side Chain Replacement in Proteins Using a Coarse-Grained Approach for Evaluating the Effects of Mutation During Evolution. J Mol Evol 2011; 73:23-33. [DOI: 10.1007/s00239-011-9454-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 07/14/2011] [Indexed: 11/28/2022]
|
14
|
Docking of calcium ions in proteins with flexible side chains and deformable backbones. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:825-38. [PMID: 19937325 DOI: 10.1007/s00249-009-0561-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 10/20/2009] [Accepted: 10/23/2009] [Indexed: 10/20/2022]
Abstract
A method of docking Ca(2+) ions in proteins with flexible side chains and deformable backbones is proposed. The energy was calculated with the AMBER force field, implicit solvent, and solvent exposure-dependent and distance-dependent dielectric function. Starting structures were generated with Ca(2+) coordinates and side-chain torsions sampled in 1000 A(3) cubes centered at the experimental Ca(2+) positions. The energy was Monte Carlo-minimized. The method was tested on fourteen Ca(2+)-binding sites. For twelve Ca(2+)-binding sites the root mean square (RMS) deviation of the apparent global minimum from the experimental structure was below 1.3 and 1.7 A for Ca(2+) ions and side-chain heavy atoms, respectively. Energies of multiple local minima correlate with the RMS deviations from the X-ray structures. Two Ca(2+)-binding sites at the surface of proteinase K were not predicted, because of underestimation of Ca(2+) hydration energy by the implicit-solvent method.
Collapse
|
15
|
Efficient and reproducible folding simulations of the Trp-cage protein with multiscale molecular dynamics. Sci Bull (Beijing) 2008. [DOI: 10.1007/s11434-008-0186-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
16
|
Lin HH, Han LY, Zhang HL, Zheng CJ, Xie B, Cao ZW, Chen YZ. Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach. BMC Bioinformatics 2006; 7 Suppl 5:S13. [PMID: 17254297 PMCID: PMC1764469 DOI: 10.1186/1471-2105-7-s5-s13] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Metal-binding proteins play important roles in structural stability, signaling, regulation, transport, immune response, metabolism control, and metal homeostasis. Because of their functional and sequence diversity, it is desirable to explore additional methods for predicting metal-binding proteins irrespective of sequence similarity. This work explores support vector machines (SVM) as such a method. SVM prediction systems were developed by using 53,333 metal-binding and 147,347 non-metal-binding proteins, and evaluated by an independent set of 31,448 metal-binding and 79,051 non-metal-binding proteins. The computed prediction accuracy is 86.3%, 81.6%, 83.5%, 94.0%, 81.2%, 85.4%, 77.6%, 90.4%, 90.9%, 74.9% and 78.1% for calcium-binding, cobalt-binding, copper-binding, iron-binding, magnesium-binding, manganese-binding, nickel-binding, potassium-binding, sodium-binding, zinc-binding, and all metal-binding proteins respectively. The accuracy for the non-member proteins of each class is 88.2%, 99.9%, 98.1%, 91.4%, 87.9%, 94.5%, 99.2%, 99.9%, 99.9%, 98.0%, and 88.0% respectively. Comparable accuracies were obtained by using a different SVM kernel function. Our method predicts 67% of the 87 metal-binding proteins non-homologous to any protein in the Swissprot database and 85.3% of the 333 proteins of known metal-binding domains as metal-binding. These suggest the usefulness of SVM for facilitating the prediction of metal-binding proteins. Our software can be accessed at the SVMProt server http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi.
Collapse
Affiliation(s)
- HH Lin
- Bioinformatics and Drug Design Group, Department of Pharmacy and Department of Computational Science, National University of Singapore, Blk SOC1, Level 7, 3 Science Drive 2, Singapore 117543
| | - LY Han
- Bioinformatics and Drug Design Group, Department of Pharmacy and Department of Computational Science, National University of Singapore, Blk SOC1, Level 7, 3 Science Drive 2, Singapore 117543
| | - HL Zhang
- Bioinformatics and Drug Design Group, Department of Pharmacy and Department of Computational Science, National University of Singapore, Blk SOC1, Level 7, 3 Science Drive 2, Singapore 117543
| | - CJ Zheng
- Bioinformatics and Drug Design Group, Department of Pharmacy and Department of Computational Science, National University of Singapore, Blk SOC1, Level 7, 3 Science Drive 2, Singapore 117543
| | - B Xie
- Bioinformatics and Drug Design Group, Department of Pharmacy and Department of Computational Science, National University of Singapore, Blk SOC1, Level 7, 3 Science Drive 2, Singapore 117543
| | - ZW Cao
- Shanghai Center for Bioinformatics Technology, 100, Qinzhou Road, Shanghai 200235 P.R. China
| | - YZ Chen
- Bioinformatics and Drug Design Group, Department of Pharmacy and Department of Computational Science, National University of Singapore, Blk SOC1, Level 7, 3 Science Drive 2, Singapore 117543
- Shanghai Center for Bioinformatics Technology, 100, Qinzhou Road, Shanghai 200235 P.R. China
| |
Collapse
|
17
|
Deng H, Chen G, Yang W, Yang JJ. Predicting calcium-binding sites in proteins - a graph theory and geometry approach. Proteins 2006; 64:34-42. [PMID: 16617426 DOI: 10.1002/prot.20973] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Identifying calcium-binding sites in proteins is one of the first steps towards predicting and understanding the role of calcium in biological systems for protein structure and function studies. Due to the complexity and irregularity of calcium-binding sites, a fast and accurate method for predicting and identifying calcium-binding protein is needed. Here we report our development of a new fast algorithm (GG) to detect calcium-binding sites. The GG algorithm uses a graph theory algorithm to find oxygen clusters of the protein and a geometric algorithm to identify the center of these clusters. A cluster of four or more oxygen atoms has a high potential for calcium binding. High performance with about 90% site sensitivity and 80% site selectivity has been obtained for three datasets containing a total of 123 proteins. The results suggest that a sphere of a certain size with four or more oxygen atoms on the surface and without other atoms inside is necessary and sufficient for quickly identifying the majority of the calcium-binding sites with high accuracy. Our finding opens a new avenue to visualize and analyze calcium-binding sites in proteins facilitating the prediction of functions from structural genomic information.
Collapse
Affiliation(s)
- Hai Deng
- Department of Computer Science, Georgia State University, Atlanta, Georgia 30302, USA
| | | | | | | |
Collapse
|