Full Text:   <781>

Summary:  <343>

Suppl. Mater.: 

CLC number: Q67

On-line Access: 2015-10-03

Received: 2015-05-02

Revision Accepted: 2015-08-04

Crosschecked: 2015-09-13

Cited: 1

Clicked: 1956

Citations:  Bibtex RefMan EndNote GB/T7714


Hua Yu


-   Go to

Article info.
Open peer comments

Journal of Zhejiang University SCIENCE B 2015 Vol.16 No.10 P.883-896


Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides

Author(s):  Hua Yu, Mao-jun Wang, Nan-xia Xuan, Zhi-cai Shang, Jun Wu

Affiliation(s):  Department of Chemistry, Zhejiang University, Hangzhou 310027, China

Corresponding email(s):   shangzc@zju.edu.cn, wujunwu@zju.edu.cn

Key Words:  Binding affinity, EHD1 EH domain, Molecular dynamics simulation, Inhibitor design, Peptide

Share this article to: More <<< Previous Article|

Hua Yu, Mao-jun Wang, Nan-xia Xuan, Zhi-cai Shang, Jun Wu. Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides[J]. Journal of Zhejiang University Science B, 2015, 16(10): 883-896.

@article{title="Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides",
author="Hua Yu, Mao-jun Wang, Nan-xia Xuan, Zhi-cai Shang, Jun Wu",
journal="Journal of Zhejiang University Science B",
publisher="Zhejiang University Press & Springer",

%0 Journal Article
%T Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides
%A Hua Yu
%A Mao-jun Wang
%A Nan-xia Xuan
%A Zhi-cai Shang
%A Jun Wu
%J Journal of Zhejiang University SCIENCE B
%V 16
%N 10
%P 883-896
%@ 1673-1581
%D 2015
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B1500106

T1 - Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides
A1 - Hua Yu
A1 - Mao-jun Wang
A1 - Nan-xia Xuan
A1 - Zhi-cai Shang
A1 - Jun Wu
J0 - Journal of Zhejiang University Science B
VL - 16
IS - 10
SP - 883
EP - 896
%@ 1673-1581
Y1 - 2015
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B1500106

Objective: To provide essential information for peptide inhibitor design, the interactions of Eps15 homology domain of Eps15 homology domain-containing protein 1 (EHD1 EH domain) with three peptides containing NPF (asparagine-proline-phenylalanine), DPF (aspartic acid-proline-phenylalanine), and GPF (glycine-proline-phenylalanine) motifs were deciphered at the atomic level. The binding affinities and the underlying structure basis were investigated. Methods: Molecular dynamics (MD) simulations were performed on EHD1 EH domain/peptide complexes for 60 ns using the GROMACS package. The binding free energies were calculated and decomposed by molecular mechanics/generalized Born surface area (MM/GBSA) method using the AMBER package. The alanine scanning was performed to evaluate the binding hot spot residues using FoldX software. Results: The different binding affinities for the three peptides were affected dominantly by van der Waals interactions. Intermolecular hydrogen bonds provide the structural basis of contributions of van der Waals interactions of the flanking residues to the binding. Conclusions: van der Waals interactions should be the main consideration when we design peptide inhibitors of EHD1 EH domain with high affinities. The ability to form intermolecular hydrogen bonds with protein residues can be used as the factor for choosing the flanking residues.


方法:用GROMACS程序对EHD1蛋白中的Eps15同源结构域与肽链形成的三个复合物进行各 60纳秒的分子动力学模拟,用AMBER程序中的MM/GBSA方法进行结合自由能计算和能量分解,用FoldX软件对三个复合物进行丙氨酸扫描实验。


Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article


[1]Ammann, L.P., Goodman, S.R., 2009. Cluster analysis for the impact of sickle cell disease on the human erythrocyte protein interactome. Exp. Biol. Med., 234(6):703-711.

[2]Benmerah, A., Gagnon, J., Bègue, B., et al., 1995. The tyrosine kinase substrate eps15 is constitutively associated with the plasma membrane adaptor AP-2. J. Cell Biol., 131(6):1831-1838.

[3]Benmerah, A., Lamaze, C., Bègue, B., et al., 1998. AP-2/Eps15 interaction is required for receptor-mediated endocytosis. J. Cell Biol., 140(5):1055-1062.

[4]Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., et al., 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys., 81(8):3684-3690.

[5]Braun, A., Pinyol, R., Dahlhaus, R., et al., 2005. EHD proteins associate with syndapin I and II and such interactions play a crucial role in endosomal recycling. Mol. Biol. Cell, 16(8):3642-3658.

[6]Caplan, S., Naslavsky, N., Hartnell, L.M., et al., 2002. A tubular EHD1-containing compartment involved in the recycling of major histocompatibility complex class I molecules to the plasma membrane. EMBO J., 21:2557-2567.

[7]Carbone, R., Fré, S., Iannolo, G., et al., 1997. eps15 and eps15R are essential components of the endocytic pathway. Cancer Res., 57(24):5498-5504.

[8]Case, D.A., Darden, T.A., Cheatham, T.E.III, et al., 2012. AMBER 13. University of California, San Francisco, p.349-369.

[9]Caswell, P., Norman, J., 2008. Endocytic transport of integrins during cell migration and invasion. Trends Cell Biol., 18(6):257-263.

[10]Cortez, K.J., Lyman, C.A., Kottilil, S., et al., 2006. Functional genomics of innate host defense molecules in normal human monocytes in response to Aspergillus fumigatus. Infect. Immun., 74(4):2353-2365.

[11]Darden, T., York, D., Pedersen, L., 1993. Particle mesh Ewald: an N∙log(N) method for Ewald sums in large systems. J. Chem. Phys., 98(12):10089-10092.

[12]Daumke, O., Lundmark, R., Vallis, Y., et al., 2007. Architectural and mechanistic insights into an EHD ATPase involved in membrane remodelling. Nature, 449(7164):923-927.

[13]de Beer, T., Hoofnagle, A.N., Enmon, J.L., et al., 2000. Molecular mechanism of NPF recognition by EH domains. Nat. Struct. Mol. Biol., 7(11):1018-1022.

[14]Delft, S.V., Schumacher, C., Hage, W., et al., 1997. Association and colocalization of Eps15 with adaptor protein-2 and clathrin. J. Cell Biol., 136(4):811-821.

[15]Dervan, E.W., Chen, H., Ho, S.L., et al., 2010. Protein macroarray profiling of serum autoantibodies in pseudoexfoliation glaucoma. Invest. Ophthalmol. Vis. Sci., 51(6):2968-2975.

[16]Doherty, K.R., Demonbreun, A.R., Wallace, G.Q., et al., 2008. The endocytic recycling protein EHD2 interacts with myoferlin to regulate myoblast fusion. J. Biol. Chem., 283(29):20252-20260.

[17]Duan, Y., Wu, C., Chowdhury, S., et al., 2003. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem., 24(16):1999-2012.

[18]Essmann, U., Perera, L., Berkowitz, M.L., et al., 1995. A smooth particle mesh Ewald method. J. Chem. Phys., 103(19):8577-8593.

[19]Fazioli, F., Minichiello, L., Matoskova, B., et al., 1993. Eps15, a novel tyrosine kinase substrate, exhibits transforming activity. Mol. Cell. Biol., 13(9):5814-5828.

[20]Galindo, C.L., Sha, J., Ribardo, D.A., et al., 2003. Identification of Aeromonas hydrophila cytotoxic enterotoxin-induced genes in macrophages using microarrays. J. Biol. Chem., 278(41):40198-40212.

[21]Grant, B.D., Caplan, S., 2008. Mechanisms of EHD/RME-1 protein function in endocytic transport. Traffic, 9(12):2043-2052.

[22]Guerois, R., Nielsen, J.E., Serrano, L., 2002. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J. Mol. Biol., 320(2):369-387.

[23]Guilherme, A., Soriano, N.A., Bose, S., et al., 2004. EHD2 and the novel EH domain binding protein EHBP1 couple endocytosis to the actin cytoskeleton. J. Biol. Chem., 279(11):10593-10605.

[24]Hansel, D.E., Rahman, A., House, M., et al., 2004. Met proto-oncogene and insulin-like growth factor binding protein 3 overexpression correlates with metastatic ability in well-differentiated pancreatic endocrine neoplasms. Clin. Cancer Res., 10(18):6152-6158.

[25]Henry, G.D., Corrigan, D.J., Dineen, J.V., et al., 2010. Charge effects in the selection of NPF motifs by the EH domain of EHD1. Biochemistry, 49(16):3381-3392.

[26]Hess, B., Bekker, H., Berendsen, H.J.C., et al., 1997. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem., 18(12):1463-1472.

[27]Hess, B., Kutzner, C., van der Spoel, D., et al., 2008. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput., 4(3):435-447.

[28]Humphrey, W., Dalke, A., Schulten, K., 1996. VMD: visual molecular dynamics. J. Mol. Graph., 14(1):33-38.

[29]Jansen, F.H., Krijgsveld, J., van Rijswijk, A., et al., 2009. Exosomal secretion of cytoplasmic prostate cancer xenograft-derived proteins. Mol. Cell. Proteomics, 8(6):1192-1205.

[30]Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., et al., 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79(2):926-935.

[31]Jović, M., Naslavsky, N., Rapaport, D., et al., 2007. EHD1 regulates β1 integrin endosomal transport: effects on focal adhesions, cell spreading and migration. J. Cell Sci., 120(5):802-814.

[32]Kabsch, W., Sander, C., 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22(12):2577-2637.

[33]Kamens, A.J., Eisert, R.J., Corlin, T., et al., 2014. Structured cyclic peptides that bind the EH domain of EHD1. Biochemistry, 53(29):4758-4760.

[34]Kieken, F., Jovic, M., Naslavsky, N., et al., 2007. EH domain of EHD1. J. Biomol. NMR, 39(4):323-329.

[35]Kieken, F., Jovic, M., Tonelli, M., et al., 2009. Structural insight into the interaction of proteins containing NPF, DPF, and GPF motifs with the C-terminal EH-domain of EHD1. Protein Sci., 18(12):2471-2479.

[36]Kieken, F., Sharma, M., Jovic, M., et al., 2010. Mechanism for the selective interaction of C-terminal Eps15 homology domain proteins with specific Asn-Pro-Phe-containing partners. J. Biol. Chem., 285(12):8687-8694.

[37]Kim, S., Cullis, D.N., Feig, L.A., et al., 2001. Solution structure of the Reps1 EH domain and characterization of its binding to NPF target sequences. Biochemistry, 40(23):6776-6785.

[38]Kollman, P.A., Massova, I., Reyes, C., et al., 2000. Calculating structures and free energies of complex molecules:  combining molecular mechanics and continuum models. Acc. Chem. Res., 33(12):889-897.

[39]Lin, S.X., Grant, B., Hirsh, D., et al., 2001. Rme-1 regulates the distribution and function of the endocytic recycling compartment in mammalian cells. Nat. Cell Biol., 3(6):567-572.

[40]Lindahl, E., Azuara, C., Koehl, P., et al., 2006. NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res., 34(Suppl. 2):W52-W56.

[41]London, N., Movshovitz-Attias, D., Schueler-Furman, O., 2010. The structural basis of peptide-protein binding strategies. Structure, 18(2):188-199.

[42]Lu, S., Jiang, Y., Lv, J., et al., 2011. Mechanism of kinase inactivation and nonbinding of fratide to GSK3β due to K85M mutation: molecular dynamics simulation and normal mode analysis. Biopolymers, 95(10):669-681.

[43]Maher, E.A., Furnari, F.B., Bachoo, R.M., et al., 2001. Malignant glioma: genetics and biology of a grave matter. Genes Dev., 15(11):1311-1333.

[44]Miliaras, N., Wendland, B., 2004. EH proteins. Cell Biochem. Biophys., 41(2):295-318.

[45]Mosesson, Y., Mills, G.B., Yarden, Y., 2008. Derailed endocytosis: an emerging feature of cancer. Nat. Rev. Cancer, 8(11):835-850.

[46]Naslavsky, N., Caplan, S., 2005. C-terminal EH-domain-containing proteins: consensus for a role in endocytic trafficking, EH? J. Cell Sci., 118(18):4093-4101.

[47]Naslavsky, N., Caplan, S., 2011. EHD proteins: key conductors of endocytic transport. Trends Cell Biol., 21(2):122-131.

[48]Naslavsky, N., Boehm, M., Backlund, P.S., et al., 2004. Rabenosyn-5 and EHD1 interact and sequentially regulate protein recycling to the plasma membrane. Mol. Biol. Cell, 15(5):2410-2422.

[49]Naslavsky, N., Rahajeng, J., Sharma, M., et al., 2006. Interactions between EHD proteins and Rab11-FIP2: a role for EHD3 in early endosomal transport. Mol. Biol. Cell, 17(1):163-177.

[50]Polo, S., Confalonieri, S., Salcini, A.E., et al., 2003. EH and UIM: endocytosis and more. Sci. Signal., 213:re17.

[51]Rose, P.W., Bi, C., Bluhm, W.F., et al., 2013. The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res., 41(D1):D475-D482.

[52]Santolini, E., Salcini, A.E., Kay, B.K., et al., 1999. The EH network. Exp. Cell Res., 253(1):186-209.

[53]Santonico, E., Panni, S., Falconi, M., et al., 2007. Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction. BMC Biochem., 8:29.

[54]Schymkowitz, J.W.H., Rousseau, F., Martins, I.C., et al., 2005. Prediction of water and metal binding sites and their affinities by using the Fold-X force field. PNAS, 102(29):10147-10152.

[55]Sharma, M., Giridharan, S.S.P., Rahajeng, J., et al., 2009. MICAL-L1 links EHD1 to tubular recycling endosomes and regulates receptor recycling. Mol. Biol. Cell, 20(24):5181-5194.

[56]Shi, A., Pant, S., Balklava, Z., et al., 2007. A novel requirement for C. elegans Alix/ALX-1 in RME-1-mediated membrane transport. Curr. Biol., 17(22):1913-1924.

[57]Shin, J., Monti, S., Aires, D.J., et al., 2007. Lesional gene expression profiling in cutaneous T-cell lymphoma reveals natural clusters associated with disease outcome. Blood, 110(8):3015-3027.

[58]Smith, C.A., Dho, S.E., Donaldson, J., et al., 2004. The cell fate determinant numb interacts with EHD/Rme-1 family proteins and has a role in endocytic recycling. Mol. Biol. Cell, 15(8):3698-3708.

[59]Stein, A., Aloy, P., 2008. Contextual specificity in peptide-mediated protein interactions. PLoS ONE, 3(7):e2524.

[60]Tripathi, A.K., Sha, W., Shulaev, V., et al., 2009. Plasmodium falciparum-infected erythrocytes induce NF-κB regulated inflammatory pathways in human cerebral endothelium. Blood, 114:4243-4252.

[61]Wang, W., Kollman, P.A., 2001. Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance. PNAS, 98(26):14937-14942.

[62]Weiser, J., Shenkin, P.S., Still, W.C., 1999. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J. Comput. Chem., 20(2):217-230.

[63]Wong, W.T., Schumacher, C., Salcini, A.E., et al., 1995. A protein-binding domain, EH, identified in the receptor tyrosine kinase substrate Eps15 and conserved in evolution. PNAS, 92(21):9530-9534.

[64]Xu, Y., Shi, H., Wei, S., et al., 2004. Mutually exclusive interactions of EHD1 with GS32 and syndapin II. Mol. Membr. Biol., 21(4):269-277.

[65]Yamabhai, M., Hoffman, N.G., Hardison, N.L., et al., 1998. Intersectin, a novel adaptor protein with two Eps15 homology and five Src homology 3 domains. J. Biol. Chem., 273(47):31401-31407.

[66]Zhang, J., Li, C., Shi, T., et al., 2009. Lys169 of human glucokinase is a determinant for glucose phosphorylation: implication for the atomic mechanism of glucokinase catalysis. PLoS ONE, 4(7):e6304.

Open peer comments: Debate/Discuss/Question/Opinion


Please provide your name, email address and a comment

Journal of Zhejiang University-SCIENCE, 38 Zheda Road, Hangzhou 310027, China
Tel: +86-571-87952783; E-mail: cjzhang@zju.edu.cn
Copyright © 2000 - Journal of Zhejiang University-SCIENCE