1
|
Loureiro RJS, Faísca PFN. The Early Phase of β2-Microglobulin Aggregation: Perspectives From Molecular Simulations. Front Mol Biosci 2020; 7:578433. [PMID: 33134317 PMCID: PMC7550760 DOI: 10.3389/fmolb.2020.578433] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/08/2020] [Indexed: 11/24/2022] Open
Abstract
Protein β2-microglobulin is the causing agent of two amyloidosis, dialysis related amyloidosis (DRA), affecting the bones and cartilages of individuals with chronic renal failure undergoing long-term hemodialysis, and a systemic amyloidosis, found in one French family, which impairs visceral organs. The protein’s small size and its biomedical significance attracted the attention of theoretical scientists, and there are now several studies addressing its aggregation mechanism in the context of molecular simulations. Here, we review the early phase of β2-microglobulin aggregation, by focusing on the identification and structural characterization of monomers with the ability to trigger aggregation, and initial small oligomers (dimers, tetramers, hexamers etc.) formed in the so-called nucleation phase. We focus our analysis on results from molecular simulations and integrate our views with those coming from in vitro experiments to provide a broader perspective of this interesting field of research. We also outline directions for future computer simulation studies.
Collapse
Affiliation(s)
- Rui J S Loureiro
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Lisbon, Portugal
| | - Patrícia F N Faísca
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Lisbon, Portugal.,Department of Physics, Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| |
Collapse
|
2
|
Narang SS, Shuaib S, Goyal D, Goyal B. In silico-guided identification of potential inhibitors against β2m aggregation in dialysis-related amyloidosis. J Biomol Struct Dyn 2019; 38:3927-3941. [DOI: 10.1080/07391102.2019.1668852] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Simranjeet Singh Narang
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Suniba Shuaib
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Deepti Goyal
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry and Biochemistry, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| |
Collapse
|
3
|
Ahmad A, Burns CS, Fink AL, Uversky VN. Peculiarities of copper binding to alpha-synuclein. J Biomol Struct Dyn 2016; 29:825-42. [PMID: 22208282 DOI: 10.1080/073911012010525023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Heavy metals have been implicated as the causative agents for the pathogenesis of the most prevalent neurodegenerative disease. Various mechanisms have been proposed to explain the toxic effects of metals ranging from metal-induced oxidation of protein to metal-induced changes in the protein conformation. Aggregation of a-synuclein is implicated in Parkinson's disease (PD), and various metals, including copper, constitute a prominent group of alpha-synuclein aggregation enhancers. In this study, we have systematically characterized the a-synuclein-Cu21 binding sites and analyzed the possible role of metal binding in a-synuclein fibrillation using a set of biophysical techniques, such as electron paramagnetic resonance (EPR), electron spin-echo envelope modulation (ESEEM), circular dichroism (CD), and size exclusion chromatography (SEC). Our analyses indicated that a-synuclein possesses at least two binding sites for Cu21. We have been able to locate one of the binding sites in the N-terminal region. Furthermore, based on the EPR studies of model peptides and Beta-synuclein, we concluded that the suspected His residue did not appear to participate in strong Cu21 binding.
Collapse
Affiliation(s)
- Atta Ahmad
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California, USA.
| | | | | | | |
Collapse
|
4
|
Abstract
The small ubiquitin-like modifier (SUMO) proteins are a kind of proteins that can be attached to a series of proteins. The sumoylation of protein is an important posttranslational modification. Thus, the prediction of the sumoylation site of a given protein is significant. Here we employed a combined method to perform this task. We predicted the sumoylation site of a protein by a two-staged procedure. At the first stage, whether a protein would be sumoylated was predicted; whereas at the second stage, the sumoylation sites of the protein were predicted if it was determined to be modified by SUMO at the first stage. At the first stage, we encoded a protein with protein families (PFAM) and trained the predictor with nearest network algorithm (NNA); at the second stage, we encoded nonapeptides (peptides that contain nine residues) of the protein containing the lysine residues, with Amino Acid Index, and trained the predictor with NNA. The predictor was tested by the k-fold cross-validation method. The highest accuracy of the second-staged predictor was 99.55% when 12 features were incorporated in the predictor. The corresponding Matthews Correlation Coefficient was 0.7952. These results indicate that the method is a promising tool to predict the sumoylation site of a protein. At last, the features used in the predictor are discussed. The software is available at request.
Collapse
Affiliation(s)
- YuDong Cai
- Institute of System Biology, Shanghai University, 99 Shangda Road, Shanghai, 200244, China.
| | | | | |
Collapse
|
5
|
Semighini EP, Resende JA, de Andrade P, Morais PAB, Carvalho I, Taft CA, Silva CHTP. Using computer-aided drug design and medicinal chemistry strategies in the fight against diabetes. J Biomol Struct Dyn 2011; 28:787-96. [PMID: 21294589 DOI: 10.1080/07391102.2011.10508606] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The aim of this work is to present a simple, practical and efficient protocol for drug design, in particular Diabetes, which includes selection of the illness, good choice of a target as well as a bioactive ligand and then usage of various computer aided drug design and medicinal chemistry tools to design novel potential drug candidates in different diseases. We have selected the validated target dipeptidyl peptidase IV (DPP-IV), whose inhibition contributes to reduce glucose levels in type 2 diabetes patients. The most active inhibitor with complex X-ray structure reported was initially extracted from the BindingDB database. By using molecular modification strategies widely used in medicinal chemistry, besides current state-of-the-art tools in drug design (including flexible docking, virtual screening, molecular interaction fields, molecular dynamics, ADME and toxicity predictions), we have proposed 4 novel potential DPP-IV inhibitors with drug properties for Diabetes control, which have been supported and validated by all the computational tools used herewith.
Collapse
Affiliation(s)
- Evandro P Semighini
- Departamento de Ciencias Farmaceuticas, Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de Sao Paulo, Av. do Cafe, s/n, Monte Alegre, 14040-903, Ribeirao Preto-SP, Brazil
| | | | | | | | | | | | | |
Collapse
|
6
|
Xu X, Su J, Chen W, Wang C. Thermal stability and unfolding pathways of Sso7d and its mutant F31A: insight from molecular dynamics simulation. J Biomol Struct Dyn 2011; 28:717-27. [PMID: 21294584 DOI: 10.1080/07391102.2011.10508601] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The thermo-stability and unfolding behaviors of a small hyperthermophilic protein Sso7d as well as its single-point mutation F31A are studied by molecular dynamics simulation at temperatures of 300 K, 371 K and 500 K. Simulations at 300 K show that the F31A mutant displays a much larger flexibility than the wild type, which implies that the mutation obviously decreases the protein's stability. In the simulations at 371 K, although larger fluctuations were observed, both of these two maintain their stable conformations. High temperature simulations at 500 K suggest that the unfolding of these two proteins evolves along different pathways. For the wild-type protein, the C-terminal alpha-helix is melted at the early unfolding stage, whereas it is destroyed much later in the unfolding process of the F31A mutant. The results also show that the mutant unfolds much faster than its parent protein. The deeply buried aromatic cluster in the F31A mutant dissociates quickly relative to the wild-type protein at high temperature. Besides, it is found that the triple-stranded antiparallel β-sheet in the wild-type protein plays an important role in maintaining the stability of the entire structure.
Collapse
Affiliation(s)
- Xianjin Xu
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | | | | | | |
Collapse
|
7
|
Majumder R, Roy S, Thakur AR. Molecular Modeling and Molecular Dynamics Simulation Studies of Delta-Notch Complex. J Biomol Struct Dyn 2011; 29:297-310. [DOI: 10.1080/07391102.2011.10507386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
8
|
Behmard E, Abdolmaleki P, Asadabadi EB, Jahandideh S. Prevalent Mutations of Human Prion Protein: A Molecular Modeling and Molecular Dynamics Study. J Biomol Struct Dyn 2011; 29:379-89. [DOI: 10.1080/07391102.2011.10507392] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
9
|
Jani V, Sonavane UB, Joshi R. Microsecond scale replica exchange molecular dynamic simulation of villin headpiece: an insight into the folding landscape. J Biomol Struct Dyn 2011; 28:845-60. [PMID: 21469746 DOI: 10.1080/07391102.2011.10508612] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Reaching the experimental time scale of millisecond is a grand challenge for protein folding simulations. The development of advanced Molecular Dynamics techniques like Replica Exchange Molecular Dynamics (REMD) makes it possible to reach these experimental timescales. In this study, an attempt has been made to reach the multi microsecond simulation time scale by carrying out folding simulations on a three helix bundle protein, Villin, by combining REMD and Amber United Atom model. Twenty replicas having different temperatures ranging from 295 K to 390 K were simulated for 1.5 µs each. The lowest Root Mean Square Deviation (RMSD) structure of 2.5 Å was obtained with respect to native structure (PDB code 1VII), with all the helices formed. The folding population landscapes were built using segment-wise RMSD and Principal Components as reaction coordinates. These analyses suggest the two-stage folding for Villin. The combination of REMD and Amber United Atom model may be useful to understand the folding mechanism of various fast folding proteins.
Collapse
Affiliation(s)
- Vinod Jani
- Bioinformatics Team, Scientific and Engineering Computing Group, Centre for Development of Advanced Computing, Pune University Campus, Ganeshkhind, Pune - 411007, Maharashtra, India
| | | | | |
Collapse
|
10
|
Su JG, Xu XJ, Li CH, Chen WZ, Wang CX. An Analysis of the Influence of Protein Intrinsic Dynamical Properties on its Thermal Unfolding Behavior. J Biomol Struct Dyn 2011; 29:105-21. [DOI: 10.1080/07391102.2011.10507377] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
|
11
|
Purohit R, Rajendran V, Sethumadhavan R. Studies on Adaptability of Binding Residues Flap Region of TMC-114 Resistance HIV-1 Protease Mutants. J Biomol Struct Dyn 2011; 29:137-52. [DOI: 10.1080/07391102.2011.10507379] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
12
|
Zhang J, Liu DD. Molecular Dynamics Studies on the Structural Stability of Wild-type Dog Prion Protein. J Biomol Struct Dyn 2011; 28:861-9. [DOI: 10.1080/07391102.2011.10508613] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
13
|
Zhou ZL, Zhao JH, Liu HL, Wu JW, Liu KT, Chuang CK, Tsai WB, Ho Y. The Possible Structural Models for Polyglutamine Aggregation: A Molecular Dynamics Simulations Study. J Biomol Struct Dyn 2011; 28:743-58. [DOI: 10.1080/07391102.2011.10508603] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
14
|
Olmez EO, Alakent B. Alpha7 Helix Plays an Important Role in the Conformational Stability of PTP1B. J Biomol Struct Dyn 2011; 28:675-93. [DOI: 10.1080/07391102.2011.10508599] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
15
|
Roy S, Thakur AR. Two models of Smad4 and Hoxa9 Complex are Proposed: Structural and Interactional Perspective. J Biomol Struct Dyn 2011; 28:729-42. [DOI: 10.1080/07391102.2011.10508602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
16
|
Zhao Y, Gong Z, Xiao Y. Improvements of the Hierarchical Approach for Predicting RNA Tertiary Structure. J Biomol Struct Dyn 2011; 28:815-26. [DOI: 10.1080/07391102.2011.10508609] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
17
|
Chakrabarti B, Bairagya HR, Mallik P, Mukhopadhyay BP, Bera AK. An Insight to Conserved Water Molecular Dynamics of Catalytic and Structural Zn+2ions in Matrix Metalloproteinase 13 of Human. J Biomol Struct Dyn 2011; 28:503-16. [DOI: 10.1080/07391102.2011.10508591] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
18
|
Banappagari S, Ronald S, Satyanarayanajois SD. A conformationally constrained peptidomimetic binds to the extracellular region of HER2 protein. J Biomol Struct Dyn 2011; 28:289-308. [PMID: 20919746 DOI: 10.1080/07391102.2010.10507360] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Human epidermal growth factor receptor 2 (HER2) is a member of the human epidermal growth factor receptor kinases (other members include EGFR or HER1, HER3, and HER4) that are involved in signaling cascades for cell growth and differentiation. It is well established that HER2-mediated heterodimerization has important implications in cancer. Deregulation of signaling pathways and overexpression of HER2 is known to occur in cancer cells, indicating a role of HER2 in tumorigenesis. Therefore, blocking HER2-mediated signaling has potential therapeutic value. We have designed several peptidomimetics to inhibit HER2-mediated signaling for cell growth. One of the compounds (HERP5, Arg-beta Naph-Phe) exhibited antiproliferative activity with IC(50) values in the micromolar-to-nanomolar range in breast cancer cell lines. Binding of fluorescently labeled HERP5 to HER2 protein was evaluated by fluorescence assay, microscopy, and circular dichroism spectroscopy. Results indicated that HERP5 binds to the extracellular region of the HER2 protein. Structure of the peptidomimetic HERP5 was studied by NMR and molecular dynamics simulations. Based on these results a model was proposed for HER2-EGFR dimerization and possible blocking by HERP5 peptidomimetic using a protein-protein docking method.
Collapse
Affiliation(s)
- Sashikanth Banappagari
- Department of Basic Pharmaceutical Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, LA 71201, USA
| | | | | |
Collapse
|
19
|
Fogolari F, Corazza A, Varini N, Rotter M, Gumral D, Codutti L, Rennella E, Viglino P, Bellotti V, Esposito G. Molecular dynamics simulation of β₂-microglobulin in denaturing and stabilizing conditions. Proteins 2010; 79:986-1001. [PMID: 21287627 DOI: 10.1002/prot.22940] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 10/22/2010] [Accepted: 11/02/2010] [Indexed: 11/11/2022]
Abstract
β₂-Microglobulin has been a model system for the study of fibril formation for 20 years. The experimental study of β₂-microglobulin structure, dynamics, and thermodynamics in solution, at atomic detail, along the pathway leading to fibril formation is difficult because the onset of disorder and aggregation prevents signal resolution in Nuclear Magnetic Resonance experiments. Moreover, it is difficult to characterize conformers in exchange equilibrium. To gain insight (at atomic level) on processes for which experimental information is available at molecular or supramolecular level, molecular dynamics simulations have been widely used in the last decade. Here, we use molecular dynamics to address three key aspects of β₂-microglobulin, which are known to be relevant to amyloid formation: (1) 60 ns molecular dynamics simulations of β₂-microglobulin in trifluoroethanol and in conditions mimicking low pH are used to study the behavior of the protein in environmental conditions that are able to trigger amyloid formation; (2) adaptive biasing force molecular dynamics simulation is used to force cis-trans isomerization at Proline 32 and to calculate the relative free energy in the folded and unfolded state. The native-like trans-conformer (known as intermediate 2 and determining the slow phase of refolding), is simulated for 10 ns, detailing the possible link between cis-trans isomerization and conformational disorder; (3) molecular dynamics simulation of highly concentrated doxycycline (a molecule able to suppress fibril formation) in the presence of β₂-microglobulin provides details of the binding modes of the drug and a rationale for its effect.
Collapse
Affiliation(s)
- Federico Fogolari
- Dipartimento di Scienze e Tecnologie Biomediche, Universita' di Udine, Piazzale Kolbe 4, 33100 Udine, Italy.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Cao Z, Liu L, Wang J. Effects of pH and Temperature on the Structural and Thermodynamic Character of a-syn12 Peptide in Aqueous Solution. J Biomol Struct Dyn 2010; 28:343-53. [DOI: 10.1080/07391102.2010.10507364] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
21
|
Huang HJ, Lee KJ, Yu HW, Chen HY, Tsai FJ, Chen CYC. A novel strategy for designing the selective PPAR agonist by the "sum of activity" model. J Biomol Struct Dyn 2010; 28:187-200. [PMID: 20645652 DOI: 10.1080/07391102.2010.10507352] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Peroxisome proliferator-activated receptors alpha, delta and gamma are a collection of ligand-activated transcription factors crucial in lipid and glucose homeostasis. The involvement of these receptors in lipid metabolism makes them perfect therapeutic target for treating obesity and stroke. In this study, 'sum of activity' model was employed to design multi-target agonists. We used a new strategy to design agonists that fit both alpha and delta but not gamma, to avoid side effect. The CoMFA and CoMSIA models were used to explore the pharmacophore features by constructing three individual models: (a) alpha-model, (b) delta-model and (c) gamma-model, and two sum models: (d) alpha, delta- model, and (e) alpha, delta and gamma-model. The CoMFA model yielded a significant cross validation value, q(2), of 0.729 and non-cross validation value, r(2), of 0.933 in the alpha, delta-model. The CoMSIA studies yielded the best predictive models with q(2) of 0.622 in A+S and with r(2) of 0.911 in the alpha, delta-model. Finally, we proposed that distinct features shown in models (a), (b), (d) but not (c) and (e) should be accounted in designing weight-controlling drugs.
Collapse
Affiliation(s)
- Hung-Jin Huang
- Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan, ROC
| | | | | | | | | | | |
Collapse
|
22
|
Abstract
Molecular shape is essential in understanding molecular function, and understanding molecular shape requires definition of molecular boundaries. In this paper, we review the conceptual evolution of three molecular boundary types: the van der Waals surface, the Connolly surface, and the Lee-Richards (accessible) surface. Then, we point out the confusion among the names of these surfaces existing in the literature. Since it is desirable to have a well-defined terminology in a discipline, we propose the standard names of the three molecular boundary types and their corresponding volumes in order to maximize consistency among researchers, respect the first individual who defined or computed a surface type, and promote collaboration between biologists and geometers.
Collapse
Affiliation(s)
- Deok-Soo Kim
- Department of Industrial Engineering, Hanyang University, 17 Haengdang-dong, Seongdong-gu, Seoul 133-791, South Korea.
| | | | | |
Collapse
|
23
|
Huang HJ, Lee KJ, Yu HW, Chen CY, Hsu CH, Chen HY, Tsai FJ, Chen CYC. Structure-based and ligand-based drug design for HER 2 receptor. J Biomol Struct Dyn 2010; 28:23-37. [PMID: 20476793 DOI: 10.1080/07391102.2010.10507341] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Human epidermal growth factor receptor 2, HER2, is a commonly over-expressed tyrosine kinase receptor found in many types of carcinoma. Despite that there are several HER2 inhibitors, namely Iressa, Tarceva and Tykerb, currently in clinical trials, all can cause several side effects. In this study, both structure-based and ligand-based drug design were employed to design novel HER2 inhibitors from traditional Chinese medicine (TCM). The HER2 structure model was built in homology modeling based on known receptors of the same family. Docking and de novo evolution experiments were performed to identify candidates and to build derivatives. A training set of 32 compounds with inhibitory activities to HER2 was used to formulate the pharmacophore hypotheses that were subsequently used to examine candidates obtained from the docking study. Hydrogen bond interactions, salt-bridge formations and pi-stacking were observed between the ligands and Phe731, Lys753, Asp863 and Asp808 of HER2 protein. Combining results from both docking and pharmacophore mapping analysis, CLC015-5, CLC604-11 and CLC604-18 were well accepted and consistent in both approaches and were considered as the most potential HER2 inhibitors.
Collapse
Affiliation(s)
- Hung-Jin Huang
- Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan, ROC
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Chang LK, Zhao JH, Liu HL, Wu JW, Chuang CK, Liu KT, Chen JT, Tsai WB, Ho Y. The Importance of Steric Zipper on the Aggregation of the MVGGVV Peptide Derived from the Amyloid β Peptide. J Biomol Struct Dyn 2010; 28:39-50. [DOI: 10.1080/07391102.2010.10507342] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
25
|
Yu Y, Wang Y, He J, Liu Y, Li H, Zhang H, Song Y. Structural and Dynamic properties of a new Amyloidogenic chicken cystatin Mutant I108T. J Biomol Struct Dyn 2010; 27:641-9. [DOI: 10.1080/07391102.2010.10508578] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
26
|
Cao Z, Wang J. A Comparative Study of Two Different Force Fields on Structural and Thermodynamics Character of H1 Peptide via Molecular Dynamics Simulations. J Biomol Struct Dyn 2010; 27:651-61. [DOI: 10.1080/07391102.2010.10508579] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|