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Qureshi R, Zou B, Alam T, Wu J, Lee VHF, Yan H. Computational Methods for the Analysis and Prediction of EGFR-Mutated Lung Cancer Drug Resistance: Recent Advances in Drug Design, Challenges and Future Prospects. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:238-255. [PMID: 35007197 DOI: 10.1109/tcbb.2022.3141697] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Lung cancer is a major cause of cancer deaths worldwide, and has a very low survival rate. Non-small cell lung cancer (NSCLC) is the largest subset of lung cancers, which accounts for about 85% of all cases. It has been well established that a mutation in the epidermal growth factor receptor (EGFR) can lead to lung cancer. EGFR Tyrosine Kinase Inhibitors (TKIs) are developed to target the kinase domain of EGFR. These TKIs produce promising results at the initial stage of therapy, but the efficacy becomes limited due to the development of drug resistance. In this paper, we provide a comprehensive overview of computational methods, for understanding drug resistance mechanisms. The important EGFR mutants and the different generations of EGFR-TKIs, with the survival and response rates are discussed. Next, we evaluate the role of important EGFR parameters in drug resistance mechanism, including structural dynamics, hydrogen bonds, stability, dimerization, binding free energies, and signaling pathways. Personalized drug resistance prediction models, drug response curve, drug synergy, and other data-driven methods are also discussed. Recent advancements in deep learning; such as AlphaFold2, deep generative models, big data analytics, and the applications of statistics and permutation are also highlighted. We explore limitations in the current methodologies, and discuss strategies to overcome them. We believe this review will serve as a reference for researchers; to apply computational techniques for precision medicine, analyzing structures of protein-drug complexes, drug discovery, and understanding the drug response and resistance mechanisms in lung cancer patients.
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Local ablation of gastric cancer by reconstituted apolipoprotein B lipoparticles carrying epigenetic drugs. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2021; 37:102450. [PMID: 34332115 DOI: 10.1016/j.nano.2021.102450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 04/28/2021] [Accepted: 07/10/2021] [Indexed: 11/21/2022]
Abstract
Epigenetic inhibitors have shown anticancer effects. Combination chemotherapy with epigenetic inhibitors has shown high effectiveness in gastric cancer clinical trials, but severe side effect and local progression are the causes of treatment failure. Therefore, we sought to develop an acidity-sensitive drug delivery system to release drugs locally to diminish unfavorable outcome of gastric cancer. In this study, we showed that, as compared with single agents, combination treatment with the demethylating agent 5'-aza-2'-deoxycytidine and HDAC inhibitors Trichostatin A or LBH589 decreased cell survival, blocked cell cycle by reducing number of S-phase cells and expression of cyclins, increased cell apoptosis by inducing expression of Bim and cleaved Caspase 3, and reexpressed tumor suppressor genes more effectively in MGCC3I cells. As a carrier, reconstituted apolipoprotein B lipoparticles (rABLs) could release drugs in acidic environments. Orally administrated embedded drugs not only showed inhibitory effects on gastric tumor growth in a syngeneic orthotopic mouse model, but also reduced the hepatic and renal toxicity. In conclusion, we have established rABL-based nanoparticles embedded epigenetic inhibitors for local treatment of gastric cancer, which have good therapeutic effects but do not cause severe side effects.
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Huang SY, Kung YA, Huang PN, Chang SY, Gong YN, Han YJ, Chiang HJ, Liu KT, Lee KM, Chang CY, Chang CC, Huang CG, Shih SR. Stability of SARS-CoV-2 Spike G614 Variant Surpasses That of the D614 Variant after Cold Storage. mSphere 2021; 6:e00104-21. [PMID: 33789940 PMCID: PMC8546686 DOI: 10.1128/msphere.00104-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/10/2021] [Indexed: 12/11/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) carrying the D614G mutation on the spike protein is the predominant circulating variant and is associated with enhanced infectivity. However, whether this dominant variant can potentially spread through the cold chain and whether the spike protein affects virus stability after cold storage remain unclear. To compare the infectivity of two SARS-CoV-2 variants, namely, SARS-CoV-2 variants with spike protein with the D614 mutation (S-D614) and G614 mutation (S-G614), after different periods of refrigeration (4°C) and freezing (-20°C). We also determined the integrity of the viral RNA and the ability of the spike protein to bind angiotensin-converting enzyme 2 (ACE2) after storage at these conditions. The results showed that SARS-CoV-2 was more stable and infectious after storage at -20°C than at 4°C. Particularly, the S-G614 variant was found to be more stable than the S-D614 variant. The spike protein of the S-G614 variant had better binding ability with the ACE2 receptor than that of the S-D614 variant after storage at -20°C for up to 30 days. Our findings revealed that SARS-CoV-2 remains stable and infectious after refrigeration or freezing, and their stability and infectivity up to 30 days depends on the spike variant. Stability and infectivity are related to each other, and the higher stability of S-G614 compared to that of S-D614 may contribute to rapid viral spread of the S-G614 variant.IMPORTANCE It has been observed that variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are more stable and infectious after storage at -20°C than at 4°C. A SARS-CoV-2 S-D614G variant is currently the most dominant variant in circulation and is associated with enhanced infectivity. We compared the stability of two SARS-CoV-2 variants: the early S-D614 variant carrying the D614 spike protein and the new S-G614 variant carrying the G614 spike protein, stored at both 4°C and -20°C for different periods. We observed that SARS-CoV-2 remains stable and infectious after refrigeration or freezing, which further depends on the spike variant, that is, the ability of the spike protein to bind with the ACE2 receptor with higher efficiency. The high stability of the S-G614 variant also explains its rapid spread and infectivity. Therefore, precautions should be taken during and after handling food preserved under cold conditions.
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Affiliation(s)
- Sheng-Yu Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yu-An Kung
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Peng-Nien Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Infectious Diseases, Department of Pediatrics, Linkou Chung Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Sheng-Yun Chang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Bachelor Program in Artificial Intelligence, College of Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Nong Gong
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yi-Ju Han
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Science, Division of Biotechnology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Huan-Jung Chiang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuan-Ting Liu
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Science, Division of Biotechnology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Ming Lee
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Yu Chang
- Department of Biological Science and Technology, College of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Chia-Ching Chang
- Department of Biological Science and Technology, College of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Department of Electrophysics, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Physics, Academia Sinica, Nankang, Taipei, Taiwan
| | - Chung-Guei Huang
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Research Center for Chinese Herbal Medicine, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Research Center for Food and Cosmetic Safety, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
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Chu HL, Cheng TM, Chen HW, Chou FH, Chang YC, Lin HY, Liu SY, Liang YC, Hsu MH, Wu DS, Li HY, Ho LP, Wu PC, Chen FR, Chen GS, Shieh DB, Chang CS, Su CH, Yao Z, Chang CC. Synthesis of apolipoprotein B lipoparticles to deliver hydrophobic/amphiphilic materials. ACS APPLIED MATERIALS & INTERFACES 2013; 5:7509-16. [PMID: 23834261 PMCID: PMC3744920 DOI: 10.1021/am401808e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/08/2013] [Indexed: 05/23/2023]
Abstract
To develop a drug delivery system (DDS), it is critical to address challenging tasks such as the delivery of hydrophobic and amphiphilic compounds, cell uptake, and the metabolic fate of the drug delivery carrier. Low-density lipoprotein (LDL) has been acknowledged as the human serum transporter of natively abundant lipoparticles such as cholesterol, triacylglycerides, and lipids. Apolipoprotein B (apo B) is the only protein contained in LDL, and possesses a binding moiety for the LDL receptor that can be internalized and degraded naturally by the cell. Therefore, synthetic/reconstituting apoB lipoparticle (rABL) could be an excellent delivery carrier for hydrophobic or amphiphilic materials. Here, we synthesized rABL in vitro, using full-length apoB through a five-step solvent exchange method, and addressed its potential as a DDS. Our rABL exhibited good biocompatibility when evaluated with cytotoxicity and cell metabolic response assays, and was stable during storage in phosphate-buffered saline at 4 °C for several months. Furthermore, hydrophobic superparamagnetic iron oxide nanoparticles (SPIONPs) and the anticancer drug M4N (tetra-O-methyl nordihydroguaiaretic acid), used as an imaging enhancer and lipophilic drug model, respectively, were incorporated into the rABL, leading to the formation of SPIONPs- and M4N- containing rABL (SPIO@rABL and M4N@rABL, respectively). Fourier transform infrared spectroscopy suggested that rABL has a similar composition to that of LDL, and successfully incorporated SPIONPs or M4N. SPIO@rABL presented significant hepatic contrast enhancement in T2-weighted magnetic resonance imaging in BALB/c mice, suggesting its potential application as a medical imaging contrast agent. M4N@rABL could reduce the viability of the cancer cell line A549. Interestingly, we developed solution-phase high-resolution transmission electron microscopy to observe both LDL and SPIO@rABL in the liquid state. In summary, our LDL-based DDS, rABL, has significant potential as a novel DDS for hydrophobic and amphiphilic materials, with good cell internalization properties and metabolicity.
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Affiliation(s)
- Hsueh-Liang Chu
- Department
of Biological Science
and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
| | - Tsai-Mu Cheng
- Department
of Biological Science
and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
- Graduate Institute of Translational
Medicine, College of Medicine and Technology, Taipei
Medical University, Taipei 11031, Taiwan
| | - Hung-Wei Chen
- Department
of Biological Science
and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
| | - Fu-Hsuan Chou
- Department
of Biological Science
and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
- Department of Materials Science
and Engineering, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Yu-Chuan Chang
- Department
of Biological Science
and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
| | - Hsin-Yu Lin
- Department
of Engineering and System Science and Nuclear Science and Technology Development
Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Shih-Yi Liu
- Department
of Engineering and System Science and Nuclear Science and Technology Development
Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yu-Chuan Liang
- Agricultural
Biotechnology Research Center and Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Ming-Hua Hsu
- Department
of Engineering and System Science and Nuclear Science and Technology Development
Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Dian-Shyeu Wu
- Department
of Biological Science
and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
| | - Hsing-Yuan Li
- Department
of Biological Science
and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
| | - Li-Ping Ho
- Department
of Biological Science
and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
| | - Ping-Ching Wu
- Institute of Oral Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Fu-Rong Chen
- Department
of Engineering and System Science and Nuclear Science and Technology Development
Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Gong-Shen Chen
- Department of Hematology, Mackay Memorial Hospital, Taipei 10449, Taiwan
| | - Dar-Bin Shieh
- Institute of Oral Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Chia-Seng Chang
- Agricultural
Biotechnology Research Center and Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Chia-Hao Su
- Center for Translational Research
in Biomedical Sciences, Kaohsiung Chang Gung Memorial
Hospital, Kaohsiung 83342, Taiwan
| | - Zemin Yao
- Department of Biochemistry,
Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Chia-Ching Chang
- Department
of Biological Science
and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
- Agricultural
Biotechnology Research Center and Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
- E-mail: . Tel: 886-3-5731633. Fax: 886-3-5733259
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CHANG CHIACHING, LIN CHIUSHEUN, CHEN MEICHUN, LIU YINCHANG, HUANG YIFU, LIN POYEN, CHEN YENFU, CHANG CHIASHENG, KAN LOUSING. FOLDING AND STRUCTURAL CHARACTERIZATION OF RECOMBINANT CYCLIN-DEPENDENT KINASE INHIBITOR p21(Cip1, Waf1, Sdi1). ACTA ACUST UNITED AC 2011. [DOI: 10.1142/s1793048006000070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
p21Cip1, Waf1, Sdi1 (p21) is a member of the cyclin-dependent kinase (CDK) family of inhibitors in eukaryotes. We report the refolding of an inclusion body of a recombinant p21 (rp21) to its native form, under an alkaline to neutral environment, via an over-critical process describable by a first-order state transition model. The secondary structure of the refolded rp21 possesses a helical-major structure as determined by circular dichroism (CD) analysis, and its diameter is around 3 nm, as measured by dynamic light scattering studies (DLS) and atomic force microscopy (AFM). The differential scanning calorimeter (DSC) measurement indicates that the folded rp21 possesses unique but weak tertiary interactions. That the function of rp21 is reinstated upon refolding under our experimental conditions is evidenced by its binding to proliferating cell nuclear antigen (PCNA) in an immuno-co-precitptation analysis. The conformational changes of the folding intermediates of rp21 are consistent with the framework of a sequential model proposed earlier. The lack of a definitive structure of p21 in acidic condition will be discussed.
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Affiliation(s)
- CHIA-CHING CHANG
- Department of Physics, National Dong Hwa University, Hualien, 97401 Taiwan, ROC
| | - CHIU-SHEUN LIN
- Department of Physics, National Dong Hwa University, Hualien, 97401 Taiwan, ROC
| | - MEI-CHUN CHEN
- Department of Physics, National Dong Hwa University, Hualien, 97401 Taiwan, ROC
| | - YIN-CHANG LIU
- Department of Life Science and Institute of Molecular Medicine, National Tsing-Hua University, Hsin-Chu, 30043 Taiwan, ROC
| | - YI-FU HUANG
- Department of Life Science and Institute of Molecular Medicine, National Tsing-Hua University, Hsin-Chu, 30043 Taiwan, ROC
| | - PO-YEN LIN
- Institute of Physics, Academia Sinica, Taipei, 11529 Taiwan, ROC
| | - YEN-FU CHEN
- Institute of Physics, Academia Sinica, Taipei, 11529 Taiwan, ROC
| | - CHIA-SHENG CHANG
- Institute of Physics, Academia Sinica, Taipei, 11529 Taiwan, ROC
| | - LOU-SING KAN
- Institute of Chemistry, Academia Sinica, Taipei, 11529 Taiwan, ROC
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Chang CC, Lin PY, Yeh XC, Deng KH, Ho YP, Kan LS. Protein folding stabilizing time measurement: A direct folding process and three-dimensional random walk simulation. Biochem Biophys Res Commun 2005; 328:845-50. [PMID: 15707956 DOI: 10.1016/j.bbrc.2005.01.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Indexed: 11/28/2022]
Abstract
Protein particles undergo Brownian motion and collisions in solution. The diffusive collisions may lead to aggregation. For proteins to fold successfully the process has to occur quickly and before significant collision takes place. The speed of protein folding was deduced by studying the correlation time of a lysozyme refolding process from autocorrelation function analysis of the mean collision time and aggregation/soluble ratio of protein. It is a measure of time before which an aggregate can be formed and also is the time measure for a protein to fold into a stable state. We report on the protein folding stabilizing time of a lysozyme system to be 25.5-27.5 micros (<+/-4%) between 295 and 279K via direct folding experimental studies, supported by a three-dimensional random walk simulation of diffusion-limited aggregation model. Aggregation is suppressed when the protein is folded to a stable form. Spontaneous folding and diffusion-limited aggregation are antagonistic in nature. Meanwhile, the resultant aggresome, suggested by Raman and mass spectroscopy, may be formed by cross-linkages of disulfide bonds and hydrophobic interactions.
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Affiliation(s)
- Chia-Ching Chang
- Department of Physics, National Dong Hwa University, Hualien 97401, Taiwan.
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Chang CC, Yeh XC, Lee HT, Lin PY, Kan LS. Refolding of lysozyme by quasistatic and direct dilution reaction paths: a first-order-like state transition. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2004; 70:011904. [PMID: 15324085 DOI: 10.1103/physreve.70.011904] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2003] [Indexed: 05/24/2023]
Abstract
A first-order-like state transition model is considered to be a global reaction mechanism to directly folded proteins from an unfolded state to its native form. In order to verify the general applicability of this mechanism, we used lysozyme as a model protein. It was fully unfolded by 4.5 M urea, 0.1 M dithiothreitol (DTT) in pH 3 and refolded to its native form by way of an overcritical reaction path (a quasistatic process) or directly crossing transition boundary path (a directly dilution process). In addition to the two states coexisting in the direct folding path, lysozyme might be trapped in a glassy state. However, it can escape from the glassy state by concentration twice. This indicates the existence of a state transition line or boundary in the direct folding reaction. However, lysozyme can continuously fold from unfolded to native by an overcritical reaction path. During the overcritical path, four stable folding intermediates and native lysozyme were obtained. The secondary structures, particle size distributions, thermal stabilities, and oxidation state of disulfide bonds of folding intermediates were analyzed by circular dichroism spectra, dynamic light scattering, differential scanning calorimetry, and Raman spectra, respectively. According to the data, the intermediates of both the overcritical reaction and the direct crossing transition boundary paths can be described by a common concept pertaining to a model that undergoes collapse, sequential, and first-order-like state transition. This indicated that protein folding by way of different reaction paths might follow a similar folding mechanism-i.e., a mechanism of overcritical folding of intermediates. A protein folding reaction diagram is postulated and discussed. In spite of a global interaction mechanism the alpha -helix is formed prior to the beta -sheet, which may indicate that protein folding is initiated by local interactions.
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Affiliation(s)
- Chia-Ching Chang
- Department of Physics, National Dong Hwa University, Hualien, Taiwan 97401.
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