1
|
Nguyen TTD, Ho QT, Le NQK, Phan VD, Ou YY. Use Chou's 5-Steps Rule With Different Word Embedding Types to Boost Performance of Electron Transport Protein Prediction Model. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1235-1244. [PMID: 32750894 DOI: 10.1109/tcbb.2020.3010975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Living organisms receive necessary energy substances directly from cellular respiration. The completion of electron storage and transportation requires the process of cellular respiration with the aid of electron transport chains. Therefore, the work of deciphering electron transport proteins is inevitably needed. The identification of these proteins with high performance has a prompt dependence on the choice of methods for feature extraction and machine learning algorithm. In this study, protein sequences served as natural language sentences comprising words. The nominated word embedding-based feature sets, hinged on the word embedding modulation and protein motif frequencies, were useful for feature choosing. Five word embedding types and a variety of conjoint features were examined for such feature selection. The support vector machine algorithm consequentially was employed to perform classification. The performance statistics within the 5-fold cross-validation including average accuracy, specificity, sensitivity, as well as MCC rates surpass 0.95. Such metrics in the independent test are 96.82, 97.16, 95.76 percent, and 0.9, respectively. Compared to state-of-the-art predictors, the proposed method can generate more preferable performance above all metrics indicating the effectiveness of the proposed method in determining electron transport proteins. Furthermore, this study reveals insights about the applicability of various word embeddings for understanding surveyed sequences.
Collapse
|
2
|
Abstract
During the last three decades or so, many efforts have been made to study the protein cleavage
sites by some disease-causing enzyme, such as HIV (Human Immunodeficiency Virus) protease
and SARS (Severe Acute Respiratory Syndrome) coronavirus main proteinase. It has become increasingly
clear <i>via</i> this mini-review that the motivation driving the aforementioned studies is quite wise,
and that the results acquired through these studies are very rewarding, particularly for developing peptide
drugs.
Collapse
Affiliation(s)
- Kuo-Chen Chou
- Gordon Life Science Institute, Boston, MA 02478, United States
| |
Collapse
|
3
|
Chou KC. An Insightful 10-year Recollection Since the Emergence of the 5-steps Rule. Curr Pharm Des 2020; 25:4223-4234. [PMID: 31782354 DOI: 10.2174/1381612825666191129164042] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/25/2019] [Indexed: 11/22/2022]
Abstract
OBJECTIVE One of the most challenging and also the most difficult problems is how to formulate a biological sequence with a vector but considerably keep its sequence order information. METHODS To address such a problem, the approach of Pseudo Amino Acid Components or PseAAC has been developed. RESULTS AND CONCLUSION It has become increasingly clear via the 10-year recollection that the aforementioned proposal has been indeed very powerful.
Collapse
Affiliation(s)
- Kuo-Chen Chou
- Gordon Life Science Institute, Boston, Massachusetts 02478, United States.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| |
Collapse
|
4
|
Zheng H, Yang H, Gong D, Mai L, Qiu X, Chen L, Su X, Wei R, Zeng Z. Progress in the Mechanism and Clinical Application of Cilostazol. Curr Top Med Chem 2020; 19:2919-2936. [PMID: 31763974 DOI: 10.2174/1568026619666191122123855] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/27/2019] [Accepted: 08/02/2019] [Indexed: 12/20/2022]
Abstract
Cilostazol is a unique platelet inhibitor that has been used clinically for more than 20 years. As a phosphodiesterase type III inhibitor, cilostazol is capable of reversible inhibition of platelet aggregation and vasodilation, has antiproliferative effects, and is widely used in the treatment of peripheral arterial disease, cerebrovascular disease, percutaneous coronary intervention, etc. This article briefly reviews the pharmacological mechanisms and clinical application of cilostazol.
Collapse
Affiliation(s)
- Huilei Zheng
- Department of Medical Examination & Health Management, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.,Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention,Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China
| | - Hua Yang
- Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention,Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China.,Department of Critical Care Medicine, Second People's Hospital of Nanning, Nanning, Guangxi, China
| | - Danping Gong
- Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention,Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China.,Elderly Cardiology Ward, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Lanxian Mai
- Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention,Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China.,Disciplinary Construction Office, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xiaoling Qiu
- Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention,Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China
| | - Lidai Chen
- Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention,Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China
| | - Xiaozhou Su
- Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention,Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China
| | - Ruoqi Wei
- Department of Computer Science and Engineering, University of Bridgeport,126 Park Ave, BRIDGEPORT, CT 06604, United States
| | - Zhiyu Zeng
- Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention,Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China.,Elderly Cardiology Ward, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| |
Collapse
|
5
|
Chou KC. Impacts of Pseudo Amino Acid Components and 5-steps Rule to Proteomics and Proteome Analysis. Curr Top Med Chem 2019; 19:2283-2300. [DOI: 10.2174/1568026619666191018100141] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 08/18/2019] [Accepted: 08/26/2019] [Indexed: 01/27/2023]
Abstract
Stimulated by the 5-steps rule during the last decade or so, computational proteomics has achieved remarkable progresses in the following three areas: (1) protein structural class prediction; (2) protein subcellular location prediction; (3) post-translational modification (PTM) site prediction. The results obtained by these predictions are very useful not only for an in-depth study of the functions of proteins and their biological processes in a cell, but also for developing novel drugs against major diseases such as cancers, Alzheimer’s, and Parkinson’s. Moreover, since the targets to be predicted may have the multi-label feature, two sets of metrics are introduced: one is for inspecting the global prediction quality, while the other for the local prediction quality. All the predictors covered in this review have a userfriendly web-server, through which the majority of experimental scientists can easily obtain their desired data without the need to go through the complicated mathematics.
Collapse
Affiliation(s)
- Kuo-Chen Chou
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| |
Collapse
|
6
|
Chou KC. Proposing Pseudo Amino Acid Components is an Important Milestone for Proteome and Genome Analyses. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09910-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
7
|
Nosik VL, Rudakova EB. Prospects of biomolecule sequencing with the techniques of translocation through nanopores: A review. CRYSTALLOGR REP+ 2013. [DOI: 10.1134/s1063774513060187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
8
|
Lin SX, Lapointe J. Theoretical and experimental biology in one<br>—A symposium in honour of Professor Kuo-Chen Chou’s 50th anniversary and Professor Richard Giegé’s 40th anniversary of their scientific careers. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/jbise.2013.64054] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
9
|
Pérez-Montoto LG, Santana L, González-Díaz H. Scoring function for DNA-drug docking of anticancer and antiparasitic compounds based on spectral moments of 2D lattice graphs for molecular dynamics trajectories. Eur J Med Chem 2009; 44:4461-9. [PMID: 19604606 PMCID: PMC7127518 DOI: 10.1016/j.ejmech.2009.06.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 06/04/2009] [Accepted: 06/05/2009] [Indexed: 02/02/2023]
Abstract
We introduce here a new class of invariants for MD trajectories based on the spectral moments pi(k)(L) of the Markov matrix associated to lattice network-like (LN) graph representations of Molecular Dynamics (MD) trajectories. The procedure embeds the MD energy profiles on a 2D Cartesian coordinates system using simple heuristic rules. At the same time, we associate the LN with a Markov matrix that describes the probabilities of passing from one state to other in the new 2D space. We construct this type of LNs for 422 MD trajectories obtained in DNA-drug docking experiments of 57 furocoumarins. The combined use of psoralens+ultraviolet light (UVA) radiation is known as PUVA therapy. PUVA is effective in the treatment of skin diseases such as psoriasis and mycosis fungoides. PUVA is also useful to treat human platelet (PTL) concentrates in order to eliminate Leishmania spp. and Trypanosoma cruzi. Both are parasites that cause Leishmaniosis (a dangerous skin and visceral disease) and Chagas disease, respectively; and may circulate in blood products collected from infected donors. We included in this study both lineal (psoralens) and angular (angelicins) furocoumarins. In the study, we grouped the LNs on two sets; set1: DNA-drug complex MD trajectories for active compounds and set2: MD trajectories of non-active compounds or no-optimal MD trajectories of active compounds. We calculated the respective pi(k)(L) values for all these LNs and used them as inputs to train a new classifier that discriminate set1 from set2 cases. In training series the model correctly classifies 79 out of 80 (specificity=98.75%) set1 and 226 out of 238 (Sensitivity=94.96%) set2 trajectories. In independent validation series the model correctly classifies 26 out of 26 (specificity=100%) set1 and 75 out of 78 (sensitivity=96.15%) set2 trajectories. We propose this new model as a scoring function to guide DNA-docking studies in the drug design of new coumarins for anticancer or antiparasitic PUVA therapy.
Collapse
Affiliation(s)
- Lázaro G. Pérez-Montoto
- Department of Microbiology & Parasitology, and Department of Organic Chemistry
- Faculty of Pharmacy, University of Santiago de Compostela, 15782, Spain
| | - Lourdes Santana
- Faculty of Pharmacy, University of Santiago de Compostela, 15782, Spain
| | - Humberto González-Díaz
- Department of Microbiology & Parasitology, and Department of Organic Chemistry
- Faculty of Pharmacy, University of Santiago de Compostela, 15782, Spain
| |
Collapse
|
10
|
Pérez-Montoto LG, Dea-Ayuela MA, Prado-Prado FJ, Bolas-Fernández F, Ubeira FM, González-Díaz H. Study of peptide fingerprints of parasite proteins and drug-DNA interactions with Markov-Mean-Energy invariants of biopolymer molecular-dynamic lattice networks. POLYMER 2009; 50:3857-3870. [PMID: 32287404 PMCID: PMC7111648 DOI: 10.1016/j.polymer.2009.05.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Revised: 05/06/2009] [Accepted: 05/14/2009] [Indexed: 11/26/2022]
Abstract
Since the advent of Molecular Dynamics (MD) in biopolymers science with the study by Karplus et al. on protein dynamics, MD has become the by foremost well established, computational technique to investigate structure and function of biomolecules and their respective complexes and interactions. The analysis of the MD trajectories (MDTs) remains, however, the greatest challenge and requires a great deal of insight, experience, and effort. Here, we introduce a new class of invariants for MDTs based on the spatial distribution of Mean-Energy values ξk (L) on a 2D Euclidean space representation of the MDTs. The procedure forces one MD trajectory to fold into a 2D Cartesian coordinates system using a step-by-step procedure driven by simple rules. The ξk (L) values are invariants of a Markov matrix (1 Π), which describes the probabilities of transition between two states in the new 2D space; which is associated to a graph representation of MDTs similar to the lattice networks (LNs) of DNA and protein sequences. We also introduce a new algorithm to perform phylogenetic analysis of peptides based on MDTs instead of the sequence of the polypeptide. In a first experiment, we illustrate this algorithm for 35 peptides present on the Peptide Mass Fingerprint (PMF) of a new protein of Leishmania infantum studied in this work. We report, by the first time, 2D Electrophoresis isolation, MALDI TOF Mass Spectroscopy characterization, and MASCOT search results for this PMF. In a second experiment, we construct the LNs for 422 MDTs obtained in DNA-Drug Docking simulations of the interaction of 57 anticancer furocoumarins with a DNA oligonucleotide. We calculated the respective ξk (L) values for all these LNs and used them as inputs to train a new classifier with Accuracy = 85.44% and 84.91% in training and validation respectively. The new model can be used as scoring function to guide DNA-Drug Docking studies in drug design of new coumarins for PUVA therapy. The new phylogenetics analysis algorithms encode information different from sequence similarity and may be used to analyze MDTs obtained in Docking or modeling experiments for any classes of biopolymers. The work opens new perspective on the analysis and applications of MD in polymer sciences.
Collapse
Affiliation(s)
- Lázaro Guillermo Pérez-Montoto
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain,Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - María Auxiliadora Dea-Ayuela
- Departamento de Atención Sanitaria, Salud Pública y Sanidad Animal, Facultad CC Experimentales y de La Salud, Universidad CEU Cardenal Herrera, 46113 Moncada (Valencia), Spain
| | - Francisco J. Prado-Prado
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain,Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | | | - Florencio M. Ubeira
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Humberto González-Díaz
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain,Corresponding author. Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| |
Collapse
|
11
|
Koleva B, Spiteller M, Kolev T. Polarized spectroscopic elucidation of N-acetyl-l-cysteine, l-cysteine, l-cystine, l-ascorbic acid and a tool for their determination in solid mixtures. Amino Acids 2009; 38:295-304. [DOI: 10.1007/s00726-009-0250-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2008] [Accepted: 01/26/2009] [Indexed: 11/28/2022]
|
12
|
Xie A, He Q, Miller L, Sclavi B, Chance MR. Low frequency vibrations of amino acid homopolymers observed by synchrotron far-ir absorption spectroscopy: Excited state effects dominate the temperature dependence of the spectra. Biopolymers 1999. [DOI: 10.1002/(sici)1097-0282(199906)49:7<591::aid-bip5>3.0.co;2-q] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
13
|
Lisy V, Miskovsky P, Brutovsky B, Chinsky L. Internal DNA modes below 25 cm-1: a resonance Raman spectroscopy observation. J Biomol Struct Dyn 1997; 14:517-23. [PMID: 9172651 DOI: 10.1080/07391102.1997.10508150] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The first resonance Raman scattering observation of the low-frequency (LF) region (below 40 up to 12 cm-1) of DNA motions is presented. Since the concentration of the studied DNA solution was very low (1 mg/ml), the spectra features reflect internal vibrations of the macromolecule. The decomposition of the spectra into Lorentzians clearly indicate three intrahelical DNA modes: the corresponding peaks are located at the frequencies 16, 19, and 23 (+/- 1) cm-1. This result is in agreement with our quasi-continuity model of the LF B-form DNA dynamics (V. Lisy, P. Miskovsky and P. Schreiber, J. Biomol. Struct. Dyn. 13, 707 (1996)). The fit of the experimental frequencies to the theory, using the Genetic Algorithms approach, allowed us to make some conclusions about the model force constants which could be found by independent conformational energy calculations. Possible positions of five lowest-frequency DNA peaks, predicted by the model, are discussed.
Collapse
Affiliation(s)
- V Lisy
- Department of Nuclear Physics and Biophysics, P.J. Safarik University, Kosice, Slovakia
| | | | | | | |
Collapse
|
14
|
Lisy V, Miskovsky P, Schreiber P. On a simple model of low-frequency vibrations in DNA macromolecules. J Biomol Struct Dyn 1996; 13:707-16. [PMID: 8906891 DOI: 10.1080/07391102.1996.10508883] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A simple quasi-continuity model of low-frequency dynamics of DNA macromolecules is presented. The model is based on the phenomenological theory by Volkov and Kosevich (J. Biomol. Struct. Dyn. 8, 1069 (1991)). We propose improvements to their theory by correcting the model energy and corresponding equations of motion, recalculating the model DNA parameters, and estimating the effects of hydration and counterion binding on the masses of DNA subunits. Comparing the calculated low-frequency vibration spectrum and the results of classical Raman scattering experiments from the literature, the values for the model force constants are determined. These values differ significantly from the estimations made by Volkov and Kosevich. A good quantitative agreement with experiment can be obtained both for the case when the "25 cm-1 mode" is an external one, and when it is considered as an intrahelical mode. Problems connected with the qualitative assignments of the calculated and experimentally observed modes are discussed.
Collapse
Affiliation(s)
- V Lisy
- Biophysics Division, P.J. Safarik University, Kosice, Slovakia.
| | | | | |
Collapse
|
15
|
Abstract
To describe low-frequency dynamics of DNA macromolecules a model is developed taking into account the hydrogen bond stretching in base pairs, the backbone flexibility and intranucleoside mobility. For double-stranded DNA the normal vibrations are found and the structure of low-frequency spectrum is determined. The agreement between theory and Raman spectroscopy data for B-DNA is demonstrated. Conformational dependences of vibration spectrum during the B----A and helix----coil DNA transitions are studied. The contribution coming from low-frequency mobility to the nucleic-protein recognition processes is discussed.
Collapse
Affiliation(s)
- S N Volkov
- Institute for Theoretical Physics, Academy of Sciences of the Ukrainian SSR, Kiev
| | | |
Collapse
|
16
|
Lisy V, Zatovsky AV. Kinetics of low-frequency excitations in globular macromolecules. J Biol Phys 1991. [DOI: 10.1007/bf00395060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
17
|
Chou KC, Maggiora GM, Mao B. Quasi-continuum models of twist-like and accordion-like low-frequency motions in DNA. Biophys J 1989; 56:295-305. [PMID: 2775828 PMCID: PMC1280479 DOI: 10.1016/s0006-3495(89)82676-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Formulae for calculating low-frequency twist-like and accordion-like modes of DNA molecules have been derived using a quasi-continuum model. The formulae can be employed in essentially all (viz. A, B, C, D, E, and Z) forms of DNA. Calculated results indicate that the experimentally observed low-frequency modes at 22 cm-1 for the A-form octanucleotide (d[CCCCGGGG]) and at 18 cm-1 for the B-form dodecanucleotide (d[CGCAA ATTTGCG]) may result from accordion-like motions, while those observed at 12 cm-1 and 15 cm-1 may result from combinations of twist-like oscillations excited in the intact segments of B- and A-DNA's, respectively. Frequency shifts in the low-frequency modes observed when DNA molecules undergo conformational changes among different forms are also discussed in terms of the current model.
Collapse
Affiliation(s)
- K C Chou
- Computational Chemistry, Upjohn Research Laboratories, Kalamazoo, Michigan 49001
| | | | | |
Collapse
|
18
|
Goichuk IA, Kukhtin VV, Petrov EG. Orientational oscillations of the peptide groups of an ?-helix. J Biol Phys 1989. [DOI: 10.1007/bf00417750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
|
19
|
|
20
|
Svirschevsky S, Apostol M. Solvent and pressure effects on transition rates of enzymatic reactions. Chem Phys Lett 1988. [DOI: 10.1016/0009-2614(88)80375-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
21
|
Abstract
The occurrence of low-frequency motion in biomacromolecules, which had long been speculated upon with a great deal of skepticism, is now a clearly established phenomenon and has been convincingly demonstrated. The next stage in the process of its elucidation appropriately concerns the determination of its origin, the development of a feasible and effective model for the calculations involved and, more importantly, the extending of investigations on its biological roles in order to gain insights into the various interesting mechanisms underlying the dynamic processes occurring in biomacromolecules. Confronted with such a task, this review has been written with the aim of stimulating further, through a systematic and comprehensive description, developments to open up this exciting frontier of molecular biology, especially from the viewpoint of biological functions.
Collapse
Affiliation(s)
- K C Chou
- Computational Chemistry, Upjohn Research Laboratories, Kalamazoo, MI 49001
| |
Collapse
|
22
|
Chou KC, Maggiora GM. Biological functions of low-frequency vibrations (phonons). 7. The impetus for DNA to accommodate intercalators. ACTA ACUST UNITED AC 1988. [DOI: 10.1002/pi.4980200209] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|