Journal of Biological Physics最新文献_第5页

Exploring the interaction of myricetin with human alpha-2-macroglobulin: biophysical and in-silico analysis 探索杨梅素与人α -2巨球蛋白的相互作用:生物物理和计算机分析

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2023-01-20 DOI: 10.1007/s10867-022-09621-z

Sana Ansari, Haseeb Ahsan, Mohammad Khalid Zia, Mansour K. Gatasheh, Fahim H. Khan

{"title":"Exploring the interaction of myricetin with human alpha-2-macroglobulin: biophysical and in-silico analysis","authors":"Sana Ansari, Haseeb Ahsan, Mohammad Khalid Zia, Mansour K. Gatasheh, Fahim H. Khan","doi":"10.1007/s10867-022-09621-z","DOIUrl":"10.1007/s10867-022-09621-z","url":null,"abstract":"<div><p>Myricetin (MYR) is a bioactive secondary metabolite found in plants that is recognized for its nutraceutical value and is an essential constituent of various foods and beverages. It is reported to exhibit a plethora of activities, including antioxidant, antimicrobial, antidiabetic, anticancer, and anti-inflammatory. Alpha-2-macroglobulin (α2M) is a major plasma anti-proteinase that can inhibit proteinases of both human and non-human origin, regardless of their specificity and catalytic mechanism. Here, we explored the interaction of MYR-α2M using various biochemical and biophysical techniques. It was found that the interaction of MYR brings subtle change in its anti-proteolytic potential and thereby alters its structure and function, as can be seen from absorbance and fluorescence spectroscopy. UV spectroscopy of α2M in presence of MYR indicated the occurrence of hyperchromism, suggesting complex formation. Fluorescence spectroscopy reveals that MYR reduces the fluorescence intensity of native α2M with a shift in the wavelength maxima. At 318.15 K, MYR binds to α2M with a binding constant of 2.4 × 10<sup>3</sup> M<sup>−1</sup>, which indicates significant binding. The Δ<i>G</i> value was found to be − 7.56 kcal mol<sup>−1</sup> at 298.15 K, suggesting the interaction to be spontaneous and thermodynamically favorable. The secondary structure of α2M does not involve any major change as was confirmed by CD analysis. The molecular docking indicates that Asp-146, Ser-172, Glu-174, and Tyr-180 were the key residues involved in α2M-MYR complex formation. This study contributes to our understanding of the function and mechanism of protein and flavonoid binding by providing a molecular basis of the interaction between MYR and α2M.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2023-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09621-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4788439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Determinant factors for residence time of kinesin motors at microtubule ends 微管末端驱动电机停留时间的决定因素

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2023-01-16 DOI: 10.1007/s10867-022-09623-x

Ping Xie

引用次数: 0

Energy-guided synapse coupling between neurons under noise 噪声下神经元间能量引导突触耦合

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2023-01-14 DOI: 10.1007/s10867-022-09622-y

Bo Hou, Jun Ma, Feifei Yang

{"title":"Energy-guided synapse coupling between neurons under noise","authors":"Bo Hou, Jun Ma, Feifei Yang","doi":"10.1007/s10867-022-09622-y","DOIUrl":"10.1007/s10867-022-09622-y","url":null,"abstract":"<div><p>From a physical viewpoint, any external stimuli including noise disturbance can inject energy into the media, and the electric response is regulated by the equivalent electric stimulus. For example, mode transition in electric activities in neurons occurs and kinds of spatial patterns are formed during the wave propagation. In this paper, a feasible criterion is suggested to explain and control the growth of electric synapse and memristive synapse between Hindmarsh-Rose neurons in the presence of noise. It is claimed that synaptic coupling can be enhanced adaptively due to energy diversity, and the coupling intensity is increased to a saturation value until two neurons reach certain energy balance. Two identical neurons can reach perfect synchronization when electric synapse coupling is further increased. This scheme is also considered in a chain neural network and uniform noise is applied on all neurons. However, reaching synchronization becomes difficult for neurons in presenting spiking, bursting, and chaotic and periodic patterns, even when the local energy balance is corrupted to continue further growth of the coupling intensity. In the presence of noise, energy diversity becomes uncertain because of spatial diversity in excitability, and development of regular patterns is blocked. The similar scheme is used to control the growth of memristive synapse for neurons, and the synchronization stability and pattern formation are controlled by the energy diversity among neurons effectively. These results provide possible guidance for knowing the biophysical mechanism for synapse growth and energy flow can be applied to control the synchronous patterns between neurons.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2023-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09622-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4570271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Computational analysis of synergism in small networks with different logic 不同逻辑下小网络协同效应的计算分析

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-12-29 DOI: 10.1007/s10867-022-09620-0

Menghan Chen, Ruiqi Wang

{"title":"Computational analysis of synergism in small networks with different logic","authors":"Menghan Chen, Ruiqi Wang","doi":"10.1007/s10867-022-09620-0","DOIUrl":"10.1007/s10867-022-09620-0","url":null,"abstract":"<div><p>Cell fate decision processes are regulated by networks which contain different molecules and interactions. Different network topologies may exhibit synergistic or antagonistic effects on cellular functions. Here, we analyze six most common small networks with regulatory logic AND or OR, trying to clarify the relationship between network topologies and synergism (or antagonism) related to cell fate decisions. We systematically examine the contribution of both network topologies and regulatory logic to the cell fate synergism by bifurcation and combinatorial perturbation analysis. Initially, under a single set of parameters, the synergism of three types of networks with AND and OR logic is compared. Furthermore, to consider whether these results depend on the choices of parameter values, statistics on the synergism of five hundred parameter sets is performed. It is shown that the results are not sensitive to parameter variations, indicating that the synergy or antagonism mainly depends on the network topologies rather than the choices of parameter values. The results indicate that the topology with “Dual Inhibition” shows good synergism, while the topology with “Dual Promotion” or “Hybrid” shows antagonism. The results presented here may help us to design synergistic networks based on network structure and regulation combinations, which has promising implications for cell fate decisions and drug combinations.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2022-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09620-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5111799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Clinical effects of 2-DG drug restraining SARS-CoV-2 infection: A fractional order optimal control study 2-DG药物抑制SARS-CoV-2感染的临床效果:分数阶最优对照研究

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-12-02 DOI: 10.1007/s10867-022-09617-9

Piu Samui, Jayanta Mondal, Bashir Ahmad, Amar Nath Chatterjee

{"title":"Clinical effects of 2-DG drug restraining SARS-CoV-2 infection: A fractional order optimal control study","authors":"Piu Samui, Jayanta Mondal, Bashir Ahmad, Amar Nath Chatterjee","doi":"10.1007/s10867-022-09617-9","DOIUrl":"10.1007/s10867-022-09617-9","url":null,"abstract":"<div><p>Fractional calculus is very convenient tool in modeling of an emergent infectious disease system comprising previous disease states, memory of disease patterns, profile of genetic variation etc. Significant complex behaviors of a disease system could be calibrated in a proficient manner through fractional order derivatives making the disease system more realistic than integer order model. In this study, a fractional order differential equation model is developed in micro level to gain perceptions regarding the effects of host immunological memory in dynamics of SARS-CoV-2 infection. Additionally, the possible optimal control of the infection with the help of an antiviral drug, viz. 2-DG, has been exemplified here. The fractional order optimal control would enable to employ the proper administration of the drug minimizing its systematic cost which will assist the health policy makers in generating better therapeutic measures against SARS-CoV-2 infection. Numerical simulations have advantages to visualize the dynamical effects of the immunological memory and optimal control inputs in the epidemic system.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2022-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09617-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4074323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Functionalization and Haemolytic analysis of pure superparamagnetic magnetite nanoparticle for hyperthermia application 用于热疗的纯超顺磁性纳米磁铁矿的功能化和溶血分析

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-11-25 DOI: 10.1007/s10867-022-09614-y

Hemalatha Kothandaraman, Alamelumangai Kaliyamoorthy, Arulmozhi Rajaram, Chandunika R. Kalaiselvan, Niroj Kumar Sahu, Parthipan Govindasamy, Muralidharan Rajaram

{"title":"Functionalization and Haemolytic analysis of pure superparamagnetic magnetite nanoparticle for hyperthermia application","authors":"Hemalatha Kothandaraman, Alamelumangai Kaliyamoorthy, Arulmozhi Rajaram, Chandunika R. Kalaiselvan, Niroj Kumar Sahu, Parthipan Govindasamy, Muralidharan Rajaram","doi":"10.1007/s10867-022-09614-y","DOIUrl":"10.1007/s10867-022-09614-y","url":null,"abstract":"<div><p>Superparamagnetic iron oxide nanoparticles (SPIONPs) are widely used in clinical research. The single domain nanoparticles are used in magnetic fluid hyperthermia (MFH) to treat cancer. When nanoparticles are exposed to an external magnetic field, it generates heat destroying tumour cells. SPIONPs have a large surface area, so the particles tend to aggregate, which leads to the destabilization of the colloidal system. To enhance the stability and biocompatibility of the nanomaterials, it is necessary to coat the surface with biocompatible material. Magnetite (Fe<sub>3</sub>O<sub>4</sub>) is a superparamagnetic nanoparticle (SPNPs) that was functionalized with oleic acid (OA) by sol–gel process using ethanol as the solvent. The oleic acid-coated magnetite (OA-Fe<sub>3</sub>O<sub>4</sub>) was characterized by X-ray powder diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), transmission electron microscopy (TEM), thermogravimetric analysis (TGA), UV–Visible diffuse reflectance spectroscopy (UV-DRS) and vibrating sample magnetometer (VSM). The haemolysis test has been used to investigate the haemocompatibility properties of nanomaterials. Hyperthermia study shows a high SAR value for the concentration of 1 mg/ml at the field of 600 Oe and frequency of 316 kHz. The OA coating enhanced the haemocompatibility of synthesized magnetite nanoparticles which can be used for magnetic fluid hyperthermia applications.\u0000</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2022-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09614-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4983430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Computational and comparative investigation of hydrophobic profile of spike protein of SARS-CoV-2 and SARS-CoV SARS-CoV-2和SARS-CoV刺突蛋白疏水性谱的计算和比较研究

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-11-23 DOI: 10.1007/s10867-022-09615-x

Uma Shekhawat, Anindita Roy Chowdhury (Chakravarty)

引用次数: 2

A pilot study of ion current estimation by ANN from action potential waveforms 基于动作电位波形的人工神经网络估计离子电流的初步研究

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-11-14 DOI: 10.1007/s10867-022-09619-7

Sevgi Şengül Ayan, Selim Süleymanoğlu, Hasan Özdoğan

{"title":"A pilot study of ion current estimation by ANN from action potential waveforms","authors":"Sevgi Şengül Ayan, Selim Süleymanoğlu, Hasan Özdoğan","doi":"10.1007/s10867-022-09619-7","DOIUrl":"10.1007/s10867-022-09619-7","url":null,"abstract":"<div><p>Experiments using conventional experimental approaches to capture the dynamics of ion channels are not always feasible, and even when possible and feasible, some can be time-consuming. In this work, the ionic current–time dynamics during cardiac action potentials (APs) are predicted from a single AP waveform by means of artificial neural networks (ANNs). The data collection is accomplished by the use of a single-cell model to run electrophysiological simulations in order to identify ionic currents based on fluctuations in ion channel conductance. The relevant ionic currents, as well as the corresponding cardiac AP, are then calculated and fed into the ANN algorithm, which predicts the desired currents solely based on the AP curve. The validity of the proposed methodology for the Bayesian approach is demonstrated by the R (validation) scores obtained from training data, test data, and the entire data set. The Bayesian regularization’s (BR) strength and dependability are further supported by error values and the regression presentations, all of which are positive indicators. As a result of the high convergence between the simulated currents and the currents generated by including the efficacy of a developed Bayesian solver, it is possible to generate behavior of ionic currents during time for the desired AP waveform for any electrical excitable cell.\u0000</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2022-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09619-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4585221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to: Non-extensitivity and criticality of atomic hydropathicity around a voltage-gated sodium channel’s pore: a modeling study 修正:电压门控钠通道孔周围原子亲水性的非广泛性和临界性:模型研究

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-11-12 DOI: 10.1007/s10867-022-09616-w

Markos N. Xenakis, Dimos Kapetis, Yang Yang, Jordi Heijman, Stephen G. Waxman, Giuseppe Lauria, Catharina G. Faber, Hubert J. Smeets, Patrick J. Lindsey, Ronald L. Westra

引用次数: 0

A dynamical model of combination therapy applied to glioma 胶质瘤联合治疗的动力学模型

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-11-11 DOI: 10.1007/s10867-022-09618-8

Handoko Handoko, Setyanto Tri Wahyudi, Ardian Arif Setyawan, Agus Kartono

{"title":"A dynamical model of combination therapy applied to glioma","authors":"Handoko Handoko, Setyanto Tri Wahyudi, Ardian Arif Setyawan, Agus Kartono","doi":"10.1007/s10867-022-09618-8","DOIUrl":"10.1007/s10867-022-09618-8","url":null,"abstract":"<div><p>Glioma is a human brain tumor that is very difficult to treat at an advanced stage. Studies of glioma biomarkers have shown that some markers are released into the bloodstream, so data from these markers indicate a decrease in the concentration of blood glucose and serum glucose in patients with glioma; these suggest an association between glucose and glioma. This decrease mechanism in glucose concentration can be described by the coupled ordinary differential equations of the early-stage glioma growth and interactions between glioma cells, immune cells, and glucose concentration. In this paper, we propose developing a new mathematical model to explain how glioma cells evolve and survive combination therapy between chemotherapy and oncolytic virotherapy, as an alternative to glioma treatment. In this study, three therapies were applied for analysis, that is, (1) chemotherapy, (2) virotherapy, and (3) a combination of chemotherapy and virotherapy. Virotherapy uses specialist viruses that only attack tumor cells. Based on the simulation results of the therapy carried out, we conclude that combination therapy can reduce the glioma cells significantly compared to the other two therapies. The simulation results of this combination therapy can be an alternative to glioma therapy.\u0000</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2022-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09618-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4476301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0