Journal of Biological Physics最新文献_第6页

Probing the binding of morin with alpha-2-macroglobulin using multi-spectroscopic and molecular docking approach 利用多光谱和分子对接方法探测桑苷与α -2巨球蛋白的结合

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2023-03-13 DOI: 10.1007/s10867-023-09629-z

Sana Ansari, Mohammad Khalid Zia, Shamila Fatima, Haseeb Ahsan, Fahim H. Khan

{"title":"Probing the binding of morin with alpha-2-macroglobulin using multi-spectroscopic and molecular docking approach","authors":"Sana Ansari, Mohammad Khalid Zia, Shamila Fatima, Haseeb Ahsan, Fahim H. Khan","doi":"10.1007/s10867-023-09629-z","DOIUrl":"10.1007/s10867-023-09629-z","url":null,"abstract":"<div>Alpha-2-macroglobulin (α2M) is an essential antiproteinase that is widely distributed in human plasma. The present study was aimed at investigating the binding of a potential therapeutic dietary flavonol, morin, with human α2M using a multi-spectroscopic and molecular docking approach. Recently, flavonoid-protein interaction has gained significant attention, because a majority of dietary bioactive components interact with proteins, thereby altering their structure and function. The results of the activity assay exhibited a 48% reduction in the antiproteolytic potential of α2M upon interaction with morin. Fluorescence quenching tests unequivocally confirmed quenching in the fluorescence of α2M in the presence of morin, conforming complex formation and demonstrating that the binding mechanism involves a dynamic mode of interaction. Synchronous fluorescence spectra of α2M with morin showed perturbation in the microenvironment around tryptophan residues. Furthermore, structural changes were observed through CD and FT-IR, showing alterations in the secondary structure of α2M induced by morin. FRET further supports the results of the dynamic mode of quenching. Moderate interaction is shown by binding constant values using Stern–Volmer’s fluorescence spectroscopy. Morin binds to α2M at 298 K with a binding constant of 2.7 × 104 M−1, indicating the strength of the association. The α2M-morin system was found to have negative ΔG values, which suggests that the binding process was spontaneous. Molecular docking also reveals the different amino acid residues involved in this binding process, revealing that the binding energy is -8.1 kcal/mol.\u0000</div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"49 2","pages":"235 - 255"},"PeriodicalIF":1.8,"publicationDate":"2023-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-023-09629-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4545438","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: 1

Neural waves and short-term memory in a neural net model 神经网络模型中的神经波和短期记忆

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2023-03-02 DOI: 10.1007/s10867-023-09627-1

Stephen Selesnick

引用次数: 0

Cellular nitric oxide synthesis is affected by disorders in the interdependent (Ca^{2+}) and (IP_{3}) dynamics during cystic fibrosis disease 在囊性纤维化疾病期间，细胞一氧化氮合成受到相互依赖的(Ca^{2+})和(IP_{3})动力学紊乱的影响

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2023-02-22 DOI: 10.1007/s10867-022-09624-w

Ankit B. Kothiya, Neeru Adlakha

{"title":"Cellular nitric oxide synthesis is affected by disorders in the interdependent (Ca^{2+}) and (IP_{3}) dynamics during cystic fibrosis disease","authors":"Ankit B. Kothiya, Neeru Adlakha","doi":"10.1007/s10867-022-09624-w","DOIUrl":"10.1007/s10867-022-09624-w","url":null,"abstract":"<div>Calcium ((Ca^{2+})), inositol trisphosphate ((IP_3)), and nitric oxide (NO) signaling are essential to maintain the structural integrity and physiological activity of fibroblast cells. The accumulation of excess quantity of NO for longer periods can lead to a variety of fibrotic disorders, including heart disease, penile fibrosis in Peyronie’s disease (PD), and cystic fibrosis. The dynamics of these three signaling processes and their interdependence in fibroblast cells are not clearly known to date. A systems biology model is proposed using reaction-diffusion equations for calcium, (IP_3), and calcium-dependent NO synthesis in fibroblast cells. The finite element method (FEM) is used to examine (Ca^{2+}), (IP_3), and NO regulation and dysregulation in cells. The results throw light on the conditions that disturb the coupled (Ca^{2+}) and (IP_3) dynamics and the influence of these factors on the levels of NO concentration in the fibroblast cell. The findings suggest that changes in source inflow, buffers, and diffusion coefficient might induce an increase or reduction in nitric oxide and (IP_3) synthesis, resulting in fibroblast cell diseases. Furthermore, the findings provide new information regarding the size and intensity of diseases in response to changes in several factors of their dynamics, which has been linked to the development of cystic fibrosis and cancer. This knowledge could be valuable for developing novel approaches to the diagnosis of diseases and therapies for various disorders of fibroblast cells.</div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"49 2","pages":"133 - 158"},"PeriodicalIF":1.8,"publicationDate":"2023-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09624-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4853328","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: 7

Adaptive behaviors of Drosophila larvae on slippery surfaces 果蝇幼虫在光滑表面的适应行为

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2023-02-15 DOI: 10.1007/s10867-023-09626-2

Li Guo, Yixuan Sun, Sijian Liu

{"title":"Adaptive behaviors of Drosophila larvae on slippery surfaces","authors":"Li Guo, Yixuan Sun, Sijian Liu","doi":"10.1007/s10867-023-09626-2","DOIUrl":"10.1007/s10867-023-09626-2","url":null,"abstract":"<div>Friction is ubiquitous but an essential force for insects during locomotion. Insects use dedicated bio-mechanical systems such as adhesive pads to modulate the intensity of friction, providing a stable grip with touching substrates for locomotion. However, how to uncover behavioral adaptation and regulatory neural circuits of friction modification is still largely understood. In this study, we devised a novel behavior paradigm to investigate adaptive behavioral alternation of Drosophila larvae under low-friction surfaces. We found a tail looseness phenotype similar to slipping behavior in humans, as a primary indicator to assess the degree of slipping. We found a gradual reduction on slipping level in wild-type larvae after successive larval crawling, coupled with incremental tail contraction, displacement, and speed acceleration. Meanwhile, we also found a strong correlation between tail looseness index and length of contraction, suggesting that lengthening tail contraction may contribute to enlarging the contact area with the tube. Moreover, we found a delayed adaptation in rut mutant larvae, inferring that neural plasticity may participate in slipping adaptation. In conclusion, our paradigm can be easily and reliably replicated, providing a feasible pathway to uncover the behavioral principle and neural mechanism of acclimation of Drosophila larvae to low-friction conditions.</div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"49 1","pages":"121 - 132"},"PeriodicalIF":1.8,"publicationDate":"2023-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-023-09626-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4603418","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

Bistability regulates TNFR2-mediated survival and death of T-regulatory cells 双稳定性调节tnfr2介导的t调节性细胞的存活和死亡

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2023-02-13 DOI: 10.1007/s10867-023-09625-3

Suvankar Halder, Samrat Chatterjee

{"title":"Bistability regulates TNFR2-mediated survival and death of T-regulatory cells","authors":"Suvankar Halder, Samrat Chatterjee","doi":"10.1007/s10867-023-09625-3","DOIUrl":"10.1007/s10867-023-09625-3","url":null,"abstract":"<div>A subgroup of T cells called T-regulatory cells (Tregs) regulates the body’s immune responses to maintain homeostasis and self-tolerance. Tregs are crucial for preventing illnesses like cancer and autoimmunity. However, contrasting patterns of Treg frequency are observed in different autoimmune diseases. The commonality of tumour necrosis factor receptor 2 (TNFR2) defects and decrease in Treg frequency on the onset of autoimmunity demands an in-depth study of the TNFR2 pathway. To unravel this mystery, we need to study the mechanism of cell survival and death in Tregs. Here, we construct an ordinary differential equation (ODE)-based model to capture the mechanism of cell survival and apoptosis in Treg cells via TNFR2 signalling. The sensitivity analysis reveals that the input stimulus, the concentration of tumour necrosis factor (TNF), is the most sensitive parameter for the model system. The model shows that the cell goes into survival or apoptosis via bistable switching. Through hysteretic switching, the system tries to cope with the changing stimuli. In order to understand how stimulus strength and feedback strength influence cell survival and death, we compute bifurcation diagrams and obtain cell fate maps. Our results indicate that the elevated TNF concentration and increased c-Jun N-terminal kinase (JNK) phosphorylation are the major contributors to the death of T-regulatory cells. Biological evidence cements our hypothesis and can be controlled by reducing the TNF concentration. Finally, the system was studied under stochastic perturbation to see the effect of noise on the system’s dynamics. We observed that introducing random perturbations disrupts the bistability, reducing the system’s bistable region, which can affect the system’s normal functioning.</div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"49 1","pages":"95 - 119"},"PeriodicalIF":1.8,"publicationDate":"2023-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-023-09625-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4536391","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: 1

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>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 × 103 M−1, which indicates significant binding. The ΔG value was found to be − 7.56 kcal mol−1 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.</div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"49 1","pages":"29 - 48"},"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>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.</div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"49 1","pages":"49 - 76"},"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>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.</div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"49 1","pages":"1 - 27"},"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>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.</div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 4","pages":"415 - 438"},"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