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Factors That Affect the Computational Prediction of Hot Spots in Protein-Protein Complexes

Computational Molecular Bioscience 2012年第1期2卷 23-34页

作者： Jianping Lin Pi Liu Hua-Zheng Yang nagarajan vaidehi College of Pharmacy Nankai University Tianjin China Department of Immunology Beckman Research Institute of the City of Hope Duarte USA State Key Laboratory of Elemento-Organic Chemistry Elemento-Organic Chemistry Institute Nankai University Tianjin China

Protein-protein complexes play an important role in the physiology and the pathology of cellular functions, and therefore are attractive therapeutic targets. A small subset of residues known as “hot spots”, accounts for most of the protein-protein binding free energy. Computational methods play a critical role in identifying the hotspots on the proteinprotein interface. In this paper, we use a computational alanine scanning method with all-atom force fields for predicting hotspots for 313 mutations in 16 protein complexes of known structures. We studied the effect of force fields, solvation models, and conformational sampling on the hotspot predictions. We compared the calculated change in the protein-protein interaction energies upon mutation of the residues in and near the protein-protein interface, to the experimental change in free energies. The AMBER force field (FF) predicted 86% of the hotspots among the three commonly used FF for proteins, namely, AMBER FF, Charmm27 FF, and OPLS-2005 FF. However, AMBER FF also showed a high rate of false positives, while the Charmm27 FF yielded 74% correct predictions of the hotspot residues with low false positives. Van der Waals and hydrogen bonding energy show the largest energy contribution with a high rate of prediction accuracy, while the desolvation energy was found to contribute little to improve the hot spot prediction. Using a conformational ensemble including limited backbone movement instead of one static structure leads to better predicttion of hotpsots.

关键词： Hotspot Prediction Computational Mutagenesis Concoord Ensemble Protein-Protein Complexes

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Masseter Vestibular evoked myogenic potentials: A new tool to assess the vestibulomasseteric reflex pathway

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Journal of Otology 2024年第1期19卷 46-54页

作者： Aishwarya nagarajan Sujeet Kumar Sinha Department of Audiology AIISHMysore06India

Purpose: This review article provides the readers with an in-depth insight in understanding and interpreting various research literatures on the masseter vestibular evoked myogenic potentials(mVEMP). The article also reviews the contemporary researches involving the clinical applications of the mVEMP. Conclusions: Masseter VEMP is an evolving yet clinically promising neuro-otology test tool that has recently gained more research interest and is considered an additional tool to diagnose various vestibular disorders. Masseter VEMP assesses the functional integrity of the acoustic-masseteric and vestibulo-masseteric reflex pathways. The mVEMP could be used as a complementary test to evaluate the same peripheral generator as the cervical VEMP but a different central pathway i.e., vestibulo-trigeminal pathway. Various research studies that have experimented on parameters such as the effect of different electrode montages(zygomatic vs mandibular configurations), stimulation rates, filter settings and stimuli used to evoke mVEMP have been discussed in this article that could assist in the optimization of a comprehensive clinical protocol. The latency and the amplitude of mVEMP waveforms serve as significant parameters in differentiating normals from those of the clinical populations. Along with the cVEMPs and oVEMPs, mVEMP might help diagnose brainstem lesions in REM Sleep behaviour disorders, Multiple Sclerosis and Parkinson's disease. However, further studies are required to probe in this area of research.

关键词： Masseter vestibular evoked myogenic potentials(mVEMP) Vestibulo-masseteric pathway Acoustic-masseteric pathway

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Magnesium-incorporated biocomposite scaffolds:A novel frontier in bone tissue engineering

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Journal of Magnesium and Alloys 2024年第6期12卷 2231-2248页

作者： Abinaya Shanmugavadivu Sundaravadhanan Lekhavadhani Sushma Babu Nivetha Suresh nagarajan Selvamurugan Department of Biotechnology School of BioengineeringCollege of Engineering and TechnologySRM Institute of Science and TechnologyKattankulathur603203Tamil NaduIndia

Nonunion represents a crucial challenge in orthopedic medicine,demanding innovative solutions beyond the scope of traditional bone grafting *** the various strategies available,magnesium(Mg)implants have been recognized for their biocompatibility and ***,their susceptibility to rapid corrosion and degradation has garnered notable research interest in bone tissue engineering(BTE),particularly in the development of Mg-incorporated biocomposite *** scaffolds gradually release Mg2+,which enhances immunomodulation,osteogenesis,and angiogenesis,thus facilitating effective bone *** review presents myriad fabrication techniques used to create Mg-incorporated biocomposite scaffolds,including electrospinning,three-dimensional printing,and sol-gel *** these advancements,the application of Mg-incorporated biocomposite scaffolds faces challenges such as controlling the degradation rate of Mg and ensuring mechanical *** limitations highlight the necessity for ongoing research aimed at refining fabrication techniques to better regulate the physicochemical and osteogenic properties of *** review provides insights into the potential of Mg-incorporated biocomposite scaffolds for BTE and the challenges that need to be addressed for their successful translation into clinical applications.

关键词： Magnesium Bone tissue engineering Immunomodulation Osteogenesis Angiogenesis

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Crosstalk between Wnt and bone morphogenetic protein signaling during osteogenic differentiati

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World Journal of Stem Cells 2024年第2期16卷 102-113页

作者： Pakkath Narayanan Arya Iyyappan Saranya nagarajan Selvamurugan Department of Biotechnology School of BioengineeringSRM Institute of Science and TechnologyKattankulathur 603203India

Mesenchymal stem cells(MSCs)originate from many sources,including the bone marrow and adipose tissue,and differentiate into various cell types,such as osteoblasts and *** studies on MSCs have revealed that many transcription factors and signaling pathways control osteogenic *** is the process by which new bones are formed;it also aids in bone ***/β-catenin and bone morphogenetic protein(BMP)signaling pathways are involved in many cellular processes and considered to be essential for ***/β-catenin and BMPs are important for bone formation in mammalian development and various regulatory activities in the *** studies have indicated that these two signaling pathways contribute to osteogenic *** Wnt signaling pathway promotes osteogenesis by activating the downstream targets of the BMP signaling ***,we briefly review the molecular processes underlying the crosstalk between these two pathways and explain their participation in osteogenic differentiation,emphasizing the canonical *** review also discusses the crosstalk mechanisms of Wnt/BMP signaling with Notch-and extracellular-regulated kinases in osteogenic differentiation and bone development.

关键词： Bone Mesenchymal stem cells Osteogenic differentiation Wnt/β-catenin Bone morphogenetic proteins

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Transcriptomic and pathological profiling of a new congenic mouse model with Lepr mutation:Evaluating susceptibility to the development of obesity and NAFLD

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Genes & Diseases 2024年第3期11卷 34-38页

作者： MJ Mahesh Kumar Shailendra Arindkar Masum Saini Perumal nagarajan National Institute of Immunology New Delhi 100067India Center for Cellular and Molecular Biology Hyderabad 500007India Regional Center for Biotechnology Faridabad 121001India

Non-alcoholic fatty liver disease(NAFLD)and type 2 diabetes mellitus(T2DM)are two disease conditions for which obesity is a risk factor.^(1)Due to the close relationship between the three pathologies,researchers frequently use the same mouse models to identify the underlying processes of obesity,NAFLD,and *** instance,leptin(Lep)-null(ob/ob)and leptin receptor(Lepr)-deficient(db/db)mice spontaneously develop NAFLD and show different phenotypes of extreme obesity and diabetes,respectively.

关键词： obesity NAFLD Lep

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Spatial Attention Integrated EfficientNet Architecture for Breast Cancer Classification with Explainable AI

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Computers, Materials & Continua 2024年第9期80卷 5029-5045页

作者： Sannasi Chakravarthy Bharanidharan nagarajan Surbhi Bhatia Khan Vinoth Kumar Venkatesan Mahesh Thyluru Ramakrishna Ahlam AlMusharraf Khursheed Aurungzeb Department of Electronics and Communication Engineering Bannari Amman Institute of TechnologySathyamangalam638402India School of Computer Science Engineering and Information Systems(SCORE) Vellore Institute of TechnologyVellore632014India School of Science Engineering and EnvironmentUniversity of SalfordManchesterM54WTUK Department of Computer Science&Engineering Faculty of Engineering and TechnologyJAIN(Deemed-to-be University)Bengaluru562112India Department of Management College of Business AdministrationPrincess Nourah Bint Abdulrahman UniversityP.O.Box 84428Riyadh11671Saudi Arabia Department of Computer Engineering College of Computer and Information SciencesKing Saud UniversityP.O.Box 51178Riyadh11543Saudi Arabia Adjunct Research Faculty Centre for Research Impact&OutcomeChitkara UniversityRajpura140401India

Breast cancer is a type of cancer responsible for higher mortality rates among *** cruelty of breast cancer always requires a promising approach for its earlier *** light of this,the proposed research leverages the representation ability of pretrained EfficientNet-B0 model and the classification ability of the XGBoost model for the binary classification of breast *** addition,the above transfer learning model is modified in such a way that it will focus more on tumor cells in the input ***,the work proposed an EfficientNet-B0 having a Spatial Attention Layer with XGBoost(ESA-XGBNet)for binary classification of *** this,the work is trained,tested,and validated using original and augmented mammogram images of three public datasets namely CBIS-DDSM,INbreast,and MIAS *** accuracy of 97.585%(CBISDDSM),98.255%(INbreast),and 98.91%(MIAS)is obtained using the proposed ESA-XGBNet architecture as compared with the existing ***,the decision-making of the proposed ESA-XGBNet architecture is visualized and validated using the Attention Guided GradCAM-based Explainable AI technique.

关键词： EfficientNet mammograms breast cancer Explainable AI deep-learning transfer learning

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Dynamic control of district heating networks with integrated emission modelling:A dynamic knowledge graph approach

Energy and AI

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Energy and AI 2024年第3期17卷 29-47页

作者： Markus Hofmeister Kok Foong Lee Yi-Kai Tsai Magnus Müller Karthik nagarajan Sebastian Mosbach Jethro Akroyd Markus Kraft Department of Chemical Engineering and Biotechnology University of CambridgePhilippa Fawcett DriveCambridgeCB30ASUnited Kingdom Cambridge Centre for Advanced Research and Education in Singapore CARES Ltd.1 Create WayCREATE Tower#05-05138602Singapore CMCL Innovations Sheraton HouseCambridgeCB30AXUnited Kingdom The Alan Turing Institute 96 Euston RoadLondonNW12DBUnited Kingdom

This paper presents a knowledge graph-based approach for the dynamic control of a district heating network with integrated emission dispersion modelling. We propose an interoperable and extensible implementation to forecast the anticipated heat demand of a municipal heating network, minimise associated total generation cost based on a previously devised methodology, and couple it with dispersion simulations for induced airborne pollutants to provide automatic insights into air quality implications of various heat sourcing strategies. We create cross-domain interoperability in the nexus of energy and air quality via newly developed ontologies and semantic software agents, which can be chained together via The World Avatar dynamic knowledge graph to resemble the behaviour of complex systems. Furthermore, we integrate the City Energy Analyst into this ecosystem to provide building-level insights into energy demand and renewable generation potential to foster strategic analyses and scenario planning. Underlying calculations use building and weather data from the knowledge graph in place of inherent assumptions in the official software release, facilitating a more data-driven approach. All use cases are implemented for a mid-size town in Germany as a proof-of-concept, and a unified visualisation interface is provided, allowing for the examination of 3D buildings alongside their corresponding energy demand and supply time series, as well as emission dispersion data. With this work, we outline the potential of Semantic Web technologies to connect digital twins for holistic energy modelling in smart cities, thereby addressing the increasing complexity of interconnected energy systems.

关键词： Knowledge graph Digital twin Inter operability Energy modelling Emi ssion dispersi on

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Isolation of Microcrystalline Cellulose from Wood and Fabrication of Polylactic Acid(PLA)Based Green Biocomposites

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Journal of Renewable Materials 2024年第8期12卷 1455-1474页

作者： Selwin Maria Sekar Rajini nagarajan Ponsuriyaprakash Selvakumar Ismail Sikiru Oluwarotimi Kumar Krishnan Faruq Mohammad Mohammed Rafi Shaik Nadir Ayrilmis Department of Mechanical Engineering Kalasalingam Academy of Research and EducationKrishnankoil626126India Department of Mechanical Engineering SSM Institute of Engineering and TechnologyDindigul624002India Department of Engineering Centre for Engineering ResearchSchool of PhysicsEngineering and Computer ScienceUniversity of HertfordshireHatfieldAL109ABUK INTI International University Persiaran Perdana BBNNilai71800Malaysia Department of Chemistry College of ScienceKing Saud UniversityP.O.Box 2455Riyadh11451Kingdom of Saudi Arabia Department of Wood Mechanics and Technology Faculty of ForestryIstanbul University–CerrahpasaBahcekoySariyerIstanbul34473Turkey

An innovative microcrystalline cellulose(MCC)natural fibre powder-reinforced PLA biocomposite was investigated using the hand lay-up *** polymer matrix composite(PMC)samples were prepared by varying the weight percentages(wt.%)of both PLA matrix and MCC reinforcement:pure PLA/100:0,90:10,80:20,70:30,60:40 and 50:50 wt.%,*** the results obtained,MCC powder,with its impressive aspect ratio,proved to be an ideal reinforcement for the PLA,exhibiting exceptional mechanical *** was evident that the 80:20 wt.%biocomposite sample exhibited the maximum improvement in the tensile,flexural,notched impact,compressive strength and hardness by 28.85%,20.00%,91.66%,21.53%and 35.82%,respectively compared to the pure PLA ***,during the thermogravimetric analysis(TGA),the same 80:20 wt.%biocomposite sample showed a minimum weight loss of 20%at 400℃,among *** morphological study using Field Emission Scanning Electron Microscopy(FE-SEM)revealed that the uniform distribution of cellulose reinforcement in the PLA matrix actively improved the mechanical properties of the biocomposites,especially the optimal 80:20 wt.%***,it was evident that the optimal PLA/cellulose biocomposite sample could be a suitable and alternative sustainable,environmentally friendly and biodegradable material for semi/structural applications,replacing synthetic and traditional components.

关键词： Polylactic acid micro crystalline cellulose biocomposite characterizations FESEM environmental pollution

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Synthesis and Crystal Structure of an Anionic Linear Trinuclear Copper(Ⅱ) Complex Containing 2-Thenoyltrifluoroacetonato and Acetato Ligands

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Chinese Journal of Structural Chemistry 2014年第1期33卷 19-26页

作者： LOGANATHAN nagarajan ROODT Andreas Department of Chemistry University of the Free State

A novel anionic trinuclear linear copper（II） complex {[Et3NH][Cul.5（CH3COO）- （TTA）3] } 2 （1, TTA = 2-thenoyltrifluoroacetonate） has been synthesized in a direct reaction involving copper（]l） acetate monohydrate, TTA and excess triethylamine base in dichloromethane solvent. Green colored X-ray quality crystals of 1 were grown from n-hexane solvent at room temperature. The data were collected at 100 K. Compound I crystallizes in the monoclinic P21/n space group （a = 11.2141（8）, b = 19.0965（13）, c = 17.3680（14） A, β = 90.225（2）°, V= 3719.3（5） A3, Mr = 1840.14, Dc = 1.643 Mg/m3, F（000） = 1866, μ = 1.129 mm^-1 and Z = 2）. The asymmetric unit of 1 contains two copper atoms, one of which lies on a crystallographic inversion center with 50% occupancy.

关键词： copper crystals acetate monoclinic 1,3-diketonates

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Facile synthesis and characterization of acetate intercalated Co-La layered double hydroxide

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Journal of Rare Earths 2017年第5期35卷 474-479页

作者： Meenakshi Pokhriyal Sitharaman Uma Rajamani nagarajan Materials Chemistry Group Department of Chemistry University of Delhi

Layered double hydroxide（LDH） comprising of Co^2＋ and La^3＋-ions with acetate counter anion was successfully synthesized by hydrogen peroxide catalyzed hydrolysis reaction and characterized extensively. The observed reflections in the powder X-ray diffraction pattern could be indexed in P3 space group with a=0.316 nm and c=2.97 nm. Lattice fringes of distances corresponding to the peaks observed in X-ray diffraction pattern were observed in high resolution transmission electron microscopic images. UV-visible diffuse reflectance spectroscopy results confirmed the presence of Co（OH）6 along with the presence of charge-transfer band due to the interlayer carboxylate anion. Magnetization measurements at room temperature indicated high spin configuration of Co^2＋-ion in the sample exhibiting paramagnetic behavior. The mixed metal oxide from calcination was used to reconstruct the parent layered structure. Intercalation experiments with other organic anions in Co-La LDH proved be successful.

关键词： layered acetate interlayer hydroxide hydrolysis anion calcination carboxylate reconstruct intercalation

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