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Suri K, Ramesh M, Bhandari M, Gupta V, Kumar V, Govindaraju T, Murugan NA. Role of Amyloidogenic and Non-Amyloidogenic Protein Spaces in Neurodegenerative Diseases and their Mitigation Using Theranostic Agents. Chembiochem 2024; 25:e202400224. [PMID: 38668376 DOI: 10.1002/cbic.202400224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/23/2024] [Indexed: 06/15/2024]
Abstract
Neurodegenerative diseases (NDDs) refer to a complex heterogeneous group of diseases which are associated with the accumulation of amyloid fibrils or plaques in the brain leading to progressive loss of neuronal functions. Alzheimer's disease is one of the major NDD responsible for 60-80 % of all dementia cases. Currently, there are no curative or disease-reversing/modifying molecules for many of the NDDs except a few such as donepezil, rivastigmine, galantamine, carbidopa and levodopa which treat the disease-associated symptoms. Similarly, there are very few FDA-approved tracers such as flortaucipir (Tauvid) for tau fibril imaging and florbetaben (Neuraceq), flutemetamol (Vizamyl), and florbetapir (Amyvid) for amyloid imaging available for diagnosis. Recent advances in the cryogenic electron microscopy reported distinctly different microstructures for tau fibrils associated with different tauopathies highlighting the possibility to develop tauopathy-specific imaging agents and therapeutics. In addition, it is important to identify the proteins that are associated with disease development and progression to know about their 3D structure to develop various diagnostics, therapeutics and theranostic agents. The current article discusses in detail the disease-associated amyloid and non-amyloid proteins along with their structural insights. We comprehensively discussed various novel proteins associated with NDDs and their implications in disease pathology. In addition, we document various emerging chemical compounds developed for diagnosis and therapy of different NDDs with special emphasis on theranostic agents for better management of NDDs.
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Affiliation(s)
- Kapali Suri
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Madhu Ramesh
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur P.O., Bengaluru, 560064, Karnataka, India
| | - Mansi Bhandari
- Department of computer science and engineering, Jamia Hamdard University, Hamdard Nagar, New Delhi, Delhi, 110062
| | - Vishakha Gupta
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Virendra Kumar
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur P.O., Bengaluru, 560064, Karnataka, India
| | - N Arul Murugan
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
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2
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Bellotto O, Kralj S, De Zorzi R, Geremia S, Marchesan S. Supramolecular hydrogels from unprotected dipeptides: a comparative study on stereoisomers and structural isomers. SOFT MATTER 2020; 16:10151-10157. [PMID: 32935720 DOI: 10.1039/d0sm01191f] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Amino acid stereoconfiguration has been shown to play a key role in the self-assembly of unprotected tripeptides into hydrogels under physiological conditions. Dramatic changes were noted for hydrophobic sequences based on the diphenylalanine motif from the formation of amorphous aggregates in the case of homochiral peptides to nanostructured and stable hydrogels in the case of heterochiral stereoisomers. Herein, we report that by further shortening the sequence to a dipeptide, the overall differences between isomers are less marked, with both homo- and hetero-chiral dipeptides forming gels, although with different stability over time. The soft materials are studied by a number of spectroscopic and microcopic techniques, and single-crystal X-ray diffraction to unveil the supramolecular interactions of these hydrogel building blocks.
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Affiliation(s)
- Ottavia Bellotto
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
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3
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Iłowska E, Sawicka J, Szymańska A. Synthesis and physicochemical studies of amyloidogenic hexapeptides derived from human cystatin C. J Pept Sci 2018; 24:e3073. [PMID: 29573035 DOI: 10.1002/psc.3073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 02/06/2018] [Accepted: 02/12/2018] [Indexed: 01/20/2023]
Abstract
Human cystatin C (hCC) is a low molecular mass protein that belongs to the cystatin superfamily. It is an inhibitor of extracellular cysteine proteinases, present in all human body fluids. At physiological conditions, hCC is a monomer, but it has a tendency to dimerization. Naturally occurring hCC mutant, with leucine in position 68 substituted by glutamine (L68Q), is directly involved in the formation of amyloid deposits, independently of other proteins. This process is the primary cause of hereditary cerebral amyloid angiopathy, observed mainly in the Icelandic population. Oligomerization and fibrillization processes of hCC are not explained equally well, but it is proposed that domain swapping is involved in both of them. Research carried out on the fibrillization process led to new hypothesis about the existence of a steric zipper motif in amyloidogenic proteins. In the hCC sequence, there are 2 fragments which may play the role of a steric zipper: the loop L1 region and the C-terminal fragment. In this work, we focused on the first of these. Nine hexapeptides covering studied hCC fragment were synthesized, and their fibrillogenic potential was assessed using an array of biophysical methods. The obtained results showed that the studied hCC fragment has strong profibrillogenic propensities because it contains 2 fragments fulfilling the requirements for an effective steric zipper located next to each other, forming 1 super-steric zipper motif. This hCC fragment might therefore be responsible for the enhanced amyloidogenic properties of dimeric or partially unfolded hCC.
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Affiliation(s)
- Emilia Iłowska
- Faculty of Chemistry, Department of Biomedical Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Justyna Sawicka
- Faculty of Chemistry, Department of Biomedical Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Aneta Szymańska
- Faculty of Chemistry, Department of Biomedical Chemistry, University of Gdańsk, Gdańsk, Poland
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4
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Pizzi A, Dichiarante V, Terraneo G, Metrangolo P. Crystallographic insights into the self-assembly of KLVFF amyloid-beta peptides. Biopolymers 2017; 110. [PMID: 29178159 DOI: 10.1002/bip.23088] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/23/2017] [Accepted: 10/30/2017] [Indexed: 02/06/2023]
Abstract
Amyloidogenic peptide fragment KLVFF (H2 N-Lys-Leu-Val-Phe-Phe-COOH, Aβ16-20 ), the core-sequence of the polypeptide Aβ40, is a well-studied model for amyloid formation. However, due to its low crystallinity, detailed atomic information of KLVFF structure is lacking. Here we report the high-resolution single-crystal X-ray structure of two monohalogenated KLVFF derivatives, KLVFF(I) and KLVFF(Br). The obtained results highlight how halogenation is a good strategy to promote crystallization and facilitate the phase determination of KLVFF(I) and KLVFF(Br) fragments. Detailed structural studies on the packing features of both monohalogenated derivatives reveal the role of the halogen atoms showing that when they are positioned on the Phe aromatic moiety at the C-terminus they do not form halogen bonds and thus do not produce any extra stabilization of the β-sheet in the self-assembly process. The structural evidences gained from these studies corroborate the various polymorphic nanostructures of the halogenated variants of KLVFF and confirm the possibility to use halogenation as innovative strategy to tune the morphology of this pentapeptide.
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Affiliation(s)
- Andrea Pizzi
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milano, I-20131, Italy
| | - Valentina Dichiarante
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milano, I-20131, Italy
| | - Giancarlo Terraneo
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milano, I-20131, Italy
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milano, I-20131, Italy
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5
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García-Bayona L, Guo MS, Laub MT. Contact-dependent killing by Caulobacter crescentus via cell surface-associated, glycine zipper proteins. eLife 2017; 6:e24869. [PMID: 28323618 PMCID: PMC5380434 DOI: 10.7554/elife.24869] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/20/2017] [Indexed: 12/18/2022] Open
Abstract
Most bacteria are in fierce competition with other species for limited nutrients. Some bacteria can kill nearby cells by secreting bacteriocins, a diverse group of proteinaceous antimicrobials. However, bacteriocins are typically freely diffusible, and so of little value to planktonic cells in aqueous environments. Here, we identify an atypical two-protein bacteriocin in the α-proteobacterium Caulobacter crescentus that is retained on the surface of producer cells where it mediates cell contact-dependent killing. The bacteriocin-like proteins CdzC and CdzD harbor glycine-zipper motifs, often found in amyloids, and CdzC forms large, insoluble aggregates on the surface of producer cells. These aggregates can drive contact-dependent killing of other organisms, or Caulobacter cells not producing the CdzI immunity protein. The Cdz system uses a type I secretion system and is unrelated to previously described contact-dependent inhibition systems. However, Cdz-like systems are found in many bacteria, suggesting that this form of contact-dependent inhibition is common.
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Affiliation(s)
- Leonor García-Bayona
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
- Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, United States
| | - Monica S Guo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
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6
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Shuaib S, Goyal B. Scrutiny of the mechanism of small molecule inhibitor preventing conformational transition of amyloid-β 42 monomer: insights from molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:663-678. [PMID: 28162045 DOI: 10.1080/07391102.2017.1291363] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that is characterized by loss of intellectual functioning of brain and memory loss. According to amyloid cascade hypothesis, aggregation of amyloid-β42 (Aβ42) peptide can generate toxic oligomers and their accumulation in the brain is responsible for the onset of AD. In spite of carrying out a large number of experimental studies on inhibition of Aβ42 aggregation by small molecules, the detailed inhibitory mechanism remains elusive. In the present study, comparable molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of a sulfonamide inhibitor C1 (2,5-dichloro-N-(4-piperidinophenyl)-3-thiophenesulfonamide), reported for its in vitro and in vivo anti-aggregation activity against Aβ42. MD simulations reveal that C1 stabilizes native α-helix conformation of Aβ42 by interacting with key residues in the central helix region (13-26) with hydrogen bonds and π-π interactions. C1 lowers the solvent-accessible surface area of the central hydrophobic core (CHC), KLVFF (16-20), that confirms burial of hydrophobic residues leading to the dominance of helical conformation in the CHC region. The binding free energy analysis with MM-PBSA demonstrates that Ala2, Phe4, Tyr10, Gln15, Lys16, Leu17, Val18, Phe19, Phe20, Glu22, and Met35 contribute maximum to binding free energy (-43.1 kcal/mol) between C1 and Aβ42 monomer. Overall, MD simulations reveal that C1 inhibits Aβ42 aggregation by stabilizing native helical conformation and inhibiting the formation of aggregation-prone β-sheet conformation. The present results will shed light on the underlying inhibitory mechanism of small molecules that show potential in vitro anti-aggregation activity against Aβ42.
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Affiliation(s)
- Suniba Shuaib
- a Department of Chemistry , School of Basic and Applied Sciences, Sri Guru Granth Sahib World University , Fatehgarh Sahib 140406 , Punjab , India
| | - Bhupesh Goyal
- a Department of Chemistry , School of Basic and Applied Sciences, Sri Guru Granth Sahib World University , Fatehgarh Sahib 140406 , Punjab , India
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7
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Ahmad A, Burns CS, Fink AL, Uversky VN. Peculiarities of copper binding to alpha-synuclein. J Biomol Struct Dyn 2016; 29:825-42. [PMID: 22208282 DOI: 10.1080/073911012010525023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Heavy metals have been implicated as the causative agents for the pathogenesis of the most prevalent neurodegenerative disease. Various mechanisms have been proposed to explain the toxic effects of metals ranging from metal-induced oxidation of protein to metal-induced changes in the protein conformation. Aggregation of a-synuclein is implicated in Parkinson's disease (PD), and various metals, including copper, constitute a prominent group of alpha-synuclein aggregation enhancers. In this study, we have systematically characterized the a-synuclein-Cu21 binding sites and analyzed the possible role of metal binding in a-synuclein fibrillation using a set of biophysical techniques, such as electron paramagnetic resonance (EPR), electron spin-echo envelope modulation (ESEEM), circular dichroism (CD), and size exclusion chromatography (SEC). Our analyses indicated that a-synuclein possesses at least two binding sites for Cu21. We have been able to locate one of the binding sites in the N-terminal region. Furthermore, based on the EPR studies of model peptides and Beta-synuclein, we concluded that the suspected His residue did not appear to participate in strong Cu21 binding.
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Affiliation(s)
- Atta Ahmad
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California, USA.
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8
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The characterization and comparison of amyloidogenic segments and non-amyloidogenic segments shed light on amyloid formation. Biochem Biophys Res Commun 2014; 447:255-62. [DOI: 10.1016/j.bbrc.2014.03.115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 03/24/2014] [Indexed: 11/30/2022]
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9
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Baftizadeh F, Pietrucci F, Biarnés X, Laio A. Nucleation process of a fibril precursor in the C-terminal segment of amyloid-β. PHYSICAL REVIEW LETTERS 2013; 110:168103. [PMID: 23679641 DOI: 10.1103/physrevlett.110.168103] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Indexed: 06/02/2023]
Abstract
By extended atomistic simulations in explicit solvent and bias-exchange metadynamics, we study the aggregation process of 18 chains of the C-terminal segment of amyloid-β, an intrinsically disordered protein involved in Alzheimer's disease and prone to form fibrils. Starting from a disordered aggregate, we are able to observe the formation of an ordered nucleus rich in beta sheets. The rate limiting step in the nucleation pathway involves crossing a barrier of approximately 40 kcal/mol and is associated with the formation of a very specific interdigitation of the side chains belonging to different sheets. This structural pattern is different from the one observed experimentally in a microcrystal of the same system, indicating that the structure of a "nascent" fibril may differ from the one of an "extended" fibril.
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10
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John S, Thangapandian S, Lee KW. Potential human cholesterol esterase inhibitor design: benefits from the molecular dynamics simulations and pharmacophore modeling studies. J Biomol Struct Dyn 2012; 29:921-36. [PMID: 22292952 DOI: 10.1080/07391102.2012.10507419] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Human pancreatic cholesterol esterase (hCEase) is one of the lipases found to involve in the digestion of large and broad spectrum of substrates including triglycerides, phospholipids, cholesteryl esters, etc. The presence of bile salts is found to be very important for the activation of hCEase. Molecular dynamic simulations were performed for the apoform and bile salt complexed form of hCEase using the co-ordinates of two bile salts from bovine CEase. The stability of the systems throughout the simulation time was checked and two representative structures from the highly populated regions were selected using cluster analysis. These two representative structures were used in pharmacophore model generation. The generated pharmacophore models were validated and used in database screening. The screened hits were refined for their drug-like properties based on Lipinski's rule of five and ADMET properties. The drug-like compounds were further refined by molecular docking simulation using GOLD program based on the GOLD fitness score, mode of binding, and molecular interactions with the active site amino acids. Finally, three hits of novel scaffolds were selected as potential leads to be used in novel and potent hCEase inhibitor design. The stability of binding modes and molecular interactions of these final hits were re-assured by molecular dynamics simulations.
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Affiliation(s)
- Shalini John
- Division of Applied Life Science_(BK21 Program), Systems and Synthetic Agrobiotech Center (SSAC) Gyeongsang National University (GNU), 501 Jinju-daero, Gazha-dong, Jinju 660-701, Republic of Korea
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11
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Wang ZJ, Si YX, Oh S, Yang JM, Yin SJ, Park YD, Lee J, Qian GY. The effect of fucoidan on tyrosinase: computational molecular dynamics integrating inhibition kinetics. J Biomol Struct Dyn 2012; 30:460-73. [PMID: 22694253 DOI: 10.1080/07391102.2012.682211] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fucoidan is a complex sulfated polysaccharide extracted from brown seaweed and has a wide variety of biological activities. In this study, we investigated the inhibitory effect of fucoidan on tyrosinase via a combination of inhibition kinetics and computational simulations. Fucoidan reversibly inhibited tyrosinase in a mixed-type manner. Time-interval kinetics showed that the inhibition was processed as first order with biphasic processes. For further insight, we simulated dockings with various sizes of molecular models (monomer to decamer) of fucoidan and showed that the best binding energy change results were obtained from the pentamer (-1.89 kcal/mol) and the hexamer (-1.97 kcal/mol) models of AutoDock Vina. The molecular dynamics simulation confirmed the binding mechanisms between tyrosinase and fucoidan and suggested that fucoidan mostly interacts with several residues including copper ions located in the active site. Our study suggests that fucoidan might be a potential natural antipigment agent.
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Affiliation(s)
- Zhi-Jiang Wang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, P.R. China
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12
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Majumder R, Roy S, Thakur AR. Analysis of Delta–Notch interaction by molecular modeling and molecular dynamic simulation studies. J Biomol Struct Dyn 2012; 30:13-29. [DOI: 10.1080/07391102.2012.674184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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13
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Thangapandian S, John S, Lee KW. Molecular Dynamics Simulation Study Explaining Inhibitor Selectivity in Different Class of Histone Deacetylases. J Biomol Struct Dyn 2012; 29:677-98. [DOI: 10.1080/07391102.2012.10507409] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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14
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Serikov R, Petyuk V, Vorobijev Y, Koval V, Fedorova O, Vlassov V, Zenkova M. Mechanism of antisense oligonucleotide interaction with natural RNAs. J Biomol Struct Dyn 2011; 29:27-50. [PMID: 21696224 DOI: 10.1080/073911011010524987] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Oligonucleotides find several numbers of applications: as diagnostic probes, RT and PCR primers and antisense agents due to their ability of forming specific interactions with complementary nucleotide sequences within nucleic acids. These interactions are strongly affected by accessibility of the target sequence in the RNA structure. In the present work the mechanism of invasion of RNA structure by oligonucleotide was investigated using a model system: yeast tRNA(Phe) and oligonucleotides complementary to the 3'-part of this molecule. Kinetics of interaction of oligonucleotides with in vitro transcript of yeast tRNAPhe was studied using stopped-flow technique with fluorescence quenching detection, 5'-DABCYL labeled oligonucleotide was hybridized with 3'-fluorescein labeled tRNA(Phe). The results evidence for a four-step invasion process of the oligonucleotide-RNA complex formation. The process is initiated by formation of transition complexes with nucleotides in the T-loop and ACCA sequence. This complex formation is followed by RNA unfolding and formation of an extended heteroduplex with the oligonucleotide via strand displacement process. Computer modeling of oligonucleotide-tRNA(Phe) interaction revealed potential factors that could favor transition complexes formation and confirmed the proposed mechanism, showing the oligonucleotide to be a molecular "wedge". Our data evidence that oligonucleotide invasion into structured RNA is initiated by loop-single strand interactions, similar to the initial step of the antisense RNA-RNA interactions. The obtained results can be used for choosing efficient oligonucleotide probes.
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Affiliation(s)
- R Serikov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., 630090 Novosibirsk, Russian Federation
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15
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Abstract
The small ubiquitin-like modifier (SUMO) proteins are a kind of proteins that can be attached to a series of proteins. The sumoylation of protein is an important posttranslational modification. Thus, the prediction of the sumoylation site of a given protein is significant. Here we employed a combined method to perform this task. We predicted the sumoylation site of a protein by a two-staged procedure. At the first stage, whether a protein would be sumoylated was predicted; whereas at the second stage, the sumoylation sites of the protein were predicted if it was determined to be modified by SUMO at the first stage. At the first stage, we encoded a protein with protein families (PFAM) and trained the predictor with nearest network algorithm (NNA); at the second stage, we encoded nonapeptides (peptides that contain nine residues) of the protein containing the lysine residues, with Amino Acid Index, and trained the predictor with NNA. The predictor was tested by the k-fold cross-validation method. The highest accuracy of the second-staged predictor was 99.55% when 12 features were incorporated in the predictor. The corresponding Matthews Correlation Coefficient was 0.7952. These results indicate that the method is a promising tool to predict the sumoylation site of a protein. At last, the features used in the predictor are discussed. The software is available at request.
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Affiliation(s)
- YuDong Cai
- Institute of System Biology, Shanghai University, 99 Shangda Road, Shanghai, 200244, China.
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Semighini EP, Resende JA, de Andrade P, Morais PAB, Carvalho I, Taft CA, Silva CHTP. Using computer-aided drug design and medicinal chemistry strategies in the fight against diabetes. J Biomol Struct Dyn 2011; 28:787-96. [PMID: 21294589 DOI: 10.1080/07391102.2011.10508606] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The aim of this work is to present a simple, practical and efficient protocol for drug design, in particular Diabetes, which includes selection of the illness, good choice of a target as well as a bioactive ligand and then usage of various computer aided drug design and medicinal chemistry tools to design novel potential drug candidates in different diseases. We have selected the validated target dipeptidyl peptidase IV (DPP-IV), whose inhibition contributes to reduce glucose levels in type 2 diabetes patients. The most active inhibitor with complex X-ray structure reported was initially extracted from the BindingDB database. By using molecular modification strategies widely used in medicinal chemistry, besides current state-of-the-art tools in drug design (including flexible docking, virtual screening, molecular interaction fields, molecular dynamics, ADME and toxicity predictions), we have proposed 4 novel potential DPP-IV inhibitors with drug properties for Diabetes control, which have been supported and validated by all the computational tools used herewith.
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Affiliation(s)
- Evandro P Semighini
- Departamento de Ciencias Farmaceuticas, Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de Sao Paulo, Av. do Cafe, s/n, Monte Alegre, 14040-903, Ribeirao Preto-SP, Brazil
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17
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Xu X, Su J, Chen W, Wang C. Thermal stability and unfolding pathways of Sso7d and its mutant F31A: insight from molecular dynamics simulation. J Biomol Struct Dyn 2011; 28:717-27. [PMID: 21294584 DOI: 10.1080/07391102.2011.10508601] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The thermo-stability and unfolding behaviors of a small hyperthermophilic protein Sso7d as well as its single-point mutation F31A are studied by molecular dynamics simulation at temperatures of 300 K, 371 K and 500 K. Simulations at 300 K show that the F31A mutant displays a much larger flexibility than the wild type, which implies that the mutation obviously decreases the protein's stability. In the simulations at 371 K, although larger fluctuations were observed, both of these two maintain their stable conformations. High temperature simulations at 500 K suggest that the unfolding of these two proteins evolves along different pathways. For the wild-type protein, the C-terminal alpha-helix is melted at the early unfolding stage, whereas it is destroyed much later in the unfolding process of the F31A mutant. The results also show that the mutant unfolds much faster than its parent protein. The deeply buried aromatic cluster in the F31A mutant dissociates quickly relative to the wild-type protein at high temperature. Besides, it is found that the triple-stranded antiparallel β-sheet in the wild-type protein plays an important role in maintaining the stability of the entire structure.
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Affiliation(s)
- Xianjin Xu
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
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18
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Majumder R, Roy S, Thakur AR. Molecular Modeling and Molecular Dynamics Simulation Studies of Delta-Notch Complex. J Biomol Struct Dyn 2011; 29:297-310. [DOI: 10.1080/07391102.2011.10507386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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19
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Behmard E, Abdolmaleki P, Asadabadi EB, Jahandideh S. Prevalent Mutations of Human Prion Protein: A Molecular Modeling and Molecular Dynamics Study. J Biomol Struct Dyn 2011; 29:379-89. [DOI: 10.1080/07391102.2011.10507392] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Jani V, Sonavane UB, Joshi R. Microsecond scale replica exchange molecular dynamic simulation of villin headpiece: an insight into the folding landscape. J Biomol Struct Dyn 2011; 28:845-60. [PMID: 21469746 DOI: 10.1080/07391102.2011.10508612] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Reaching the experimental time scale of millisecond is a grand challenge for protein folding simulations. The development of advanced Molecular Dynamics techniques like Replica Exchange Molecular Dynamics (REMD) makes it possible to reach these experimental timescales. In this study, an attempt has been made to reach the multi microsecond simulation time scale by carrying out folding simulations on a three helix bundle protein, Villin, by combining REMD and Amber United Atom model. Twenty replicas having different temperatures ranging from 295 K to 390 K were simulated for 1.5 µs each. The lowest Root Mean Square Deviation (RMSD) structure of 2.5 Å was obtained with respect to native structure (PDB code 1VII), with all the helices formed. The folding population landscapes were built using segment-wise RMSD and Principal Components as reaction coordinates. These analyses suggest the two-stage folding for Villin. The combination of REMD and Amber United Atom model may be useful to understand the folding mechanism of various fast folding proteins.
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Affiliation(s)
- Vinod Jani
- Bioinformatics Team, Scientific and Engineering Computing Group, Centre for Development of Advanced Computing, Pune University Campus, Ganeshkhind, Pune - 411007, Maharashtra, India
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Su JG, Xu XJ, Li CH, Chen WZ, Wang CX. An Analysis of the Influence of Protein Intrinsic Dynamical Properties on its Thermal Unfolding Behavior. J Biomol Struct Dyn 2011; 29:105-21. [DOI: 10.1080/07391102.2011.10507377] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Purohit R, Rajendran V, Sethumadhavan R. Studies on Adaptability of Binding Residues Flap Region of TMC-114 Resistance HIV-1 Protease Mutants. J Biomol Struct Dyn 2011; 29:137-52. [DOI: 10.1080/07391102.2011.10507379] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Zhang J, Liu DD. Molecular Dynamics Studies on the Structural Stability of Wild-type Dog Prion Protein. J Biomol Struct Dyn 2011; 28:861-9. [DOI: 10.1080/07391102.2011.10508613] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Zhou ZL, Zhao JH, Liu HL, Wu JW, Liu KT, Chuang CK, Tsai WB, Ho Y. The Possible Structural Models for Polyglutamine Aggregation: A Molecular Dynamics Simulations Study. J Biomol Struct Dyn 2011; 28:743-58. [DOI: 10.1080/07391102.2011.10508603] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Olmez EO, Alakent B. Alpha7 Helix Plays an Important Role in the Conformational Stability of PTP1B. J Biomol Struct Dyn 2011; 28:675-93. [DOI: 10.1080/07391102.2011.10508599] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Roy S, Thakur AR. Two models of Smad4 and Hoxa9 Complex are Proposed: Structural and Interactional Perspective. J Biomol Struct Dyn 2011; 28:729-42. [DOI: 10.1080/07391102.2011.10508602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Zhao Y, Gong Z, Xiao Y. Improvements of the Hierarchical Approach for Predicting RNA Tertiary Structure. J Biomol Struct Dyn 2011; 28:815-26. [DOI: 10.1080/07391102.2011.10508609] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Mittal A, Jayaram B. Backbones of Folded Proteins Reveal Novel Invariant Amino Acid Neighborhoods. J Biomol Struct Dyn 2011; 28:443-54. [DOI: 10.1080/073911011010524954] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Chakrabarti B, Bairagya HR, Mallik P, Mukhopadhyay BP, Bera AK. An Insight to Conserved Water Molecular Dynamics of Catalytic and Structural Zn+2ions in Matrix Metalloproteinase 13 of Human. J Biomol Struct Dyn 2011; 28:503-16. [DOI: 10.1080/07391102.2011.10508591] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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