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Journal of Molecular Recognition: JMR

Rana Shadjou, Mohammad Hasanzadeh, Mohammad Heidar-Poor, Nasrin Shadjou
Aflatoxins are potential food pollutants produced by fungi. One of important toxins is aflatoxin M1 (AFM1). A great deal of concern is associated with AFM1 toxicity. In the present study, an innovative electrochemical interface for quantitation of AFM1 based on ternary signal amplification strategy was fabricated. In this work, silver nanoparticles was electrodeposited onto green and biocompatible nanocomposite containing α-cyclodextrin as conductive matrix and graphene quantum dots as amplification element...
January 17, 2018: Journal of Molecular Recognition: JMR
Huan Zhang, Chong Zhang, Xiao-Yan Dong, Jie Zheng, Yan Sun
Dysfunctional accumulation of amyloid β-protein (Aβ) mediated by Cu2+ exhibits higher neurotoxicity and accelerates the progress of Alzheimer's disease, so inhibition of Cu2+ -mediated Aβ aggregation and cytotoxicity has been considered as a therapeutic strategy for the disease. Herein, a nonapeptide was designed by linking HH to the C-terminus of a peptide inhibitor of Aβ aggregation, LVFFARK (LK7). We found that the nonapeptide, LK7-HH, possessed dual functionality, including enhanced inhibition capability on Aβ aggregation as compared to LK7, and chelating Cu2+ with a dissociation constant of 5...
January 10, 2018: Journal of Molecular Recognition: JMR
David A Spivak
No abstract text is available yet for this article.
January 9, 2018: Journal of Molecular Recognition: JMR
Hongping Wu, Hai Wang, Wuqi Jiang, Zhengxing Lian
Toll-like receptors (TLRs) are an important part of the innate immune system, acting as a first line of defense against many invading pathogens. The ligand known to bind Gallus toll-like receptor 21 (gTLR21) is the unmethylated cytosine phosphate guanine dideoxy nucleotide motif; however, the evolutionary characteristics and structural biology of gTLR21 are poorly elaborated. Our results suggest that gTLR21 is phylogenetically and evolutionarily related to the TLR11 family and is perhaps a close ortholog of the Mus TLR13...
December 27, 2017: Journal of Molecular Recognition: JMR
Mei-Ling Sun, Li-Mei Sun, Yong-Qing Wang
The human HtrA family of serine proteases (HtrA1, HtrA2, HtrA3, and HtrA4) are the key enzymes associated with pregnancy and closely related to the development and progression of many pathological events. Previously, it was found that halogen substitution at the indole moiety of peptide Trp-1 residue can form a geometrically satisfactory halogen bond with the Drosophila discs large, zona occludens-1 (PDZ) domain of HtrA proteases. Here, we attempt to systematically investigate the effect of substitution with 4 halogen types and 2 indole positions on the binding affinity and specificity of peptide ligands to the 4 HtrA PDZ domains...
December 20, 2017: Journal of Molecular Recognition: JMR
Paromita Bhattacharjee, Tapas Ghosh, Sarita Sarkar, Prateek Pandya, Kakali Bhadra
The work focuses towards interaction of harmaline, with nucleic acids of different motifs by multispectroscopic and calorimetric techniques. Findings of this study suggest that binding constant varied in the order single-stranded (ss) poly(A) > double-stranded calf thymus (CT) DNA > double-stranded poly(G)·poly(C) > clover leaf tRNAPhe . Prominent structural changes of ss poly(A), CT DNA, and poly(G)· poly(C) with concomitant induction of optical activity in the bound achiral alkaloid molecule was observed, while with tRNAPhe , very weak induced circular dichroism perturbation was seen...
December 15, 2017: Journal of Molecular Recognition: JMR
Vineeta Kaushik, Ved Vrat Verma, Manisha Goel
Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated (CRISPR-Cas) systems present in genomes of bacteria and archaea have been the focus of many research studies recently. The Cas4 proteins of these systems are thought to be responsible for the adaptation step in the CRISPR mechanism. Cas4 proteins exhibit low sequence similarity among themselves and are currently classified into 2 main classes: DUF83 and DUF911. The characteristic features of Cas4 proteins belonging to DUF83 class have been elucidated by determining the structures of Cas4 protein from Sulfolobus solfataricus and Pyrobaculum calidifontis...
December 15, 2017: Journal of Molecular Recognition: JMR
A Kulandaisamy, Ambuj Srivastava, R Nagarajan, M Michael Gromiha
Protein-DNA interactions are involved in various fundamental biological processes such as replication, transcription, DNA repair, and gene regulation. To understand the interaction in protein-DNA complexes, the integrative study of binding and stabilizing residues is important. In the present study, we have identified key residues that play a dual role in both binding and stability from a nonredundant dataset of 319 protein-DNA complexes. We observed that key residues are identified in very less number of complexes (29%) and only about 4% of stabilizing/binding residues are identified as key residues...
December 12, 2017: Journal of Molecular Recognition: JMR
Siew Wen Leong, Theam Soon Lim, Asma Ismail, Yee Siew Choong
With the development of de novo binders for protein targets from non-related scaffolds, many possibilities for therapeutics and diagnostics have been created. In this study, we described the use of de novo design approach to create single-chain fragment variable (scFv) for Salmonella enterica subspecies enterica serovar Typhi TolC protein. Typhoid fever is a global health concern in developing and underdeveloped countries. Rapid typhoid diagnostics will improve disease management and therapy. In this work, molecular dynamics simulation was first performed on a homology model of TolC protein in POPE membrane bilayer to obtain the central structure that was subsequently used as the target for scFv design...
December 12, 2017: Journal of Molecular Recognition: JMR
Meryl Wang, David Zhu, Jianwei Zhu, Ruth Nussinov, Buyong Ma
Deciphering antibody-protein antigen recognition is of fundamental and practical significance. We constructed an antibody structural dataset, partitioned it into human and murine subgroups, and compared it with nonantibody protein-protein complexes. We investigated the physicochemical properties of regions on and away from the antibody-antigen interfaces, including net charge, overall antibody charge distributions, and their potential role in antigen interaction. We observed that amino acid preference in antibody-protein antigen recognition is entropy driven, with residues having low side-chain entropy appearing to compensate for the high backbone entropy in interaction with protein antigens...
December 8, 2017: Journal of Molecular Recognition: JMR
Cheng-Zhang Yang, Lin-Yi Li, Xiao-Han Wang, Si-Qian Yu, Yan-Jun Hu
Tremendous research efforts have been dedicated to fabricating high-quality Zn-doped CdTe quantum dots (QDs) for any potential biomedical applications. In particular, the correlation of issues regarding how QDs interact with DNA is of greatest importance. Herein, a pH-responsive study of the interactions between CdTe:Zn2+ quantum dots with 4 different sizes and calf thymus DNA (ctDNA) was conducted using multispectroscopic techniques and electrochemical investigation. Fluorescence studies revealed that this interaction process is predominantly a static process and groove binding was the main binding mode for CdTe:Zn2+ QDs to ctDNA...
December 6, 2017: Journal of Molecular Recognition: JMR
Izabela Behrendt, Martyna Prądzińska, Marta Spodzieja, Paulina Czaplewska, Aleksandra S Kołodziejczyk, Aneta Szymańska, Franciszek Kasprzykowski, Susanna L Lundström, Roman A Zubarev, Sylwia Rodziewicz-Motowidło
Amyloid formation is associated with a number of neurodegenerative diseases that affect the independence and quality of life of aging populations. One of rather atypical, occurring at a young age amyloidosis is hereditary cystatin C amyloid angiopathy (HCCAA) related to aggregation of L68Q variant of human cystatin C (hCC). Human cystatin C plays a very important role in many aspects of human health; however, its amyloidogenic properties manifested in HCCAA present a real, lethal threat to some populations and any work on factors that can affect possible influencing hCC aggregation is not to overestimate...
December 5, 2017: Journal of Molecular Recognition: JMR
H Benachour, J Leroy-Dudal, R Agniel, J Wilson, M Briand, F Carreiras, O Gallet
Changes in glycosylation have been associated with human cancer, but their complexity poses an analytical challenge. Ovarian cancer is a major cause of death in women because of an often late diagnosis. At least one-third of patients presents ascites fluid at diagnosis, and almost all have ascites at recurrence. Vitronectin (Vn) is a multifunctional glycoprotein that is suggested to be implicated in ovarian cancer metastasis and is found within ascites. The present study evaluated the potential of using lectin affinity for characterizing the glycosylation pattern of Vn...
December 4, 2017: Journal of Molecular Recognition: JMR
Anas Shamsi, Azaj Ahmed, Bilqees Bano
In our study, we have characterized the prefibrillar aggregates of human serum albumin (HSA) induced by temsirolimus, anti-renal cancer drug. Molecular docking was retorted to confirm binding of HSA and temsirolimus. Temsirolimus caused the structural transition of native HSA to non-native species after prolonged incubation of 20 days. These non-native species were characterized as prefibrillar aggregates as evident by decreased intrinsic fluorescence and enhanced 8-anilino-1-naphthalene-sulphonic acid (ANS) fluorescence...
November 27, 2017: Journal of Molecular Recognition: JMR
Yan Zheng, Qing Wang, Xiaohai Yang, Zhiping Li, Lei Gao, Hua Zhang, Wenyan Nie, Xiuhua Geng, Kemin Wang
Increasing knowledge on the understanding interactions of aptamer with misfolded proteins (including monomer, oligomer, and amyloid fibril) is crucial for development of aggregation inhibitors and diagnosis of amyloid diseases. Herein, the interactions of lysozyme monomer-, oligomer-, and amyloid fibril-aptamer were investigated using single-molecule force spectroscopy. The results revealed that the aptamer screened against lysozyme monomer could also bind to oligomer and amyloid fibril, in spite of the recognition at a lower binding probability...
November 16, 2017: Journal of Molecular Recognition: JMR
S Dhivya, V Baskar, S R Kumar, R Sathishkumar
The role of polyketide and non-ribosomal proteins from the class of small molecule metabolism of Mycobacterium tuberculosis is well documented in envelope organization, virulence, and pathogenesis. Consequently, the identification of T cell epitopes from these proteins could serve to define potential antigens for the development of vaccines. Fourty-one proteins from polyketide and non-ribosomal peptide synthesis of small molecule metabolism proteins of M tuberculosis H37Rv were analyzed computationally for the presence of HLA class I binding nanomeric peptides...
November 16, 2017: Journal of Molecular Recognition: JMR
Christopher Dobie, Andrew P Montgomery, Rémi Szabo, Danielle Skropeta, Haibo Yu
Sialyltransferase (ST) upregulation and the resultant hypersialylation of tumour cell surfaces is an established hallmark of many cancers including lung, breast, ovarian, pancreatic and prostate cancer. The role of ST enzymes in tumour cell growth and metastasis, as well as links to multi-drug resistance, has seen ST inhibition emerge as a target for potential antimetastatic cancer treatments. The most potent of these reported inhibitors are transition-state analogues. Although there are several examples of these in the literature, many have suspected poor pharmacokinetic properties and are not readily synthetically accessible...
November 9, 2017: Journal of Molecular Recognition: JMR
John W Schrader, Gary R McLean
Recombinant monoclonal antibodies (Ab's) have widespread application as research tools, diagnostic reagents and as biotherapeutics. Whilst studying the cellular molecular switch protein m-ras, a recombinant monoclonal antibody to m-ras was generated for use as a research tool. Antibody genes from a single rabbit B cell secreting IgG to an m-ras specific peptide sequence were expressed in mammalian cells, and monoclonal rabbit IgG binding was characterized by ELISA and peptide array blotting. Although the monoclonal Ab was selected for specificity to m-ras peptide, it also bound to both recombinant full-length m-ras and h-ras proteins...
November 8, 2017: Journal of Molecular Recognition: JMR
Zhengshan Tian, Zechun Wang, Xinxin Han, Ning Wang, Ruiyong Wang
The interaction between cannabinol (CBN) and herring-sperm deoxyribonucleic acid was investigated by using acridine orange as a fluorescence probe in this work. UV-Vis spectroscopy, fluorescence spectroscopy, and DNA melting techniques were used. The fluorescence of DNA acridine orange was quenched by CBN. The results indicated that CBN can bind to DNA. The binding constant for the CBN and herring-sperm deoxyribonucleic acid was obtained at 3 temperatures, respectively. Results of molecular docking corroborated the experimental results obtained from spectroscopic investigations...
October 25, 2017: Journal of Molecular Recognition: JMR
Susana R Sousa, Pierre Parot, Jean-Luc Pellequer
No abstract text is available yet for this article.
October 12, 2017: Journal of Molecular Recognition: JMR
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