Abstract:Missense mutations in the coding region of d-amino acid oxidase (DAO) have been found in patients suffering from amyotrophic lateral sclerosis (ALS). Mutations primarily impair the enzymatic activity of DAO and cause neurodegeneration due to an abnormal accumulation of d-serine in the spinal cord. However, the structural and dynamic changes that lead to impaired enzymatic activity are not fully understood. We present here extensive molecular dynamics simulations of wild-type, and all reported ALS-associated DA… Show more
“…Our integrated study including MD simulations and in silico approaches reveal that certain structural and dynamic attributes corresponding to the active site residues, an active site loop comprising residues 216–228 and binding with cofactor FAD, contribute to the plausible loss of enzymatic activity, thus likely to be predisposing the individuals carrying these variations to ALS. This report and our earlier study 23 , employing MD simulations and other informatics-based analyses clearly demonstrate that certain Project MinE based rare DAAO variants are also loss-of-function type and could cause ALS through an unusual deposition of D-serine in the spinal cord. Figure 1 Graphic representation of human D-amino acid oxidase showing its functional sites and rare DAAO variants.…”
Section: Introductionsupporting
confidence: 62%
“…First, only the missense variants with rare variant burden of 0.5% were extracted and variants for which the functional mechanisms are not known were selected for our study. Out of a total of 20 variants (V5A, R38H, D46N, H78Y, F90V, P103L, R115W, P119L, R199W, R199Q, L215F, P268S, R279Q, R283Q, R286C, L329F, G331E, S340F, S345F and S345C), the R38H, R199W and R199Q variants were not included in this study because they were previously studied by us and others 13,14,23 . Further, variants S345F and S345C were excluded because the crystal structure of WT-DAAO (PDB ID: 2E49) contains residues until Ser340 only.…”
Section: Methodsmentioning
confidence: 99%
“…The loss of enzymatic activity, and excessive accumulation of D-serine in the spinal cord was further observed in sALS patients and in SOD1 G93A -ALS mouse model 14 . Because compromised enzymatic activity of DAAO happens to play a vital role in manifestation of ALS, as a result of excessive accumulation of D-serine, we recently demonstrated that certain structural and dynamic changes disrupts the enzymatic activity in ALS associated DAAO variants, leading to the disease causation 23 . This encouraged us to investigate if any of the Project MinE derived rare DAAO variants could also exhibit loss of enzymatic functions and if so, how and by what molecular mechanisms.…”
Impaired enzymatic activity in D-amino acid oxidase (DAAO) caused by missense mutations has been shown to trigger amyotrophic lateral sclerosis (ALS) through an abnormal accumulation of D-serine in the spinal cord. While loss of enzymatic functions of certain ALS-causing DAAO variants have been studied before, a detailed understanding of structure-dynamics-function relationship of the rare DAAO variants has not been investigated hitherto. To address this, we carried out a comprehensive study of all the reported rare DAAO variants. By employing a spectrum of bioinformatics analyses along with extensive structural dynamics simulations, we show that certain rare variants disrupted key interactions with the active site and decreased the conformational flexibility of active site loop comprising residues 216–228, which is essential for substrate binding and product release. Moreover, these variants lost crucial interactions with the cofactor flavin-adenine-dinucleotide, resulting in weaker binding affinity. A detailed inspection revealed that these variants exhibited such characteristics due to the abrogation of specific salt bridges. Taken together, our study provides a gateway into the structural-dynamic features of the rare DAAO variants and highlights the importance of informatics-based integrated analyses in the screening and prioritization of variants a priori to the clinical-functional characterization.
“…Our integrated study including MD simulations and in silico approaches reveal that certain structural and dynamic attributes corresponding to the active site residues, an active site loop comprising residues 216–228 and binding with cofactor FAD, contribute to the plausible loss of enzymatic activity, thus likely to be predisposing the individuals carrying these variations to ALS. This report and our earlier study 23 , employing MD simulations and other informatics-based analyses clearly demonstrate that certain Project MinE based rare DAAO variants are also loss-of-function type and could cause ALS through an unusual deposition of D-serine in the spinal cord. Figure 1 Graphic representation of human D-amino acid oxidase showing its functional sites and rare DAAO variants.…”
Section: Introductionsupporting
confidence: 62%
“…First, only the missense variants with rare variant burden of 0.5% were extracted and variants for which the functional mechanisms are not known were selected for our study. Out of a total of 20 variants (V5A, R38H, D46N, H78Y, F90V, P103L, R115W, P119L, R199W, R199Q, L215F, P268S, R279Q, R283Q, R286C, L329F, G331E, S340F, S345F and S345C), the R38H, R199W and R199Q variants were not included in this study because they were previously studied by us and others 13,14,23 . Further, variants S345F and S345C were excluded because the crystal structure of WT-DAAO (PDB ID: 2E49) contains residues until Ser340 only.…”
Section: Methodsmentioning
confidence: 99%
“…The loss of enzymatic activity, and excessive accumulation of D-serine in the spinal cord was further observed in sALS patients and in SOD1 G93A -ALS mouse model 14 . Because compromised enzymatic activity of DAAO happens to play a vital role in manifestation of ALS, as a result of excessive accumulation of D-serine, we recently demonstrated that certain structural and dynamic changes disrupts the enzymatic activity in ALS associated DAAO variants, leading to the disease causation 23 . This encouraged us to investigate if any of the Project MinE derived rare DAAO variants could also exhibit loss of enzymatic functions and if so, how and by what molecular mechanisms.…”
Impaired enzymatic activity in D-amino acid oxidase (DAAO) caused by missense mutations has been shown to trigger amyotrophic lateral sclerosis (ALS) through an abnormal accumulation of D-serine in the spinal cord. While loss of enzymatic functions of certain ALS-causing DAAO variants have been studied before, a detailed understanding of structure-dynamics-function relationship of the rare DAAO variants has not been investigated hitherto. To address this, we carried out a comprehensive study of all the reported rare DAAO variants. By employing a spectrum of bioinformatics analyses along with extensive structural dynamics simulations, we show that certain rare variants disrupted key interactions with the active site and decreased the conformational flexibility of active site loop comprising residues 216–228, which is essential for substrate binding and product release. Moreover, these variants lost crucial interactions with the cofactor flavin-adenine-dinucleotide, resulting in weaker binding affinity. A detailed inspection revealed that these variants exhibited such characteristics due to the abrogation of specific salt bridges. Taken together, our study provides a gateway into the structural-dynamic features of the rare DAAO variants and highlights the importance of informatics-based integrated analyses in the screening and prioritization of variants a priori to the clinical-functional characterization.
“…MD simulation provides a complete understanding of the phenotypic expressions of mutations by generating detailed information on conformational and structural consequences at a reasonable quality and adequate time scale 52 . Several recent studies have investigated the correlation between experimental studies and MDS analysis, and have suggested MDS studies are helpful for uncovering underlying mutation-associated disease mechanisms, especially in the context of neurodegeneration 40,[53][54][55][56][57] . It has been suggested in previous MD simulation studies that R47H is responsible for loop distortions in TREM2 58 and to induce flexibility, particularly in CDR2 loops 59 .…”
Section: Mechanistic Insights Into Conformational Remodeling Intra-rmentioning
Recently, the critical roles played by genetic variants of TREM2 (Triggering Receptor Expressed on Myeloid cells 2) in Alzheimer's disease have been aggressively highlighted. However, few studies have focused on the deleterious roles of Nasu-Hakola disease (NHD) associated TREM2 variants. In order to get insights into the contributions made by these variants to neurodegeneration, we investigated the influences of four NHD associated TREM2 mutations (Y38C, W50C, T66M, and V126G) on loss-offunction, and followed this with in silico prediction and conventional molecular dynamics simulation. NHD mutations were predicted to be highly deleterious by eight different in silico bioinformatics tools and found to induce conformational changes by molecular dynamics simulation. As compared with the wild-type, the four variants produced substantial differences in the collective motions of loop regions, which not only promoted structural remodeling in the CDR2 (complementarity-determining region 2) loop but also in the CDR1 loop, by changing inter-and intra-loop hydrogen bonding networks. In addition, structural studies in a free energy landscape analysis showed that Y38, T66, and V126 are crucial for maintaining the structural features of CDR1 and CDR2 loops, and that mutations in these positions produced steric clashes and loss of ligand binding. These results showed the presence of mutations in the TREM2 ectodomain induced flexibility and caused structural alterations. Dynamical scenarios, as provided by the present study, may be critical to our understanding of the roles of these TREM2 mutations in neurodegenerative diseases. The accumulation of amyloid-β (Aβ) in brain parenchyma is the main hallmark of Alzheimer's disease (AD), which results in a slow progressive decline of cognitive function by causing the formation of intracellular neurofibrillary tangles, synapse loss, and cell death 1,2. Although the precise mechanisms and molecular determinants of this neurodegenerative disease are incomplete, recent whole-genome sequencing studies have demonstrated altered genetic loci including those in TREM2 (Triggering Receptor Expressed on Myeloid cells 2) are associated with a markedly higher risk of progression to AD 3,4. TREM2 is a V-type immunoglobulin (Ig) domain-containing transmembrane protein that is expressed in osteoclasts, microglia, alveolar macrophages, and other mononuclear phagocytes 4. The activation of TREM2 is initiated by anionic lipids, such as bacterial lipopolysaccharide (LPS) and phospholipids, and several putative ligands like apolipoprotein J (ApoJ) and apolipoprotein E (ApoE) have been reported to bind to TREM2 5-7. Upon ligand binding, TREM2 recruits protein tyrosine kinase SYK through an adapter protein known as DNAX-activating protein of 12 kDa (DAP12), which interacts with the transmembrane region of TREM2 8-10. This binding is followed by a cascade of signaling events, which include the activations of MAPK and PI3K, and regulates the phagocytosis of cellular debris and the inflammatory responses of ...
“…The structures and functions of DAAO have received intense attention in recent years due to its versatility. [26][27][28][29][30] In 1995, Schell et al discovered that D-Ser was localized principally within glial cells. Specifically, they found that type-2 astrocytes, which were cultured from cerebral cortex, expressed particularly high levels of D-Ser.…”
Section: Natural Occurrence and Biological Functions Of D-amino Acidsmentioning
AbstractThis review covers the recent development on the natural occurrence, functional elucidations, and analysis of amino acids of the D (dextro) configuration. In the pharmaceutical field, amino acids are not only used directly as clinical drugs and nutriments, but also widely applied as starting materials, catalysts, or chiral ligands for the synthesis of active pharmaceutical ingredients. Earler belief hold that only L-amino acids exist in nature and D-amino acids were artificial products. However, increasing evidence indicates that D-amino acids are naturally occurring in living organisms including human beings, plants, and microorganisms, playing important roles in biological processes. While D-amino acids have similar physical and chemical characteristics with their respective L-enantiomers in an achiral measurement, the biological functions of D-amino acids are remarkably different from those of L-ones. With the rapid development of chiral analytical techniques for D-amino acids, studies on the existence, formation mechanisms, biological functions as well as relevant physiology and pathology of D-amino acids have achieved great progress; however, they are far from being sufficiently explored.
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