Source and target enzyme signature in serine protease inhibitor active site sequences

Amino acid sequences of proteinaceous proteinase inhibitors have been extensively analysed for deriving information regarding the molecular evolution and functional relationship of these proteins. These sequences have been grouped into several well defined families. It was found that the phylogeny constructed with the sequences corresponding to the exposed loop responsible for inhibition has several branches that resemble those obtained from comparisons using the entire sequence. The major branches of the unrooted tree corresponded to the families to which the inhibitors belonged. Further branching is related to the enzyme specificity of the inhibitor. Examination of the active site loop sequences of trypsin inhibitors revealed that here are strong preferences for specific amino acids at different positions of the loop. These preferences are inhibitor class specific. Inhibitors active against more than one enzyme occur within a class and confirm to class specific sequence in their loops. Hence, only a few positions in the loop seem to determine the specificity. The ability to inhibit the same enzyme by inhibitors that belong to different classes appears to be a result of convergent evolution

Structural stabilization of GTP-binding domains in circularly permuted GTPases: Implications for RNA binding

GTP hydrolysis by GTPases requires crucial residues embedded in a conserved G-domain as sequence motifs G1–G5. However, in some of the recently identified GTPases, the motif order is circularly permuted. All possible circular permutations were identified after artificially permuting the classical GTPases and subjecting them to profile Hidden Markov Model searches. This revealed G4–G5–G1–G2–G3 as the only possible circular permutation that can exist in nature. It was also possible to recognize a structural rationale for the absence of other permutations, which either destabilize the invariant GTPase fold or disrupt regions that provide critical residues for GTP binding and hydrolysis, such as Switch-I and Switch-II. The circular permutation relocates Switch-II to the C-terminus and leaves it unfastened, thus affecting GTP binding and hydrolysis. Stabilizing this region would require the presence of an additional domain following Switch-II. Circularly permuted GTPases (cpGTPases) conform to such a requirement and always possess an ‘anchoring’ C-terminal domain. There are four sub-families of cpGTPases, of which three possess an additional domain N-terminal to the G-domain. The biochemical function of these domains, based on available experimental reports and domain recognition analysis carried out here, are suggestive of RNA binding. The features that dictate RNA binding are unique to each subfamily. It is possible that RNA-binding modulates GTP binding or vice versa. In addition, phylogenetic analysis indicates a closer evolutionary relationship between cpGTPases and a set of universally conserved bacterial GTPases that bind the ribosome. It appears that cpGTPases are RNA-binding proteins possessing a means to relate GTP binding to RNA binding

Transforaminal percutaneous endoscopic lumbar discectomy versus microdiscectomy: an Indian rural experience

Background: The objective of the study was to compare surgical outcome of micro-discectomy with transforaminal percutaneous endoscopic lumbar discectomy for single level lumbar disc herniation in Indian rural population.Methods: Retrospective comparative study was designed during the period of October 2012 to June 2015, patients in the age group of 22-75 years with unremitting sciatica with/without back pain, and/or a neurological deficit that correlated with appropriate level and side of neural compression as revealed on MRI, with single level lumbar disc herniation who underwent either microdiscectomy or TPELD were included in the study. Patients were assessed on visual analogue scale (VAS) for back and leg pain, modified macnabs criteria, the Oswestry Disability Index (ODI).Results: Group I (MD) included 44 patients and Group II (TPELD) included 20 patients. Significant improvement was seen in claudication symptom post-operatively in both MD and TPELD. Mean operating time was significantly shorter in MD group (1.11 hrs vs. 1.32 hrs; p<0.01). According to modified MacNab's criteria, outcome were excellent (81.8%), good (9.09%) and fair (9.09%) in MD. Similarly, in TPELD, 80%, 15% and 5% patients had excellent, good and fair outcome respectively. In both groups, no one had a poor outcome. Thus, overall success rate was 100% in the study.Conclusions: TPELD and MD have comparable post-operative outcome in most of the efficacy parameters in Indian rural patients undergoing treatment of single level lumbar disc herniation. Additionally, TPELD offers distinct advantages such as performed under local anaesthesia, preservation of structure, lesser post-operative pain and early mobilization and discharge from hospital

Adaptive Wind Driven Optimization based Energy Aware Clustering Scheme for Wireless Sensor Networks

Wireless Sensor Networks (WSNs) are utilised in a variety of applications due to their capacity to capture and transmit environmental data. Clustering has emerged as an efficient method for improving energy efficiency in WSNs. To resolve these issues, we propose an Adaptive Wind Driven Optimisation based Energy Aware Clustering Scheme (AWDO-EACS) for WSNs. The AWDO-EACS model presents an extended form of the Wind Driven Optimisation (WDO) algorithm, designated AWDO, with optimised inherent term values. The proposed model takes into account multiple objectives, such as energy consumption, distance, and end-to-end latency, in order to achieve superior energy efficiency and an extended network lifetime. To validate the efficacy of the AWDO-EACS model, extensive experiments with varying node counts were carried out. In terms of network stability, energy efficiency, end-to-end latency, packet delivery ratio, throughput, packet loss rate, and network lifetime, the results demonstrate that the AWDO-EACS outperforms contemporary clustering strategies. Specifically, the AWDO-EACS obtained a significant increase in energy efficiency, with a 27.35 percent improvement over existing clustering techniques for 20 nodes and an 83.41 percent improvement for 100 nodes. In addition, the end-to-end latency was considerably reduced, with a 96-round lifetime for 20 nodes and a 74-round lifetime for 100 nodes, compared to 37 and 20 rounds, respectively, for GA-LEACH and MW-LEACH. In addition, the AWDO-EACS demonstrated superior packet delivery performance, with a 99.32% delivery ratio for 100 nodes, eclipsing the 76.90% and 82.65% of GA-LEACH and MW-LEACH, respectively. Moreover, the AWDO-EACS model demonstrated a remarkably low packet loss rate of 0.68 percent for 100 nodes, compared to 23.10 percent for GA-LEACH and 17.35 percent for MW-LEACH. The effectiveness of the proposed AWDO-EACS model in enhancing the overall performance of WSNs is demonstrated

A charge reversal differentiates (p)ppGpp synthesis by monofunctional and bifunctional Rel proteins

A major regulatory mechanism evolved by microorganisms to combat stress is the regulation mediated by (p)ppGpp (the stringent response molecule), synthesized and hydrolyzed by Rel proteins. These are divided into bifunctional and monofunctional proteins based on the presence or absence of the hydrolysis activity. Although these proteins require Mg2+ for (p)ppGpp synthesis, high Mg2+ was shown to inhibit this reaction in bifunctional Rel proteins from Mycobacterium tuberculosis and Streptococcus equisimilis. This is not a characteristic feature in enzymes that use a dual metal ion mechanism, such as DNA polymerases that are known to carry out a similar pyrophosphate transfer reaction. Comparison of polymerase Polβ and RelSeq structures that share a common fold led to the proposal that the latter would follow a single metal ion mechanism. Surprisingly, in contrast to bifunctional Rel, we did not find inhibition of guanosine 5′-triphosphate, 3′-diphosphate (pppGpp) synthesis at higher Mg2+ in the monofunctional RelA from Escherichia coli. We show that a charge reversal in a conserved motif in the synthesis domains explains this contrast; an RXKD motif in the bifunctional proteins is reversed to an EXDD motif. The differential response of these proteins to Mg2+ could also be noticed in fluorescent nucleotide binding and circular dichroism experiments. In mutants where the motifs were reversed, the differential effect could also be reversed. We infer that although a catalytic Mg2+ is common to both bifunctional and monofunctional proteins, the latter would utilize an additional metal binding site formed by EXDD. This work, for the first time, brings out differences in (p)ppGpp synthesis by the two classes of Rel proteins

Distribution and Depth-Aware Transformers for 3D Human Mesh Recovery

Precise Human Mesh Recovery (HMR) with in-the-wild data is a formidable challenge and is often hindered by depth ambiguities and reduced precision. Existing works resort to either pose priors or multi-modal data such as multi-view or point cloud information, though their methods often overlook the valuable scene-depth information inherently present in a single image. Moreover, achieving robust HMR for out-of-distribution (OOD) data is exceedingly challenging due to inherent variations in pose, shape and depth. Consequently, understanding the underlying distribution becomes a vital subproblem in modeling human forms. Motivated by the need for unambiguous and robust human modeling, we introduce Distribution and depth-aware human mesh recovery (D2A-HMR), an end-to-end transformer architecture meticulously designed to minimize the disparity between distributions and incorporate scene-depth leveraging prior depth information. Our approach demonstrates superior performance in handling OOD data in certain scenarios while consistently achieving competitive results against state-of-the-art HMR methods on controlled datasets.Comment: Submitted to 21st International Conference on Robots and Vision (CRV'24), Guelph, Ontario, Canad

Extended C-terminus and length of the linker connecting the G-domains are species-specific variations in the EngA family of GTPases

AbstractEngA is an essential protein involved in ribosome biogenesis. It is an unique GTPase, possessing two consecutive G-domains. Using sequence and phylogenetic analysis, we found two intriguing variants among EngA homologues – one with a shorter linker joining the G-domains and another with a longer linker, which additionally possesses an extended C-terminus. Interestingly, while the former variant is mainly restricted to firmicutes, the latter is found in nonfirmicutes. Chimeric proteins with interchanged linkers and extensions were generated to gauge the importance of these elements. Ribosome interaction experiments employing the chimeric proteins suggest that a precise combination of the linker and C-terminal extension are important features regulating EngA ribosome interactions in a variant-specific manner

Differential regulation of intracellular factors mediating cell cycle, DNA repair and inflammation following exposure to silver nanoparticles in human cells

10.1186/2041-9414-3-2Genome Integrity3

Structure of N-acetylglucosamine-1-phosphate uridyltransferase (GlmU) from Mycobacterium tuberculosis in a cubic space group

The structure of M. tuberculosis N-acetylglucosamine-1-phosphate uridyltransferase (GlmU) was determined by the molecular-replacement method to 3.4 Å resolution in space group I432 and was refined to a final R work and R free of 0.285 and 0.321, respectively