Journal of Molecular Biology最新文献_第8页

Tracing the Origin of the Genetic Code and Thermostability to Dipeptide Sequences in Proteomes 追踪遗传密码和热稳定性的起源到蛋白质组中的二肽序列。

IF 4.5 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Biology

Pub Date : 2026-02-15 Epub Date: 2025-08-14 DOI: 10.1016/j.jmb.2025.169396

Minglei Wang, M. Fayez Aziz, Gustavo Caetano-Anollés

The safekeeping of the genetic code has been entrusted to interactions between aminoacyl-tRNA synthetases and their cognate tRNA. In a previous phylogenomic study, chronologies of RNA substructures, protein domains and dipeptide sequences uncovered the early emergence of an ‘operational’ code in the acceptor arm of tRNA prior to the implementation of the 'standard' genetic code in the anticodon loop of the molecule. This history likely originated in peptide–synthesizing urzymes but was driven by episodes of molecular co-evolution and recruitment that promoted flexibility and protein folding. Here, we show that dipeptide sequences offer deep-time insights into the chronology of code emergence. A phylogeny describing the evolution of the repertoire of 400 canonical dipeptides reconstructed from an analysis of 4.3 billion dipeptide sequences across 1,561 proteomes revealed the overlapping temporal emergence of dipeptides containing Leu, Ser and Tyr, followed by those containing Val, Ile, Met, Lys, Pro, and Ala, all of which supported the operational RNA code. This strengthened a timeline of genetic code entry. The synchronous appearance of dipeptide–antidipeptide sequences along the dipeptide chronology supported an ancestral duality of bidirectional coding operating at the proteome level. Tracing determinants of thermal adaptation showed protein thermostability was a late evolutionary development and bolstered an origin of proteins in the mild environments typical of the Archaean eon. Our study uncovers a hidden evolutionary link between a protein code of dipeptides – arising from the structural demands of emerging proteins – and an early operational code shaped by co-evolution, editing, catalysis and specificity.

遗传密码的安全保存被委托于氨基酰基tRNA合成酶与其同源tRNA之间的相互作用。在之前的系统基因组学研究中，RNA亚结构、蛋白质结构域和二肽序列的年表揭示了tRNA受体臂中“操作”密码的早期出现，早于分子反密码子环中“标准”遗传密码的实施。这段历史可能起源于肽合成酶，但由促进柔韧性和蛋白质折叠的分子共同进化和招募事件驱动。在这里，我们表明，二肽序列提供了深入的时间洞察代码出现的年表。通过对1561个蛋白质组中43亿个二肽序列的分析，描述了400个典型二肽库的进化系统发育，揭示了包含Leu、Ser和Tyr的二肽的重叠时间出现，其次是包含Val、Ile、Met、Lys、Pro和Ala的二肽，所有这些二肽都支持可操作的RNA代码。这加强了遗传密码进入的时间轴。值得注意的是，二肽-抗二肽序列的同步出现表明在蛋白质组水平上具有祖先遗传的二元性。最后，沿着二肽年表追踪热适应的已知决定因素表明，蛋白质的热稳定性是一个较晚的进化发展，并支持了蛋白质在太古宙典型的温和环境中的起源。我们的研究揭示了二肽的蛋白质代码（源于新兴蛋白质的结构需求）与由共同进化、编辑、催化和特异性形成的早期操作代码之间隐藏的进化联系。

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引用次数: 0

Stability and Adaptation of Proteins, Membranes and Cells to Extreme Temperature and Pressure 蛋白质、膜和细胞对极端温度和压力的稳定性和适应性。

IF 4.5 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Biology

Pub Date : 2026-02-15 Epub Date: 2025-10-06 DOI: 10.1016/j.jmb.2025.169477

J. Peters , J.G. LoRicco , M. Saracco , A. Caliò , P. Oger

All biological systems, from low complexity (single molecules) to high complexity (whole cells), must find a way to maintain stability and function under a wide array of environmental conditions. Archaea have been found to be particularly effective at inhabiting the most extreme environments found on Earth. Proto-cells at the origin of life are hypothesised to have originated under even harsher conditions. Therefore, in this review, we summarise our recent works which have provided insights into the molecular bases for adaptation in various archaeal and proto-cell systems, to temperature and high hydrostatic pressure. First, we discuss adaptation in archaeal membranes, which differ significantly from membranes of Bacteria and eukaryotes, having been adapted by evolution to extreme environments. Next, we consider how functionality could have arisen and been maintained in simple proto-membranes. Finally, we discuss proteome and cell-wide adaptation strategies seen in adapted vs non-adapted species.

所有生物系统，从低复杂性（单分子）到高复杂性（整个细胞），都必须找到一种在各种环境条件下保持稳定性和功能的方法。人们发现古细菌在地球上最极端的环境中生存得特别有效。据推测，生命起源时的原始细胞是在更为恶劣的条件下产生的。因此，在本文中，我们总结了我们最近的研究成果，为各种古细菌和原细胞系统适应温度和高静水压力的分子基础提供了见解。首先，我们讨论了古细菌膜的适应性，它与细菌和真核生物的膜有很大的不同，它们通过进化适应了极端环境。接下来，我们考虑功能是如何在简单的原膜中产生和维持的。最后，我们讨论了在适应和非适应物种中观察到的蛋白质组和细胞范围的适应策略。

引用次数: 0

Unraveling the Link Between Thermal Adaptation and Latent Allostery in Malate Dehydrogenase From Methanococcales 揭示甲烷球菌苹果酸脱氢酶的热适应与潜伏变构之间的联系。

IF 4.5 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Biology

Pub Date : 2026-02-15 Epub Date: 2025-11-20 DOI: 10.1016/j.jmb.2025.169552

Caroline Simões Pereira , Sandrine Coquille , Céline Brochier-Armanet , Fabio Sterpone , Dominique Madern

Malate dehydrogenase (MalDH) (EC.1.1.1.37) is an enzyme engaged in the central metabolism of cells, catalyzing the interconversion between oxaloacetate and malate using NADH or NADPH as coenzyme. These enzymes are particularly interesting models for studying how proteins adapt to physical and chemical environmental constraints. In this study, we investigated the molecular mechanisms that have enabled MalDHs to adapt to changes in temperature, using Methanococcales archaea as a model organism. We solved the crystal structure of ancestral MalDHs in these archaea. Structural comparison with present-day MalDHs such as those from Methanocaldococcus infernus (M. inf) and Methanocaldococcus jannaschii (M. jan), highlights the role salt-bridges in thermal adaptation. We also found that present-day MalDHs from M. inf and M. jan, show structural features that resemble the extended or compact states typical of allosteric lactate dehydrogenases. To test hypotheses about a possible link between thermal adaptation and the emergence of allosteric regulation, we characterized structurally two M. jan MalDH mesophilic-like mutants. Molecular dynamics simulations using the Wt M. jan and mutant MalDHs were used to rationalize the experimental data. The results indicate that uncompetent and competent catalytic site configurations are in an equilibrium that depends on temperature conditions. At low temperature the Wt M. jan MalDH select non-competent conformers, whereas high temperature favors active conformers. In contrast, the M. jan MalDH mutants explore competent conformers for catalysis at a lowest temperature, a phenomenon that fits well with their biochemical behavior. Our work reveals that thermal adaptation and evolution of allostery are strongly linked via the modulation of the protein conformational landscape.

苹果酸脱氢酶（MalDH）（EC.1.1.1.37）是一种参与细胞中心代谢的酶，以NADH或NADPH作为辅酶，催化草酰乙酸与苹果酸之间的相互转化。这些酶是研究蛋白质如何适应物理和化学环境约束的特别有趣的模型。在这项研究中，我们研究了使MalDHs适应温度变化的分子机制，以甲烷球菌古细菌为模式生物。我们解决了这些古细菌祖先maldh的晶体结构。与现今的MalDHs结构比较，如来自infernus Methanocaldococcus （M. inf）和jannaschii Methanocaldococcus （M. jan）的MalDHs，突出了盐桥在热适应中的作用。我们还发现，来自M. inf和M. jan的现今MalDHs显示出类似于变构乳酸脱氢酶典型的扩展或紧凑状态的结构特征。为了验证热适应和变构调节之间可能存在联系的假设，我们对两个M. jan MalDH中温样突变体进行了结构表征。利用Wt M. jan和突变体MalDHs进行分子动力学模拟，对实验数据进行合理化。结果表明，在不同的温度条件下，非活性位点和活性位点构型处于平衡状态。在低温下，Wt M. jan MalDH选择非活性构象，而高温有利于活性构象。相比之下，M. jan MalDH突变体在最低温度下探索有能力的构象进行催化，这一现象与它们的生化行为非常吻合。我们的研究表明，热适应和变构的进化是通过调节蛋白质构象景观紧密联系在一起的。

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引用次数: 0

Allostery in Biomolecular Condensates 生物分子凝聚体中的变构。

IF 4.5 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Biology

Pub Date : 2026-02-15 Epub Date: 2025-09-15 DOI: 10.1016/j.jmb.2025.169446

Ruth Nussinov , Clil Regev , Hyunbum Jang

Allosteric proteins and membrane-less biomolecular condensates are physics-governed pivotal functional components. Allosteric regulation is an inherent physical property of dynamic proteins, and dynamic proteins are allosteric. Thus, in biomolecular condensates (like everywhere else in the cell), allostery is at play, and often missing in condensate descriptions is that the cooperative transitions can involve allosteric effects. The condensate environment can be especially conducive to allostery. Condensed settings can increase the chance of protein interaction and allosteric encounters in function-specific condensates. Specific protein–protein interactions provide the structural framework for signals to transmit cooperatively and dynamically, ultimately modulating cell activity. Their interfaces are commonly enriched in nonpolar (hydrophobic) surface. With abundant functionally specific proteins, and surfaces accommodating multiple hydrophobic patches, interconnected multivalent molecular networks are expected. Lacking hydrophobic cores, disordered proteins’ folding-upon-binding scenarios often form strong hydrophobic interfaces, and cooperative (partially disordered) multimers are also common. Repelling water is a major force in condensate formation, albeit not the sole. Here we emphasize dilution as functional and allosteric determinant. Extremely high dilution in rapidly growing proliferating cells can stimulate senescence; lower dilution increases concentration, thus, higher probability of increased proximity and reduced separation, driving protein–protein interactions, and allostery. Is there then effective allostery in condensates? We believe that it depends on the cell state. Under normal physiological conditions, with condensates water content around 40% of total cell mass–yes; over 70% could be too diluted. If too low—it can become function-poor aggregate-like. Effective allostery and signaling require specific interactions, extending from clustered receptors to the cytoskeleton.

无膜生物分子凝聚物是关键的物理控制的功能组件。尽管如此，一个关键因素却被忽视了。功能通常涉及动态蛋白，而动态蛋白是变构的。因此，在生物分子凝聚体中（和其他任何地方一样），变构在起作用，而在凝聚体描述中通常遗漏的是，合作转变可能涉及变构效应。凝结水环境特别有利于变构。冷凝设置可以增加蛋白质相互作用的机会，并在功能特异性冷凝物变构遭遇。特定的蛋白质-蛋白质相互作用为信号的协同和动态传递提供了结构框架，最终调节细胞活性。它们的界面通常富集在非极性（疏水）表面。由于具有丰富的功能特异性蛋白质和容纳多个疏水斑块的表面，相互连接的多价分子网络有望实现。缺乏疏水核心，无序蛋白质的结合折叠场景通常形成强疏水界面，合作（部分无序）多聚体也很常见。拒水是凝析油形成的主要力量，尽管不是唯一的力量。这里我们强调稀释是功能性和变构性的决定因素。在快速生长的增殖细胞中，高度稀释可刺激衰老；较低的稀释增加了浓度，因此，增加接近和减少分离的可能性更高，驱动蛋白质相互作用和变构。凝析油是否存在有效变构？我们认为这取决于细胞的状态。在正常生理条件下，凝析液含水量约占细胞总质量的40%；超过70%可能会被稀释。如果太低，它会变成功能差的聚合体。有效的变构和信号需要特定的相互作用，从集群受体延伸到细胞骨架。

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引用次数: 0

Adaptation of Folding and Function of a Nuclease from the Cold Deep Sea 一种低温深海核酸酶的折叠适应性及其功能。

IF 4.5 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Biology

Pub Date : 2026-02-15 Epub Date: 2025-12-22 DOI: 10.1016/j.jmb.2025.169602

Tejaswi Koduru , Philippe Barthe , Noam Hantman , Karine De Guillen , Scott A. McCallum , Joel E. Morgan , Estella F. Yee , Pierce Leonardi , Jack Foland , Christian Roumestand , Catherine A. Royer

The majority of the Earth’s microbial biomass is found in high pressure environments, raising the question of how protein sequences adapt to such environments. Pressure adaptation is more complex, and less well-understood, than adaptation to extreme temperatures since in high pressure environments, these two thermodynamic parameters are often coupled, as in the cold deep-sea or at hydrothermal vents. To begin to address this question, we investigated the functional and folding properties of an exonuclease, Cnase, from the first Gram positive piezophile to be sequenced, Carnobacterium sp. AT7, isolated at 2500 m depth and at ∼2 °C in the Aleutian trench in the North Pacific. We find that Cnase is a bonafide exonuclease, despite its high negative charge. We also find that Cnase largely conserves the structure and folding mechanism of its mesophilic and well-studied homolog, staphylococcal nuclease, Snase, despite significant differences in their sequences.

地球上的大部分微生物是在高压环境中发现的，这就提出了蛋白质序列如何适应这种环境的问题。压力适应比对极端温度的适应更复杂，也更不容易理解，因为在高压环境中，这两个热力学参数通常是耦合的，比如在寒冷的深海或热液喷口。为了开始解决这个问题，我们研究了第一个革兰氏阳性亲压菌Carnobacterium sp. AT7的外切酶nase的功能和折叠特性，该细菌在北太平洋阿留申海沟2500米深、~ 2°C下分离。我们发现nase是一种真正的外切酶，尽管它的负电荷很高。我们还发现，尽管在序列上存在显著差异，但nase在很大程度上保留了其中温性同源物葡萄球菌核酸酶Snase的结构和折叠机制。

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引用次数: 0

Protein Intrinsic Disorder and Adaptation to Extreme Environments: Resilience of Chaos 蛋白质内在紊乱和对极端环境的适应：混乱的恢复力。

IF 4.5 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Biology

Pub Date : 2026-02-15 Epub Date: 2025-11-14 DOI: 10.1016/j.jmb.2025.169547

Vladimir N. Uversky

Extremophiles are organisms adapted not only to survive in harsh conditions but thrive in environments considered extreme or uninhabitable by most life forms. They serve as a living reflection of a popular motto “What doesn’t kill you makes you stronger” and show that life on Earth is spread well outside the human-centric comfort zone. In fact, extremophiles, being found in deep crustal and oceanic depths, outer space, highly acidic and basic conditions, extreme temperatures (+122 °C to −20 °C), and in the presence of toxins and high radiation, demonstrate life’s remarkable adaptability. Polyextremophiles, capable of enduring multiple extreme conditions, further highlight this adaptability, whereas super-extremophiles, exhibiting resilience in seemingly impossible environments, showcase the extraordinary capacity of life to endure and thrive. Even though they inhabit vastly different environments, extremophiles, polyextremophiles, and super-extremophiles are all Earth organisms. They are made of the same elements found on our planet and share basic biological similarities with other life forms. Their survival in extreme conditions is due to adaptations and changes in their existing cellular structures and metabolic processes, and not because they use entirely new fundamental components or chemical reactions. While extremophiles employ a multitude of factors, mechanisms, and survival strategies to withstand harsh environments, this study addresses a specific aspect of extremophile adaptation by concentrating solely on the functions of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs).

极端微生物是一种不仅适应在恶劣条件下生存，而且在大多数生命形式认为极端或不适合居住的环境中茁壮成长的生物。它们生动地反映了一句流行的格言：“杀不死你的，让你更强大”，并表明地球上的生命远远超出了以人类为中心的舒适区。事实上，在地壳深处和海洋深处、外太空、强酸性和碱性条件、极端温度（+122°C至-20°C）以及存在毒素和高辐射的环境中发现的极端微生物表明，生命具有非凡的适应性。能够忍受多种极端条件的多极端生物进一步突出了这种适应性，而超级极端生物在看似不可能的环境中表现出弹性，展示了生命生存和繁衍的非凡能力。尽管它们生活在截然不同的环境中，但极端微生物、多极端微生物和超级极端微生物都是地球上的生物。它们由地球上发现的相同元素组成，与其他生命形式有着基本的生物相似性。它们在极端条件下的生存是由于它们现有的细胞结构和代谢过程的适应和变化，而不是因为它们使用了全新的基本成分或化学反应。虽然极端微生物利用多种因素、机制和生存策略来抵御恶劣环境，但本研究通过仅关注内在无序蛋白（IDPs）和内在无序区域（IDRs）的功能，解决了极端微生物适应的一个特定方面。

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引用次数: 0

From Extreme Environments in Nature to Molecular and Cellular Adaptation and Functional Regulation 从自然界的极端环境到分子和细胞的适应和功能调节。

IF 4.5 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Biology

Pub Date : 2026-02-15 Epub Date: 2026-01-12 DOI: 10.1016/j.jmb.2026.169639

Igor N. Berezovsky , Ruth Nussinov

引用次数: 0

Integrating Sequence, Structure, and Graph-based Features for Elucidating the Stability of Thermophilic Proteins 整合序列、结构和基于图的特征来阐明嗜热蛋白的稳定性。

IF 4.5 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Biology

Pub Date : 2026-02-15 Epub Date: 2025-12-12 DOI: 10.1016/j.jmb.2025.169593

P. Ramakrishna Reddy, Fathima Ridha, M. Michael Gromiha

Proteins from thermophilic organisms exhibit remarkable stability under extreme thermal conditions. Understanding the molecular mechanisms underlying thermostability is essential for studying protein evolution and engineering robust enzymes. In this study, we systematically analyzed four sets of mesophilic–thermophilic protein pairs to investigate the molecular basis of thermal adaptation. We have constructed independent datasets of mesophilic–thermophilic protein pairs defined by sequence identity and optimal growth temperature (OGT): (a) >90% identity and 60–80 °C OGT, (b) 50–90% identity and >80 °C OGT, (c) 50–90% identity and 60–80 °C OGT, and (d) 50–90% identity and 40–60 °C OGT. Mutational analysis revealed that thermophilic proteins consistently reduced polar, uncharged residues while enriching charged, hydrophobic, and aromatic residues, particularly in extreme thermophiles (>80 °C). Further, by integrating multiple known protein features into a hierarchical rule-based classifier, we identified the thermostable protein from a pair of sequences and also assessed the relative importance of features across datasets to provide interpretable insights into protein thermostability. The hierarchical rule-based method identified stabilizing residues as the primary distinguishing factor, followed by electrostatic energy, volume, and localized electrical effects, which correctly classified 99% of thermophilic proteins. A bagging model trained on the same features achieved a balanced accuracy of 92% in 5-fold cross-validation and 91% on the 20% hold-out test set. Furthermore, independent validation using multiple mutations in proteins accurately identified 94% of stabilizing and destabilizing mutations. The results obtained in this work provide valuable insights to understand the thermal adaptation of proteins and reliably identify thermostable proteins.

来自嗜热生物的蛋白质在极端热条件下表现出显著的稳定性。了解热稳定性的分子机制对于研究蛋白质进化和构建健壮酶至关重要。在这项研究中，我们系统地分析了四组中温-嗜热蛋白对，以探讨热适应的分子基础。我们构建了由序列一致性和最佳生长温度（OGT）定义的中温-嗜热蛋白对的独立数据集：(a) >90%一致性和60-80°C OGT， (b) 50-90%一致性和>80°C OGT, (C) 50-90%一致性和60-80°C OGT， (d) 50-90%一致性和40-60°C OGT。突变分析显示，在极端嗜热菌（bb0 ~ 80°C）中，嗜热蛋白持续减少极性、不带电的残基，同时富集带电、疏水和芳香残基。此外，通过将多个已知的蛋白质特征整合到基于分层规则的分类器中，我们从一对序列中确定了热稳定性蛋白质，并评估了数据集中特征的相对重要性，以提供对蛋白质热稳定性的可解释性见解。基于分层规则的方法将稳定残基作为主要区分因素，其次是静电能、体积和局部电效应，正确分类了99%的嗜热蛋白。在相同特征上训练的装袋模型在5倍交叉验证中实现了92%的平衡精度，在20%的保留测试集上实现了91%的平衡精度。此外，使用蛋白质中多个突变的独立验证准确地识别了94%的稳定和不稳定突变。本研究结果为了解蛋白质的热适应性和可靠地鉴定热稳定性蛋白质提供了有价值的见解。

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引用次数: 0

On the Molecular Basis of the Hypersaline Adaptation of Halophilic Proteins 嗜盐蛋白适应高盐环境的分子基础。

IF 4.5 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Biology

Pub Date : 2026-02-15 Epub Date: 2025-09-13 DOI: 10.1016/j.jmb.2025.169439

Gabriel Ortega-Quintanilla , Oscar Millet

Halophilic organisms have adapted to survive in environments with extremely high salinity, such as saline lakes. To achieve this, they modify their proteome to withstand salt concentrations that inactivate non-adapted mesophilic proteins. The surfaces of halophilic proteins feature a very characteristic amino acid composition, favoring short, polar, and acidic amino acids—such as aspartate, glutamate, and threonine—while disfavoring bulky, hydrophobic amino acids—such as lysine, methionine, and leucine. In this work, we review our understanding of the molecular basis of haloadaptation. We critically examine the role of electrostatic interactions in stabilizing halophilic proteins, while underlining the importance of other contributions from hydrophobic solvation and preferential ion exclusion. Finally, we describe the mechanistic link by which the halophilic amino acid composition optimizes function in hypersaline environments, balancing the trade-off between stability, solubility, and catalytic function.

嗜盐生物已经适应了在极高盐度的环境中生存，比如盐湖。为了实现这一目标，它们修改了蛋白质组，以承受盐浓度，使非适应性中温性蛋白质失活。嗜盐蛋白的表面具有非常特殊的氨基酸组成，有利于短的、极性的和酸性的氨基酸，如天冬氨酸、谷氨酸和苏氨酸，而不利于大的、疏水的氨基酸，如赖氨酸、蛋氨酸和亮氨酸。在这项工作中，我们回顾了我们对光适应的分子基础的理解。我们批判性地研究了静电相互作用在稳定亲盐蛋白中的作用，同时强调了疏水溶剂化和优先离子排斥的其他贡献的重要性。最后，我们描述了嗜盐氨基酸组成在高盐环境中优化功能的机制联系，平衡了稳定性、溶解度和催化功能之间的权衡。

引用次数: 0

PERCEPTRON-PTMKB: A Web Server for Residue-Based Post-Translational Modification Analysis and Propensity Scoring. PERCEPTRON-PTMKB：基于残基的翻译后修饰分析和倾向评分的Web服务器。

IF 4.5 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Biology

Pub Date : 2026-02-12 DOI: 10.1016/j.jmb.2026.169709

Abdullah Bin Faiz, Muhammad Shoaib, Safee Ullah Chaudary

The identification of post-translational modifications (PTMs) of protein residues is vital for understanding protein functions and their subsequent role in cellular processes. Researchers have collected substantial experimental data on PTMs along with their validation and assortment into online databases. However, these databases do not offer integration with protein search and identification tools which then prevent researchers from seamlessly employing them in deciphering PTMs in biological samples. Additionally, there is a lack of tools that evaluate protein residues in light of their neighborhoods for the variety of PTMs found in PTM databases. Here, we propose PERCEPTRON-PTMKB, a web server designed for the analysis and evaluation of PTM sites using empirical datasets. PERCEPTRON-PTMKB provides a quantitative evaluation of per-residue PTM site through its propensity scoring algorithm. The search and propensity calculation pipelines are also served via a secure RESTful API, which enables their seamless integration into protein sequence search engines. PERCEPTRON-PTMKB is available freely at https://perceptronptmkb.lums.edu.pk.

鉴定蛋白质残基的翻译后修饰（PTMs）对于理解蛋白质的功能及其在细胞过程中的后续作用至关重要。研究人员已经收集了大量关于ptm的实验数据，并将其验证和分类到在线数据库中。然而，这些数据库不提供与蛋白质搜索和鉴定工具的集成，从而阻止研究人员无缝地使用它们来破译生物样品中的PTMs。此外，缺乏根据PTM数据库中发现的各种PTM的邻域来评估蛋白质残基的工具。在这里，我们提出了PERCEPTRON-PTMKB，这是一个用于使用经验数据集分析和评估PTM站点的web服务器。PERCEPTRON-PTMKB通过其倾向评分算法提供了每残基PTM位点的定量评估。搜索和倾向计算管道也通过安全的RESTful API提供服务，这使得它们能够无缝集成到蛋白质序列搜索引擎中。PERCEPTRON-PTMKB可在https://perceptronptmkb.lums.edu.pk免费获得。

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引用次数: 0