Proteins[JOURNAL]
Sun
200 papers
SARS-CoV-2 Mpro Dihedral Angles Reveal Allosteric Signaling.
Evans D, Sheraz S, Lau AY
Proteins · 2025 Jul · PMID 40026279 · Full text
In allosteric proteins, identifying the pathways that signals take from allosteric ligand-binding sites to enzyme active sites or binding pockets and interfaces remains challenging. This avenue of research is motivated b...
In allosteric proteins, identifying the pathways that signals take from allosteric ligand-binding sites to enzyme active sites or binding pockets and interfaces remains challenging. This avenue of research is motivated by the goals of understanding particular macromolecular systems of interest and creating general methods for their study. An especially important protein that is the subject of many investigations in allostery is the SARS-CoV-2 main protease (Mpro), which is necessary for coronaviral replication. It is both an attractive drug target and, due to intense interest in it for the development of pharmaceutical compounds, a gauge of the state of the art approaches in studying protein inhibition. Here we develop a computational method for characterizing protein allostery and use it to study Mpro. We propose a role of the protein's C-terminal tail in allosteric modulation and warn of unintuitive traps that can plague studies of the role of protein dihedral angles in transmitting allosteric signals.
Structural Implications of HIV-1 Protease Subtype C Bound to Darunavir: A Molecular Dynamics Study.
Venkatachalam S, Krishnan SR, Pandian R … +2 more , Sayed Y, Gromiha MM
Proteins · 2025 Sep · PMID 40026243 · Publisher ↗
In recent years, Human Immunodeficiency Virus (HIV) remains a significant global health challenge, with millions affected worldwide, particularly in Africa and sub-Saharan regions. Despite advances in antiretroviral ther...
In recent years, Human Immunodeficiency Virus (HIV) remains a significant global health challenge, with millions affected worldwide, particularly in Africa and sub-Saharan regions. Despite advances in antiretroviral therapies, the genetic variability of HIV, including different subtypes and drug-resistant strains, poses persistent obstacles in the development of universally effective treatments. This study focuses on the dynamics of HIV protease, a key enzyme in viral replication and maturation, particularly targeting subtype C and its double insertion (HL) variant L38HL, in the context of interaction with Darunavir (DRV), a second-generation nonpeptidic protease inhibitor approved by the FDA in 2006. Through molecular dynamics simulations, structural analyses, dynamic cross-correlation analyses, and binding energy calculations, we investigated differences in the binding of DRV to WT and L38HL HIV-1 protease. The findings highlight that the double insertion at the hinge induces variation in Φ and Ψ angles, leading to increased residue fluctuations, solvent-accessible surface area (SASA), and radius of gyration (R). This alters the overall structural compactness and the hydrophobic core crucial for drug binding. Subtle structural changes result in the loss of hydrogen bond interactions, reducing the binding energy of L38HL HIV-1 protease subtype C bound to DRV, leading to drug resistance.
Skittles: GNN-Assisted Pseudo-Ligands Generation and Its Application for Binding Sites Classification and Affinity Prediction.
Evteev S, Ereshchenko A, Adjugim D … +5 more , Vyacheslavov A, Pastukhova A, Malyshev A, Terentiev V, Ivanenkov Y
Proteins · 2025 Jul · PMID 40017403 · Publisher ↗
Nowadays, multiple solutions are known for identifying ligand-protein binding sites. Another important task is labeling each point of a binding site with the appropriate atom type, a process known as pseudo-ligand genera...
Nowadays, multiple solutions are known for identifying ligand-protein binding sites. Another important task is labeling each point of a binding site with the appropriate atom type, a process known as pseudo-ligand generation. The number of solutions for pseudo-ligand generation is limited, and, to our knowledge, the influence of machine learning techniques has not been studied previously. Here, we describe Skittles, a new graph neural network-assisted pseudo-ligand generation approach, and compare it with known force-field-based methods. We also demonstrate the application of Skittles-based data for solving several important problems in structural biology, including ligand-protein binding site classification and ligand-protein affinity prediction.
Evaluation of the Ability of Wasp Venom Bioinspired Peptides (Fraternine-10 and Octovespin) in the Disaggregation and Anti-Aggregation of Amyloid-β Fibrils.
de Oliveira Só YA, Costa CVS, Camargo LC … +4 more , Veras LG, Júnior LAR, Mortari MR, Gargano R
Proteins · 2025 Jul · PMID 39989313 · Publisher ↗
Many neurodegenerative diseases are directly related to the formation of toxic protein aggregates, such as Alzheimer's disease, which is associated with the aggregation of amyloid-beta (Aβ). In this context, protein fibr...
Many neurodegenerative diseases are directly related to the formation of toxic protein aggregates, such as Alzheimer's disease, which is associated with the aggregation of amyloid-beta (Aβ). In this context, protein fibrils are the hallmark of these neurodegenerative diseases. In this sense, developing compounds capable of preventing or reducing the formation of protein aggregation in the brain can be of fundamental importance for the curative treatment of these diseases. Animals' venom compounds are known to be selected for nervous system targets, therefore, they are considered an interesting platform for developing pharmacological tools. This work presents a study of the ligands Octovespin (bioinspired by the wasp venom Polybia occidentalis) and Fraternine-10 (bioinspired by the wasp venom Parachartergus fraternus) concerning the disaggregation and anti-aggregation of fibrils of Aβ(17-42) sheets. First, we performed in silico calculations using molecular docking and molecular dynamics simulations with 200 ns. The results indicate that Octovespin and Fraternine-10 interact with the Aβ protein fibrils throughout all simulation time. The RMSD, RMSF, number of hydrogen and radius of gyration values and the interactions with amino acids responsible for fibril aggregation demonstrate that both Octovespin and Fraternine-10 have a significant disaggregation potential, which corroborates the in vitro and in vivo experimental observations. Furthermore, experimental data of Fraternine-10 demonstrated an anti-aggregation effect, indicating that it can promote fibril disaggregation and prevent them from aggregating again to form oligomers. However, in vivo data of Fraternine-10 did not show improvement. Even though in vivo results were not promising, the in vitro and in silico discoveries qualify these molecules as potential sources for developing new candidates to become medicines against Alzheimer's disease.
Enhancing Functional Protein Design Using Heuristic Optimization and Deep Learning for Anti-Inflammatory and Gene Therapy Applications.
Patat AS, Nalbantoğlu ÖU
Proteins · 2025 Jul · PMID 39985803 · Full text
Protein sequence design is a highly challenging task, aimed at discovering new proteins that are more functional and producible under laboratory conditions than their natural counterparts. Deep learning-based approaches...
Protein sequence design is a highly challenging task, aimed at discovering new proteins that are more functional and producible under laboratory conditions than their natural counterparts. Deep learning-based approaches developed to address this problem have achieved significant success. However, these approaches often do not adequately emphasize the functional properties of proteins. In this study, we developed a heuristic optimization method to enhance key functionalities such as solubility, flexibility, and stability, while preserving the structural integrity of proteins. This method aims to reduce laboratory demands by enabling a design that is both functional and structurally sound. This approach is particularly valuable for the synthetic production of proteins with anti-inflammatory properties and those used in gene therapy. The designed proteins were initially evaluated for their ability to preserve natural structures using recovery and confidence metrics, followed by assessments with the AlphaFold tool. Additionally, natural protein sequences were mutated using a genetic algorithm and compared with those designed by our method. The results demonstrate that the protein sequences generated by our method exhibit much greater similarity to native protein sequences and structures. The code and sequences for the designed proteins are available at https://github.com/aysenursoyturk/HMHO.
Double the Double: Revisiting BCL11B's Multimerization.
Susemihl A, Geist N, Grabarczyk P … +3 more , Schmidt CA, Delcea M, Schulig L
Proteins · 2025 Jul · PMID 39976228 · Full text
The transcription factor B Cell Lymphoma/Leukemia 11B (BCL11B) exerts a bi-directional function in cancer, with its role as an emerging therapeutic target in cancer treatment being particularly intriguing. BCL11B knockou...
The transcription factor B Cell Lymphoma/Leukemia 11B (BCL11B) exerts a bi-directional function in cancer, with its role as an emerging therapeutic target in cancer treatment being particularly intriguing. BCL11B knockouts in cultured T cells revealed the acquisition of properties characteristic of natural killer cells, hinting at its importance in innate versus adaptive immune regulation. Our previous studies using Förster Resonance Energy Transfer-assisted Fluorescence-Activated Cell Sorting and Hybrid Solvent Replica-Exchange Simulations indicated that BCL11B forms dimers, with this being a prerequisite for its activity. However, size exclusion chromatography and crosslinking experiments have challenged this view, suggesting that BCL11B forms tetramers instead. An atypical CCHC zinc finger motif within the N-terminal region of the protein mediates multimerization and a novel 3D structure is presented based on extensive replica-exchange simulations in strong agreement with experimental data. The physiological relevance of multimer formation of this zinc finger protein has been demonstrated previously. Therefore, understanding the nature of BCL11B's multimerization could potentially enhance our ability to target this protein effectively, hopefully paving the way for novel BCL11B-targeted therapies.
Cloning, Characterization, and Computer-Aided Evolution of a Thermostable Laccase of the DUF152 Family From Klebsiella michiganensis.
Cui T, Brückner K, Schilling S … +1 more , Mägert HJ
Proteins · 2025 Jul · PMID 39950717 · Full text
Bacterial laccases exhibit relatively high optimal reaction temperatures and possess a broad substrate spectrum, thereby expanding the range of potential applications for laccase enzymes. This study aims to investigate t...
Bacterial laccases exhibit relatively high optimal reaction temperatures and possess a broad substrate spectrum, thereby expanding the range of potential applications for laccase enzymes. This study aims to investigate the molecular evolution of bacterial laccases using computational 3D-structure prediction and molecular docking tools such as AlphaFold2, Metal3D, AutoDockVina, and Rosetta. We isolated a bacterium with laccase activities from fecal samples from a Hermann's tortoise (Testudo hermanni), identified it as Klebsiella michiganensis using 16S rRNA sequencing and nanopore genome sequencing, and then identified a sequence encoding a laccase with a predicted molecular weight of approximately 27.5 kDa. Expression of the corresponding, chemically synthesized DNA fragment resulted in the isolation of an active laccase. The enzyme showed considerable thermostability, retaining 21% of its activity after boiling for 30 min. Using state-of-the-art information technology and machine learning techniques, we conducted 3D-structure prediction on this sequence, predicted its copper-ion binding sites, and validated these predictions through site-directed mutagenesis and expression. Subsequently, we performed computer-aided evolution studies on this sequence and found that 90% of the results from the selected mutations exhibited improved performance. In summary, this study not only revealed a novel laccase but also demonstrated an efficient approach for advancing research on the molecular evolution of bacterial laccases using cutting-edge machine learning, next-generation sequencing, traditional bioinformatics approaches, and laboratory techniques, providing an effective strategy for discovering and design new bacterial laccases.
Simpler Protein Domain Identification Using Spectral Clustering.
Cazals F, Herrmann J, Sarti E
Proteins · 2025 Jul · PMID 39945423 · Publisher ↗
The decomposition of a biomolecular complex into domains is an important step to investigate biological functions and ease structure determination. A successful approach to do so is the SPECTRUS algorithm, which provides...
The decomposition of a biomolecular complex into domains is an important step to investigate biological functions and ease structure determination. A successful approach to do so is the SPECTRUS algorithm, which provides a segmentation based on spectral clustering applied to a graph coding inter-atomic fluctuations derived from an elastic network model. We present SPECTRALDOM, which makes three straightforward and useful additions to SPECTRUS. For single structures, we show that high quality partitionings can be obtained from a graph Laplacian derived from pairwise interactions-without normal modes. For sets of homologous structures, we introduce a Multiple Sequence Alignment mode, exploiting both the sequence based information (MSA) and the geometric information embodied in experimental structures. Finally, we propose to analyze the clusters/domains delivered using the so-called -family-matching algorithm, which establishes a correspondence between domains yielded by two decompositions, and can be used to handle fragmentation issues. Our domains compare favorably to those of the original SPECTRUS, and those of the deep learning based method Chainsaw. Using two complex cases, we show in particular that SPECTRALDOM is the only method handling complex conformational changes involving several sub-domains. Finally, a comparison of SPECTRALDOM and Chainsaw on the manually curated domain classification ECOD as a reference shows that high quality domains are obtained without using any evolutionary related piece of information. SPECTRALDOM is provided in the Structural Bioinformatics Library, see http://sbl.inria.fr and https://sbl.inria.fr/doc/Spectral_domain_explorer-user-manual.html.
Structural Insight Into the SKP1-CUL1-FBXO3-RBX1 Complex.
Wei J, Xu C
Proteins · 2025 Jul · PMID 39921442 · Publisher ↗
The cryo-EM structure of human SCF, which consists of CUL1, RBX1, SKP1 and FBXO3 was solved at a nominal resolution of 3.70 Å. Although a previous study reported the crystal structure of the FBXO3 ApaG domain, how FBXO3...
The cryo-EM structure of human SCF, which consists of CUL1, RBX1, SKP1 and FBXO3 was solved at a nominal resolution of 3.70 Å. Although a previous study reported the crystal structure of the FBXO3 ApaG domain, how FBXO3 is incorporated into the SCF complex remains elusive. In the cryo-EM structure of SCF, the F-box domain of FBXO3 primarily associates with SKP1 via extensive hydrophobic interactions and interacts with the N-terminal region of CUL1 via hydrophobic interactions. The weak cryo-EM map of the RBX1 globular region is close to the FBXO3 ApaG domain, suggesting that unmodified SCF exhibits a closed conformation and that CUL1 neddylation is likely required to achieve high E3 activity. The structural study provides insight into the assembly of SCF and its activation mediated by CUL1 neddylation.
Performance of Hybrid Strategies Combining MDockPP and AlphaFold2 in CAPRI Rounds 47-55.
Duan R, Xu X, Qiu L … +2 more , Zhang S, Zou X
Proteins · 2025 Feb · PMID 39902622 · Full text
CAPRI challenges offer a range of blind tests for biomolecule interaction prediction. This study evaluates the performance of our prediction protocols for the human group Zou and the server group MDockPP in CAPRI rounds...
CAPRI challenges offer a range of blind tests for biomolecule interaction prediction. This study evaluates the performance of our prediction protocols for the human group Zou and the server group MDockPP in CAPRI rounds 47-55, highlighting the impact of AlphaFold2 (AF2) and the effectiveness of massive sampling approaches. Prior to AlphaFold2's release, our methods relied on homology modeling and docking-based protocols, achieving limited accuracy due to constraints in structural templates and inherent docking limitations. After AlphaFold2's public release, which demonstrated breakthrough accuracy in protein structure prediction, we integrated its multimer models and massive sampling techniques into our protocols. This integration significantly improved prediction accuracy, with human predictions increasing from 1 correct interface of 19 pre-AlphaFold2 to 4 of 8 post-AlphaFold2. The massive sampling approach further enhanced performance, particularly for targets T231 and T233, yielding medium-quality models that default parameters could not achieve.
Correction to Rigidifying Flexible Sites: A Promising Strategy to Improve Thermostability of Lysophospholipase From Pyrococcus abyssi.
Proteins · 2025 Jul · PMID 39888703 · Publisher ↗
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Massive Sampling Strategy for Antibody-Antigen Targets in CAPRI Round 55 With MassiveFold.
Raouraoua N, Lensink MF, Brysbaert G
Proteins · 2025 Jan · PMID 39868877 · Publisher ↗
Massive sampling with AlphaFold2 improves protein-protein complex predictions. This has been shown during the last CASP15-CAPRI blind prediction round by the AFsample tool. However, more difficult targets including antib...
Massive sampling with AlphaFold2 improves protein-protein complex predictions. This has been shown during the last CASP15-CAPRI blind prediction round by the AFsample tool. However, more difficult targets including antibody-antigen binding remain challenging. CAPRI Round 55 consisted of three antibody-antigen targets and one heterotrimer. We used our AlphaFold2-based MassiveFold, running 6 prediction pools, each with their own set of parameters, to produce in total more than 6000 predictions per target. We show here that massive sampling categorically produces acceptable to high quality predictions, however it is clear that the AlphaFold2 confidence score cannot be used to identify the best models in the set. We also show that, contrary to what was done before for CASP15-CAPRI with AFsample, increasing the sampling without activating the dropout provides the best models for most of the targets of Round 55.
The Pseudoenzyme β-Amylase9 From Arabidopsis Activates α-Amylase3: A Possible Mechanism to Promote Stress-Induced Starch Degradation.
Berndsen CE, Storm AR, Sardelli AM … +5 more , Hossain SR, Clermont KR, McFather LM, Connor MA, Monroe JD
Proteins · 2025 Jun · PMID 39846389 · Full text
Starch accumulation in plants provides carbon for nighttime use, for regrowth after periods of dormancy, and for times of stress. Both ɑ- and β-amylases (AMYs and BAMs, respectively) catalyze starch hydrolysis, but their...
Starch accumulation in plants provides carbon for nighttime use, for regrowth after periods of dormancy, and for times of stress. Both ɑ- and β-amylases (AMYs and BAMs, respectively) catalyze starch hydrolysis, but their functional roles are unclear. Moreover, the presence of catalytically inactive amylases that show starch excess phenotypes when deleted presents questions on how starch degradation is regulated. Plants lacking one of these catalytically inactive β-amylases, BAM9, have enhanced starch accumulation when combined with mutations in BAM1 and BAM3, the primary starch degrading BAMs in response to stress and at night, respectively. BAM9 has been reported to be transcriptionally induced by stress although the mechanism for BAM9 function is unclear. From yeast two-hybrid experiments, we identified the plastid-localized AMY3 as a potential interaction partner for BAM9. We found that BAM9 interacted with AMY3 in vitro and that BAM9 enhances AMY3 activity about three-fold. Modeling of the AMY3-BAM9 complex predicted a previously undescribed alpha-alpha hairpin in AMY3 that could serve as a potential interaction site. Additionally, AMY3 lacking the alpha-alpha hairpin is unaffected by BAM9. Structural analysis of AMY3 showed that it can form a homodimer in solution and that BAM9 appears to replace one of the AMY3 monomers to form a heterodimer. The presence of both BAM9 and AMY3 in many vascular plant lineages, along with model-based evidence that they heterodimerize, suggests that the interaction is conserved. Collectively these data suggest that BAM9 is a pseudoamylase that activates AMY3 in response to cellular stress, possibly facilitating stress recovery.
Structure, Oligomerization, and Thermal Stability of a Recently Discovered Old Yellow Enzyme.
Polidori N, Babin P, Daniel B … +1 more , Gruber K
Proteins · 2025 Jun · PMID 39840754 · Full text
The Old Yellow Enzyme from Ferrovum sp. JA12 (FOYE) displays an unusual thermal stability for an enzyme isolated from a mesophilic organism. We determined the crystal structure of this enzyme and performed bioinformatic...
The Old Yellow Enzyme from Ferrovum sp. JA12 (FOYE) displays an unusual thermal stability for an enzyme isolated from a mesophilic organism. We determined the crystal structure of this enzyme and performed bioinformatic characterization to get insights into its thermal stability. The enzyme displays a tetrameric quaternary structure; however, unlike the other tetrameric homologs, it clusters in a separate phylogenetic group and possesses unique interactions that stabilize this oligomeric state. The thermal stability of this enzyme is mainly due to an unusually high number of intramolecular hydrogen bonds. Finally, this study provides a general analysis of the forces driving the oligomerization in Old Yellow Enzymes.
DisDock: A Deep Learning Method for Metal Ion-Protein Redocking.
Lin M, Li K, Zhang Y … +3 more , Pan F, Wu W, Zhang J
Proteins · 2025 Jun · PMID 39838957 · Publisher ↗
The structures of metalloproteins are essential for comprehending their functions and interactions. The breakthrough of AlphaFold has made it possible to predict protein structures with experimental accuracy. However, th...
The structures of metalloproteins are essential for comprehending their functions and interactions. The breakthrough of AlphaFold has made it possible to predict protein structures with experimental accuracy. However, the type of metal ion that a metalloprotein binds and the binding structure are still not readily available, even with the predicted protein structure. In this study, we present DisDock, a deep learning method for predicting protein-metal docking. DisDock takes distogram of randomly initialized protein-ligand configuration as input and outputs the distogram of the predicted binding complex. It combines the U-net architecture with self-attention modules to enhance model performance. Taking inspiration from the physical principle that atoms in closer proximity display a stronger mutual attraction, this predictor capitalizes on geometric information to uncover latent characteristics indicative of atom interactions. To train our model, we employ a high-quality metalloprotein dataset sourced from the Mother of All Databases (MOAD). Experimental results demonstrate that our approach outperforms other existing methods in prediction accuracy for various types of metal ions.
AlphaFold and Docking Approaches for Antibody-Antigen and Other Targets: Insights From CAPRI Rounds 47-55.
Gowthaman R, Park M, Yin R … +2 more , Guest JD, Pierce BG
Proteins · 2025 Jan · PMID 39831331 · Full text
Accurate modeling of the structures of protein-protein complexes and other biomolecular interactions represents a longstanding and important challenge for computational biology. The Critical Assessment of PRedicted Inter...
Accurate modeling of the structures of protein-protein complexes and other biomolecular interactions represents a longstanding and important challenge for computational biology. The Critical Assessment of PRedicted Interactions (CAPRI) experiment has served for over two decades as a key means to assess and compare current approaches and methods through blind predictive scenarios, highlighting useful strategies, and new developments. Here we describe the performance of our laboratory's team in recent CAPRI rounds, which included submissions for 10 modeling targets. Our team utilized a range of docking and modeling approaches, including ZDOCK, Rosetta, and ZRANK, to model, refine, and score protein-protein and protein-DNA complexes. For recent targets we utilized adaptations of AlphaFold to generate models, leading to near-native models for an antibody-peptide target, and a highly accurate (but low ranked) model for an antibody-MHC complex. These results underscore the utility of AlphaFold-based protocols for predictive protein complex modeling, including for immune recognition, and highlight considerations regarding the use of AlphaFold confidence metrics in model selection.
Unraveling the Molecular Architecture of Mosquito D1-Like Dopamine Receptors: Insights Into Ligand Binding and Structural Dynamics for Insecticide Development.
Dasgupta S, Bhaumik P
Proteins · 2025 Jun · PMID 39825718 · Publisher ↗
Vector-borne diseases pose a severe threat to human life, contributing significantly to global mortality. Understanding the structure-function relationship of the vector proteins is pivotal for effective insecticide deve...
Vector-borne diseases pose a severe threat to human life, contributing significantly to global mortality. Understanding the structure-function relationship of the vector proteins is pivotal for effective insecticide development due to their involvement in drug resistance and disease transmission. This study reports the structural and dynamic features of D1-like dopamine receptors (DARs) in disease-causing mosquito species, such as Aedes aegypti , Culex quinquefasciatus , Anopheles gambiae , and Anopheles stephensi. Through molecular modeling and simulations, we describe the common structural fold of mosquito DARs within the G-protein-coupled receptor family, highlighting the importance of an orthosteric and enlarged binding pocket. The orthosteric binding pocket, resembling a cage-like structure, is situated ~15 Å deep within the protein, with two serine residues forming the roof and an aspartate residue, along with two conserved water molecules (W1 and W2), forming the floor. The side walls are composed of two phenylalanine residues on one side and a valine residue on the other. The antagonist binding site, an enlarged binding pocket (EBP) near the entrance cavity, can accommodate ligands of varying sizes. The binding energy of dopamine is observed to be ~2-3 kcal/mol higher than that of the antagonist molecules amitriptyline, asenapine, and flupenthixol in mosquito DARs. These antagonist molecules bind to EBP, which obstructs dopamine movement toward the active site, thereby inhibiting signal transduction. Our findings elucidate the molecular architecture of the binding pockets and the versatility of DARs in accommodating diverse ligands, providing a foundational framework for future drug and insecticide development.
Sucrose and Gibberellic Acid Binding Stabilize the Inward-Open Conformation of AtSWEET13: A Molecular Dynamics Study.
Palmai Z
Proteins · 2025 Jun · PMID 39815685 · Publisher ↗
In plants, sugar will eventually be exported transporters (SWEETs) facilitate the translocation of mono- and disaccharides across membranes and play a critical role in modulating responses to gibberellin (GA3), a key gro...
In plants, sugar will eventually be exported transporters (SWEETs) facilitate the translocation of mono- and disaccharides across membranes and play a critical role in modulating responses to gibberellin (GA3), a key growth hormone. However, the dynamic mechanisms underlying sucrose and GA3 binding and transport remain elusive. Here, we employed microsecond-scale molecular dynamics (MD) simulations to investigate the influence of sucrose and GA3 binding on SWEET13 transporter motions. While sucrose exhibits high flexibility within the binding pocket, GA3 remains firmly anchored in the central cavity. Binding of both ligands increases the average channel radius along the transporter's principal axis. In contrast to the apo form, which retains its initial conformation throughout the simulation, ligand-bound complexes undergo a significant conformational transition characterized by further opening of the intracellular gate relative to the inward-open crystal structure (5XPD). This opening is driven by ligand-induced bending of helix V, stabilizing the inward-open state. Sucrose binding notably enhances the flexibility of the intracellular gate and amplifies anticorrelated motions between the N- and C-terminal domains at the intracellular side, suggesting an opening-closing motion of these domains. Principal component analysis revealed that this gating motion is most pronounced in the sucrose complex and minimal in the apo form, highlighting sucrose's ability to induce high-amplitude gating. Our binding free energy calculations indicate that SWEET13 has lower binding affinity for sucrose compared to GA3, consistent with its role in sugar transport. These results provide insight into key residues involved in sucrose and GA3 binding and transport, advancing our understanding of SWEET13 dynamics.
High-Throughput Evaluation of Natural Diversity of F-Type ATP Synthase Rotor Ring Stoichiometries.
Osipov SD, Zinovev EV, Anuchina AA … +5 more , Kuzmin AS, Minaeva AV, Ryzhykau YL, Vlasov AV, Gushchin IY
Proteins · 2025 Jun · PMID 39810702 · Publisher ↗
Adenosine triphosphate (ATP) synthases are large enzymes present in every living cell. They consist of a transmembrane and a soluble domain, each comprising multiple subunits. The transmembrane part contains an oligomeri...
Adenosine triphosphate (ATP) synthases are large enzymes present in every living cell. They consist of a transmembrane and a soluble domain, each comprising multiple subunits. The transmembrane part contains an oligomeric rotor ring (c-ring), whose stoichiometry defines the ratio between the number of synthesized ATP molecules and the number of ions transported through the membrane. Currently, c-rings of F-Type ATP synthases consisting of 8-17 (except 16) subunits have been experimentally demonstrated, but it is not known whether other stoichiometries are present in natural organisms. Here, we present an easy-to-use high-throughput computational approach based on AlphaFold that allows us to estimate the stoichiometry of all homo-oligomeric c-rings, whose sequences are present in genomic databases. We validate the approach on the available experimental data, obtaining the correlation as high as 0.94 for the reference dataset and use it to predict the existence of c-rings with stoichiometry varying at least from 8 to 27. We then conduct molecular dynamics simulations of two c-rings with stoichiometry above 17 to corroborate the machine learning-based predictions. Our work strongly suggests existence of rotor rings with previously undescribed high stoichiometry in natural organisms and highlights the utility of AlphaFold-based approaches for studying homo-oligomeric proteins.
Exploring the Conformational Space of MPS1 Kinase Using Metadynamics.
Singh A, Lakkaniga NR
Proteins · 2025 Jun · PMID 39786318 · Publisher ↗
MPS1 kinase is a dual specificity kinase that plays an important role in the spindle assembly checkpoint mechanism during cell division. Overexpression of MPS1 kinase is reported in several cancers. However, drug discove...
MPS1 kinase is a dual specificity kinase that plays an important role in the spindle assembly checkpoint mechanism during cell division. Overexpression of MPS1 kinase is reported in several cancers. However, drug discovery and development efforts targeting MPS1 kinase did not result in any clinically successful candidates. All the reported crystal structures of MPS1 kinase adopt the DFG "in" conformation. Knowledge of the other conformations of the kinase would be beneficial in the structure-based drug design of novel inhibitors. This work employs well-tempered metadynamics simulations to explore the conformational space of MPS1 kinase by using its experimentally determined DFG "in" conformation as the starting structure. The simulation could successfully predict the DFG "out" conformation and identify the possible transition states. The key interactions that stabilize the kinase in various conformations were identified, and the effect of phosphorylation of the key residues on the conformation of the kinase was determined.
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