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Proceedings of the National Academy of... May 2024Protein-protein and protein-water hydrogen bonding interactions play essential roles in the way a protein passes through the transition state during folding or...
Protein-protein and protein-water hydrogen bonding interactions play essential roles in the way a protein passes through the transition state during folding or unfolding, but the large number of these interactions in molecular dynamics (MD) simulations makes them difficult to analyze. Here, we introduce a state space representation and associated "rarity" measure to identify and quantify transition state passage (transit) events. Applying this representation to a long MD simulation trajectory that captured multiple folding and unfolding events of the GTT WW domain, a small protein often used as a model for the folding process, we identified three transition categories: Highway (faster), Meander (slower), and Ambiguous (intermediate). We developed data sonification and visualization tools to analyze hydrogen bond dynamics before, during, and after these transition events. By means of these tools, we were able to identify characteristic hydrogen bonding patterns associated with "Highway" versus "Meander" versus "Ambiguous" transitions and to design algorithms that can identify these same folding pathways and critical protein-water interactions directly from the data. Highly cooperative hydrogen bonding can either slow down or speed up transit. Furthermore, an analysis of protein-water hydrogen bond dynamics at the surface of WW domain shows an increase in hydrogen bond lifetime from folded to unfolded conformations with Ambiguous transitions as an outlier. In summary, hydrogen bond dynamics provide a direct window into the heterogeneity of transits, which can vary widely in duration (by a factor of 10) due to a complex energy landscape.
Topics: Hydrogen Bonding; Protein Folding; Molecular Dynamics Simulation; Proteins; Water; WW Domains; Protein Conformation; Algorithms
PubMed: 38768341
DOI: 10.1073/pnas.2319094121 -
Journal of Molecular Modeling May 2024Ubiquitin-like with PHD and RING finger domain containing protein 1 (UHRF1) is responsible for preserving the stability of genomic methylation through the recruitment of...
CONTEXT
Ubiquitin-like with PHD and RING finger domain containing protein 1 (UHRF1) is responsible for preserving the stability of genomic methylation through the recruitment of DNA methyltransferase 1 (DNMT1). However, the interaction between Developmental pluripotency associated 3 (DPPA3) and the pre-PHD-PHD (PPHD) domain of UHRF1 hinders the nuclear localization of UHRF1. This disruption has implications for potential cancer treatment strategies. Drugs that mimic the binding pattern between DPPA3 and PPHD could offer a promising approach to cancer treatment. Our study reveals that DPPA3 undergoes dissociation from the C-terminal through three different modes of helix unfolding. Furthermore, we have identified key residue pairs involved in this dissociation process and potential drug-targeting residues. These findings offer valuable insights into the dissociation mechanism of DPPA3 from PPHD and have the potential to inform the design of novel drugs targeting UHRF1 for cancer therapy.
METHODS
To comprehend the dissociation process and binding patterns of PPHD-DPPA3, we employed enhanced sampling techniques, including steered molecular dynamics (SMD) and conventional molecular dynamics (cMD). Additionally, we utilized self-organizing maps (SOM) and time-resolved force distribution analysis (TRFDA) methodologies. The Gromacs software was used for performing molecular dynamics simulations, and the AMBER FF14SB force field was applied to the protein.
Topics: Ubiquitin-Protein Ligases; Molecular Dynamics Simulation; CCAAT-Enhancer-Binding Proteins; Protein Binding; Humans; Binding Sites
PubMed: 38767734
DOI: 10.1007/s00894-024-05946-9 -
BioRxiv : the Preprint Server For... May 2024Site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) using nitroxide spin labels is a well-established technology for mapping site-specific secondary...
Site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) using nitroxide spin labels is a well-established technology for mapping site-specific secondary and tertiary structure and for monitoring conformational changes in proteins of any degree of complexity, including membrane proteins, with high sensitivity. SDSL-EPR also provides information on protein dynamics in the time scale of ps-µs using continuous wave lineshape analysis and spin lattice relaxation time methods. However, the functionally important time domain of µs-ms, corresponding to large-scale protein motions, is inaccessible to those methods. To extend SDSL-EPR to the longer time domain, the perturbation method of pressure-jump relaxation is implemented. Here, we describe a complete high-pressure EPR system at Q-band for both static pressure and millisecond-timescale pressure-jump measurements on spin-labeled proteins. The instrument enables pressure jumps both up and down from any holding pressure, ranging from atmospheric pressure to the maximum pressure capacity of the system components (~3500 bar). To demonstrate the utility of the system, we characterize a local folding-unfolding equilibrium of T4 lysozyme. The results illustrate the ability of the system to measure thermodynamic and kinetic parameters of protein conformational exchange on the millisecond timescale.
PubMed: 38766191
DOI: 10.1101/2024.05.07.593074 -
ACS Omega May 2024DNA topoisomerase 2-binding protein 1 (Topbp1) plays a crucial role in activating the ataxia-telangiectasia mutated and rad3-related (ATR) complex to initiate DNA damage...
DNA topoisomerase 2-binding protein 1 (Topbp1) plays a crucial role in activating the ataxia-telangiectasia mutated and rad3-related (ATR) complex to initiate DNA damage repair responses. For this process to occur, it is necessary for PHF8 to dissociate from Topbp1. Topbp1 binds to the acidic patch sequence (APS) of PHF8 through its C-terminal BRCT7/8 domain, and disrupting this interaction could be a promising strategy for cancer treatment. To investigate the dissociation process and binding pattern of BRCT7/8-PHF8, we employed enhanced sampling techniques, such as steered molecular dynamics (SMD) simulations and accelerated molecular dynamics (aMD) simulations, along with self-organizing maps (SOM) and time-resolved force distribution analysis (TRFDA) methodologies. Our results demonstrate that the dissociation of PHF8 from BRCT7/8 starts from the N-terminus, leading to the unfolding of the N-terminal helix. Additionally, we identified critical residues that play a pivotal role in this dissociation process. These findings provide valuable insights into the disassociation of PHF8 from BRCT7/8, which could potentially guide the development of novel drugs targeting Topbp1 for cancer therapy.
PubMed: 38764655
DOI: 10.1021/acsomega.3c09433 -
Free Radical Biology & Medicine May 2024Non-small cell lung cancer (NSCLC), particularly lung adenocarcinoma (LUAD), significantly influences cancer-related mortality and is frequently considered by poor...
Non-small cell lung cancer (NSCLC), particularly lung adenocarcinoma (LUAD), significantly influences cancer-related mortality and is frequently considered by poor therapeutic responses due to genetic alterations. Cancer cells possess an inclination to develop resistance to individual treatment modalities, thus it is necessary to investigate several pathways simultaneously to obtain insights that will aid in the establishment of improved therapeutic approaches. Exploring regulated cell death (RCD) mechanisms offers promising avenues to augment immunotherapy by reshaping the tumor microenvironment (TME). Here, we investigated the prospective of microwave plasma-infused nitric oxide water (NOW) to initiate immunogenic cell death (ICD) while concurrently modulating autophagy and ferroptosis signaling in LUAD-associated A549 cells. Plasma treatment results in stable NO species nitrite/nitrate (NO/NO) in the water, altering its physicochemical properties. Analysis of ICD markers reveals increased expression of damage-associated molecular patterns (DAMPs) at both protein and mRNA levels post-NOW exposure. Intracellular reactive oxygen and nitrogen species (RONS) accumulation suggests NO-mediated mitochondrial dysfunction, triggering autophagy induction. Flow cytometry and western blotting confirm alterations in autophagy regulators Beclin 1 and SQSTM1. Furthermore, NOW treatment induces lipid peroxidation and upregulates ferroptosis-associated genes, as determined by qRT-PCR. Transmission electron microscopy (TEM) imaging reveals autophagosome formation and loss of cristae structures, corroborating the occurrence of autophagy and ferroptosis. Our findings propose that NOW may considered as inducer of ICD and the stimulation of other RCD-related proteins may enhance the anti-tumor immunogenicity.
PubMed: 38763209
DOI: 10.1016/j.freeradbiomed.2024.05.033 -
Journal of Dairy Science May 2024Milk fan cheese, a type of stretched -cheese, presents challenges in its stretch-forming. This study investigated the impacts of complex phosphates (sodium...
Milk fan cheese, a type of stretched -cheese, presents challenges in its stretch-forming. This study investigated the impacts of complex phosphates (sodium tripolyphosphate and sodium dihydrogen phosphate, STPP-DSP) on the gelling properties of acid-induced milk fan gel and the mechanisms contributing to its stretch-forming. The treatment of milk fan gel with STPP-DSP resulted in improved functional and textural properties compared with the control group. In particular, drawing length increased significantly from 69.67 nm to 80.33 nm, and adhesiveness increased from 1737.89 g/mm to 1969.79 g/mm. The addition of STPP-DSP also led to increased viscosity, elastic modulus (G'), and viscous modulus (G"). Microstructural analysis revealed the formation of a fibrous structure within the gel after STPP-DSP treatment, facilitating uniform embedding of fat globules and emulsification. Structural analysis showed that the addition of STPP-DSP increased β-fold and decreased random coiling of the gel, facilitating the unfolding of protein structures. Additionally, UV absorption spectroscopy and excitation-emission matrix spectroscopy results indicated the formation of a chelate between STPP-DSP and milk fan gel, increasing protein-protein molecular interactions. Evidence from differential scanning calorimetry and x-ray diffraction demonstrated the formation of sodium caseinate chelate. Fourier transform infrared spectroscopy and zeta potential analysis revealed that the sodium caseinate chelate formed through hydrophobicity, hydrogen bonding, and electrostatic forces. These findings provided theoretical insights into how phosphates can improve the stretch-forming of milk fan gel, facilitating the application of phosphate additives in stretched -cheese processing.
PubMed: 38762104
DOI: 10.3168/jds.2024-24737 -
Journal of Pharmaceutical Sciences May 2024The Arrhenius energy of activation of unfolding Ea and Gibbs free energy of unfolding ΔG have been calculated utilizing DSC differential scanning calorimetry for 4...
The Arrhenius energy of activation of unfolding Ea and Gibbs free energy of unfolding ΔG have been calculated utilizing DSC differential scanning calorimetry for 4 mAbs (1 biosimilar) in 3 formulations. DSC derived ΔTm melting temperature changes for each mAb domain (CH2, Fab, CH3) at calorimetric scan rates at 60 °C, 90 °C, 150 °C and 200 °C / hr. were utilized to calculate the kinetic Ea. The DSC derived Ea trend with observed aggregate formation and can be used to predict%HMW formation post 9-month storage at 5 °C and 40 °C for all formulations analyzed. Additionally, thermodynamic ΔG energies were also derived (Tm, ΔCp and ΔH measurements) for each mAb at every scan rate to observe scan rate dependence of ΔG and for extrapolation to 0 °C/hr. (to report ΔG at true equilibrium conditions). Both derived thermodynamic ΔG and kinetic Ea energies were combined to build full energetic landscapes for mAb unfolding and aggregation. Statistical multivariate analysis of kinetic (Ea CH2, Ea Fab, Ea CH3) energies, thermodynamic (ΔG ° and ΔG °) energies and in-silico modeled surface properties was also performed. Analysis revealed key significant parameters contributing to aggregation. These parameters were utilized to build predictive aggregation models for 25 mg/mL mAb formulations stored 9-months at 5 °C and 40 °C.
PubMed: 38761862
DOI: 10.1016/j.xphs.2024.05.009 -
Nature Aging May 2024Hyaline cartilage fibrosis is typically considered an end-stage pathology of osteoarthritis (OA), which results in changes to the extracellular matrix. However, the...
Hyaline cartilage fibrosis is typically considered an end-stage pathology of osteoarthritis (OA), which results in changes to the extracellular matrix. However, the mechanism behind this is largely unclear. Here, we found that the RNA helicase DDX5 was dramatically downregulated during the progression of OA. DDX5 deficiency increased fibrosis phenotype by upregulating COL1 expression and downregulating COL2 expression. In addition, loss of DDX5 aggravated cartilage degradation by inducing the production of cartilage-degrading enzymes. Chondrocyte-specific deletion of Ddx5 led to more severe cartilage lesions in the mouse OA model. Mechanistically, weakened DDX5 resulted in abundance of the Fn1-AS-WT and Plod2-AS-WT transcripts, which promoted expression of fibrosis-related genes (Col1, Acta2) and extracellular matrix degradation genes (Mmp13, Nos2 and so on), respectively. Additionally, loss of DDX5 prevented the unfolding Col2 promoter G-quadruplex, thereby reducing COL2 production. Together, our data suggest that strategies aimed at the upregulation of DDX5 hold significant potential for the treatment of cartilage fibrosis and degradation in OA.
Topics: Animals; DEAD-box RNA Helicases; Mice; Osteoarthritis; G-Quadruplexes; Fibrosis; Alternative Splicing; Humans; Cartilage, Articular; Chondrocytes; Disease Models, Animal; Male
PubMed: 38760576
DOI: 10.1038/s43587-024-00624-0 -
Science Advances May 2024Understanding how the amino acid sequence dictates protein structure and defines its stability is a fundamental problem in molecular biology. It is especially...
Understanding how the amino acid sequence dictates protein structure and defines its stability is a fundamental problem in molecular biology. It is especially challenging for membrane proteins that reside in the complex environment of a lipid bilayer. Here, we obtain an atomic-level picture of the thermally induced unfolding of a membrane-embedded α-helical protein, human aquaporin 1, using solid-state nuclear magnetic resonance spectroscopy. Our data reveal the hierarchical two-step pathway that begins with unfolding of a structured extracellular loop and proceeds to an intermediate state with a native-like helical packing. In the second step, the transmembrane domain unravels as a single unit, resulting in a heterogeneous misfolded state with high helical content but with nonnative helical packing. Our results show the importance of loops for the kinetic stabilization of the whole membrane protein structure and support the three-stage membrane protein folding model.
Topics: Protein Unfolding; Humans; Membrane Proteins; Aquaporin 1; Nuclear Magnetic Resonance, Biomolecular; Magnetic Resonance Spectroscopy; Models, Molecular; Protein Folding; Kinetics; Thermodynamics
PubMed: 38758787
DOI: 10.1126/sciadv.adm7907 -
Protein Science : a Publication of the... Jun 2024The de novo design of miniprotein inhibitors has recently emerged as a new technology to create proteins that bind with high affinity to specific therapeutic targets....
The de novo design of miniprotein inhibitors has recently emerged as a new technology to create proteins that bind with high affinity to specific therapeutic targets. Their size, ease of expression, and apparent high stability makes them excellent candidates for a new class of protein drugs. However, beyond circular dichroism melts and hydrogen/deuterium exchange experiments, little is known about their dynamics, especially at the elevated temperatures they seemingly tolerate quite well. To address that and gain insight for future designs, we have focused on identifying unintended and previously overlooked heat-induced structural and chemical changes in a particularly stable model miniprotein, EHEE_rd2_0005. Nuclear magnetic resonance (NMR) studies suggest the presence of dynamics on multiple time and temperature scales. Transiently elevating the temperature results in spontaneous chemical deamidation visible in the NMR spectra, which we validate using both capillary electrophoresis and mass spectrometry (MS) experiments. High temperatures also result in greatly accelerated intrinsic rates of hydrogen exchange and signal loss in NMR heteronuclear single quantum coherence spectra from local unfolding. These losses are in excellent agreement with both room temperature hydrogen exchange experiments and hydrogen bond disruption in replica exchange molecular dynamics simulations. Our analysis reveals important principles for future miniprotein designs and the potential for high stability to result in long-lived alternate conformational states.
Topics: Hot Temperature; Nuclear Magnetic Resonance, Biomolecular; Molecular Dynamics Simulation; Protein Conformation; Proteins; Protein Stability
PubMed: 38757381
DOI: 10.1002/pro.4991