The relationship between structure and property is central to chemistry and enables the understanding of chemical phenomena and processes. Need for an efficient conformational sampling of chemical systems arises from the presence of solvents and the existence of non-zero temperatures. However, conformational sampling of structures to compute molecular quantum mechanical properties is computationally expensive because a large number of electronic structure calculations are required. In this work, the development and implementation of the effective stochastic potential (ESP) method is presented to perform efficient conformational sampling of molecules. The overarching goal of this work is to alleviate the computational bottleneck associated with performing a large number of electronic structure calculations required for conformational sampling. We introduce the concept of a deformation potential and demonstrate its existence by the proof-by-construction approach. A statistical description of the fluctuations in the deformation potential due to non-zero temperature was obtained using infinite-order moment expansion of the distribution. The formal mathematical definition of the ESP was derived using the functional minimization approach to match the infinite-order moment expansion for the deformation potential. Practical implementation of the ESP was obtained using the random-matrix theory method. The developed method was applied to two proof-of-concept calculations of the distribution of HOMO-LUMO gaps in water molecules and solvated CdSe clusters at 300 K. The need for large sample size to obtain statistically meaningful results was demonstrated by performing 10 ESP calculations. The results from these prototype calculations demonstrated the efficacy of the ESP method for performing efficient conformational sampling. We envision that the fundamental nature of this work will not only extend our knowledge of chemical systems at non-zero temperatures but also generate new insights for innovative technological applications.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1063/1.5026027 | DOI Listing |
Pharm Res
January 2025
BioDev Department WuXi Biologics USA, 1 Cedarbrook Dr, Cranbury, NJ, 08512, USA.
Background: High concentration protein formulation (HCPF) development needs to balance protein stability attributes such as conformational/colloidal stability, chemical stability, and solution properties such as viscosity and osmolality.
Methodology: A three-phase design is established in this work. In Phase 1, conformational and colloidal stability are measured by 384-well-based high-throughput (HT) biophysical screening while viscosity reduction screening is performed with HT viscosity screening.
Nat Commun
January 2025
Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Biomedical Engineering, The University of Illinois Chicago, 851 South Morgan Street, Chicago, IL, 60607, USA.
The bottleneck in enhanced sampling lies in finding collective variables that effectively accelerate protein conformational changes; true reaction coordinates that accurately predict the committor are the well-recognized optimal choice. However, identifying them requires unbiased natural reactive trajectories, which, paradoxically, require effective enhanced sampling. Using the generalized work functional method, we uncover that true reaction coordinates control both conformational changes and energy relaxation, enabling us to compute them from energy relaxation simulations.
View Article and Find Full Text PDFNeurol Neuroimmunol Neuroinflamm
March 2025
Neuroimmunology Laboratory and Neuroimmunology Research Section, IRCCS Mondino Foundation, Pavia, Italy.
Background And Objectives: Antibodies to proteolipid protein-1 (PLP1-IgG), a major central myelin protein also expressed in the peripheral nervous system (PNS) as the isoform DM20, have been previously identified mostly in patients with multiple sclerosis (MS), with unclear clinical implications. However, most studies relied on nonconformational immunoassays and included few patients with non-MS CNS autoimmune demyelinating disorders (ADDs). We aimed to investigate conformational PLP1-IgG in the whole ADD spectrum.
View Article and Find Full Text PDFJ Sci Food Agric
January 2025
Division of Medicine, University College London, London, UK.
Background: The escalating global prevalence of food allergies has intensified the need for hypoallergenic food products. Transglutaminase (TGase)-mediated crosslinking has garnered significant attention for its potential to reduce the allergenicity of food proteins. This study aimed to investigate the effects of TGase crosslinking on the potential allergenicity and conformational changes in a dual-protein system composed of β-lactoglobulin (β-LG) and soy protein isolate (SPI) at varying mass ratios (10:0, 7:3, 5:5, 3:7 and 0:10 (w/w)).
View Article and Find Full Text PDFBlood Adv
January 2025
Sanquin, Amsterdam, Netherlands.
In Immune-mediated Thrombotic Thrombocytopenic Purpura (iTTP), patients develop antibodies against ADAMTS13. The majority of patients exhibit inhibitory anti-spacer antibodies. Non-inhibitory antibodies binding to the carboxy-terminal CUB domains have been suggested to enhance the clearance of ADAMTS13 in iTTP.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!