On the Three-Dimensional Structure of the Flow through Deterministic Lateral Displacement Devices and Its Effects on Particle Separation

Experiments have shown that a suspension of particles of different dimensions pushed through a periodic lattice of micrometric obstacles can be sorted based on particle size. This label-free separation mechanism, referred to as Deterministic Lateral Displacement (DLD), has been explained hinging on the structure of the 2D solution of the Stokes flow through the patterned geometry, thus neglecting the influence of the no-slip conditions at the top and bottom walls of the channel hosting the obstacle lattice. We show that the no-slip conditions at these surfaces trigger the onset of off-plane velocity components, which impart full three-dimensional character to the flow. The impact of the 3D flow structure on particle transport is investigated by enforcing an excluded volume approach for modelling the interaction between the finite-sized particles and the solid surfaces. We find that the combined action of particle diffusion and of the off-plane velocity component causes the suspended particles to migrate towards the top and bottom walls of the channel. Preliminary results suggest that this effect makes the migration angle of the particles significantly different from that obtained by assuming a strictly two-dimensional structure for the flow of the suspending fluid.

Download Full-text

Susceptibility of protein therapeutics to spontaneous chemical modifications by oxidation, cyclization, and elimination reactions

Amino Acids ◽

10.1007/s00726-019-02787-2 ◽

2019 ◽

Vol 51 (10-12) ◽

pp. 1409-1431 ◽

Cited By ~ 5

Author(s):

Luigi Grassi ◽

Chiara Cabrele

Keyword(s):

Small Molecules ◽

Three Dimensional ◽

Drug Market ◽

Structure And Function ◽

Dimensional Structure ◽

Chemical Modifications ◽

Small Molecule Drugs ◽

And Function ◽

The Impact

Abstract Peptides and proteins are preponderantly emerging in the drug market, as shown by the increasing number of biopharmaceutics already approved or under development. Biomolecules like recombinant monoclonal antibodies have high therapeutic efficacy and offer a valuable alternative to small-molecule drugs. However, due to their complex three-dimensional structure and the presence of many functional groups, the occurrence of spontaneous conformational and chemical changes is much higher for peptides and proteins than for small molecules. The characterization of biotherapeutics with modern and sophisticated analytical methods has revealed the presence of contaminants that mainly arise from oxidation- and elimination-prone amino-acid side chains. This review focuses on protein chemical modifications that may take place during storage due to (1) oxidation (methionine, cysteine, histidine, tyrosine, tryptophan, and phenylalanine), (2) intra- and inter-residue cyclization (aspartic and glutamic acid, asparagine, glutamine, N-terminal dipeptidyl motifs), and (3) β-elimination (serine, threonine, cysteine, cystine) reactions. It also includes some examples of the impact of such modifications on protein structure and function.

Download Full-text

SphereCon—a method for precise estimation of residue relative solvent accessible area from limited structural information

Bioinformatics ◽

10.1093/bioinformatics/btaa159 ◽

2020 ◽

Vol 36 (11) ◽

pp. 3372-3378

Author(s):

Alexander Gress ◽

Olga V Kalinina

Keyword(s):

Protein Function ◽

Structural Information ◽

Solvent Accessibility ◽

Three Dimensional ◽

Structural Data ◽

Supplementary Information ◽

Dimensional Structure ◽

Relative Solvent Accessibility ◽

Precise Measure ◽

The Impact

Abstract Motivation In proteins, solvent accessibility of individual residues is a factor contributing to their importance for protein function and stability. Hence one might wish to calculate solvent accessibility in order to predict the impact of mutations, their pathogenicity and for other biomedical applications. A direct computation of solvent accessibility is only possible if all atoms of a protein three-dimensional structure are reliably resolved. Results We present SphereCon, a new precise measure that can estimate residue relative solvent accessibility (RSA) from limited data. The measure is based on calculating the volume of intersection of a sphere with a cone cut out in the direction opposite of the residue with surrounding atoms. We propose a method for estimating the position and volume of residue atoms in cases when they are not known from the structure, or when the structural data are unreliable or missing. We show that in cases of reliable input structures, SphereCon correlates almost perfectly with the directly computed RSA, and outperforms other previously suggested indirect methods. Moreover, SphereCon is the only measure that yields accurate results when the identities of amino acids are unknown. A significant novel feature of SphereCon is that it can estimate RSA from inter-residue distance and contact matrices, without any information about the actual atom coordinates. Availability and implementation https://github.com/kalininalab/spherecon. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

Download Full-text

Combining Electrostatic, Hindrance and Diffusive Effects for Predicting Particle Transport and Separation Efficiency in Deterministic Lateral Displacement Microfluidic Devices

Biosensors ◽

10.3390/bios10090126 ◽

2020 ◽

Vol 10 (9) ◽

pp. 126

Author(s):

Valentina Biagioni ◽

Giulia Balestrieri ◽

Alessandra Adrover ◽

Stefano Cerbelli

Keyword(s):

Particle Transport ◽

Separation Efficiency ◽

Lateral Displacement ◽

Operating Conditions ◽

Separation Performance ◽

Label Free ◽

Deterministic Lateral Displacement ◽

Promising Tool ◽

Label Free Detection ◽

Diffusive Effects

Microfluidic separators based on Deterministic Lateral Displacement (DLD) constitute a promising technique for the label-free detection and separation of mesoscopic objects of biological interest, ranging from cells to exosomes. Owing to the simultaneous presence of different forces contributing to particle motion, a feasible theoretical approach for interpreting and anticipating the performance of DLD devices is yet to be developed. By combining the results of a recent study on electrostatic effects in DLD devices with an advection–diffusion model previously developed by our group, we here propose a fully predictive approach (i.e., ideally devoid of adjustable parameters) that includes the main physically relevant effects governing particle transport on the one hand, and that is amenable to numerical treatment at affordable computational expenses on the other. The approach proposed, based on ensemble statistics of stochastic particle trajectories, is validated by comparing/contrasting model predictions to available experimental data encompassing different particle dimensions. The comparison suggests that at low/moderate values of the flowrate the approach can yield an accurate prediction of the separation performance, thus making it a promising tool for designing device geometries and operating conditions in nanoscale applications of the DLD technique.

Download Full-text

Microfluidic label-free bioprocessing of human reticulocytes from erythroid culture

Lab on a Chip ◽

10.1039/c9lc01128e ◽

2020 ◽

Vol 20 (18) ◽

pp. 3445-3460

Author(s):

Kerwin Kwek Zeming ◽

Yuko Sato ◽

Lu Yin ◽

Nai-Jia Huang ◽

Lan Hiong Wong ◽

...

Keyword(s):

Stem Cells ◽

Hematopoietic Stem Cells ◽

Closed Loop ◽

Lateral Displacement ◽

Label Free ◽

Hematopoietic Stem ◽

Deterministic Lateral Displacement ◽

Dean Flow ◽

Flow Fractionation ◽

Human Rbcs

Developments in Dean flow fractionation (DFF) and deterministic lateral displacement (DLD) for label-free purification of cultured RBCs from human hematopoietic stem cells. An advancement in sorting and closed-loop manufacturing of viable human RBCs.

Download Full-text

A Stochastic Rockfall Model Related to Random Ground Roughness Based on Three-Dimensional Discontinuous Deformation Analysis

Frontiers in Earth Science ◽

10.3389/feart.2021.819751 ◽

2021 ◽

Vol 9 ◽

Author(s):

Lu Zheng ◽

Zhiyuan Zhu ◽

Qi Wei ◽

Kaihui Ren ◽

Yihan Wu ◽

...

Keyword(s):

Dynamic Behavior ◽

Lateral Displacement ◽

Grid Point ◽

Slope Angle ◽

Three Dimensional ◽

Discontinuous Deformation Analysis ◽

Cumulative Distribution ◽

Deformation Analysis ◽

Discontinuous Deformation ◽

The Impact

The use of feasible 3-D numerical methods has become essential for addressing problems related to rockfall hazard. Although several models with various degrees of complexity are available, certain trajectories and impact dynamics related to some model inputs could fall in the rockfall observations area but are rarely calibrated against reflecting its range, especially the lateral deviations. A major difficulty exists in the lack of simulating the apparent randomness during the impact-rebound process leading to both ground roughness and block irregularities. The model presented here is based on three-dimensional discontinuous deformation analysis (3-D DDA). Despite similarities to previous simulations using 3-D DDA, the model presented here incorporates several novel concepts: (1) ground roughness is represented as a random change of slope angle by height perturbation at a grid point in DEM terrain; (2) block irregularities are modelled directly using polyhedron data; (3) a scaled velocity restitution relationship is introduced to consider incident velocity and its angle. Lateral deviations of rebound velocity, both direction and value, at impact are similarly accounted for by perturbing the ground orientation laterally, thus inducing scatter of run-out directions. With these features, the model is capable to describe the stochastic rockfall dynamics. In this study, 3-D DDA was then conducted to investigate the dynamic behavior of the rockfall and examine the role of sphericity of the rock block travelling on bench slopes with different ground roughness levels. Parametric analyses were carried out in terms of cumulative distribution function (CDF) to investigate for spatial distribution (both runout distance and lateral displacement), velocity and jumping height. The effects of block shape and ground roughness revealed by these factors were discussed. It suggests that ground roughness amplifies the randomness and plays important roles on the dynamic behavior of the system; irregularity from block sphericity will further amplify the randomness especially when the size of the rock is relatively small compared to the roughness level. Both irregularities should be taken into consideration in simulating rockfall problems. Further calibration of the new model against a range of field datasets is essential.

Download Full-text

Two Pathogenic Gene Mutations Identified Associating with Congenital Cataract and Iris Coloboma Respectively in a Chinese Family

Journal of Ophthalmology ◽

10.1155/2020/7054315 ◽

2020 ◽

Vol 2020 ◽

pp. 1-9

Author(s):

Bin Li ◽

Bin Lu ◽

Xuewen Guo ◽

Shenghui Hu ◽

Guihu Zhao ◽

...

Keyword(s):

Congenital Cataract ◽

Three Dimensional ◽

Gene Mutations ◽

Dimensional Structure ◽

Chinese Family ◽

Control Group ◽

Three Dimensional Structure ◽

Han Ethnicity ◽

The Family ◽

The Impact

Purpose. To screen out pathogenic genes in a Chinese family with congenital cataract and iris coloboma. Material and Methods. A three-generation family with congenital cataract and iris coloboma from a Han ethnicity was recruited. DNA was extracted from peripheral blood samples collected from all individuals in the family. Whole exon sequencing was employed for screening the disease-causing gene mutations in the proband, and Sanger sequencing was used for other members of the family and a control group of 500 healthy individuals. Bioinformatics analysis and three-dimensional structure predictions were used to predict the impact of amino acid changes on protein structure and function. Results. The candidate genes of cataract and iris coloboma were successfully screened out. A heterozygote mutation, CRYGD c.70C>A (p.P24T), was identified as cosegregating with congenital cataracts, while another heterozygous mutation, WFS1 c.1514G>C (p.C505S), which had not been reported previously, cosegregated with congenital iris coloboma. Bioinformatic analyses and three-dimensional structure prediction proved that the three-dimensional structures of WFS1 p.C505S and CRYGD p.P24T changed markedly and may contribute significantly to iris coloboma and congenital cataract, respectively. Conclusions. We report a novel mutation, WFS1 p.C505S, and a known mutation, CRYGD p.P24T, that cosegregate with iris coloboma and congenital cataract, respectively, in a Chinese family. This is the first time the association of WFS1 p.C505S with iris coloboma has been demonstrated, although CRYGD p.P24T has been widely reported as being associated with congenital cataract, especially in the Eastern Asian population. These findings may have future therapeutic benefit for the diagnosis of iris coloboma and congenital cataract. The results may also be relevant in further studies aiming to investigate the molecular pathogenesis of iris coloboma and congenital cataract.

Download Full-text

Novel biological implication of a strictly monomorphic GCC repeat in the human PRKACB gene

10.21203/rs.3.rs-428458/v1 ◽

2021 ◽

Author(s):

Safoura Khamse ◽

Zahra Jafarian ◽

Ali Bozorgmehr ◽

Mostafa Tavakoli ◽

Hossein Afshar Iranian ◽

...

Keyword(s):

Late Onset ◽

Human Subjects ◽

Three Dimensional ◽

Dna Structure ◽

Dimensional Structure ◽

Protein Coding ◽

Three Dimensional Structure ◽

Significant Divergence ◽

The Impact ◽

The Brain

Abstract Across human protein-coding genes, PRKACB (Protein Kinase CAMP-Activated Catalytic Subunit Beta) contains one of the longest GCC-repeats, and is predominantly expressed in the brain. Here we studied this STR in 300 human subjects, consisting of late-onset neurocognitive disorder (NCD) (N = 150) and controls (N = 150). We also studied the impact of this STR on the three-dimensional structure of DNA. While the PRKACB GCC-STR was strictly monomorphic at 7-repeats, we detected two 7/8 genotypes only in the NCD group. In comparison to all other lengths, (GCC)7 had the least effect on the three-dimensional structure of DNA, evidenced by minimal divergence between 0 and 7-repeats (divergence score = 0.04) and significant divergence between 0 and 8 repeats (divergence score = 0.50). A similar inert effect to the GCC-repeat was not detected in other classes of STRs such as GA and CA repeats. In conclusion, we report monomorphism of an exceptionally long GCC repeat in the PRKACB gene in human, its inert effect on DNA structure, and divergence in two cases of late-onset NCD. This is the first indication of natural selection for an exceptionally long monomorphic GCC-repeat, which probably evolved to function as an “epigenetic knob”, without changing the regional DNA structure.

Download Full-text

Deep geometric representations for modeling effects of mutations on protein-protein binding affinity

PLoS Computational Biology ◽

10.1371/journal.pcbi.1009284 ◽

2021 ◽

Vol 17 (8) ◽

pp. e1009284

Author(s):

Xianggen Liu ◽

Yunan Luo ◽

Pengyong Li ◽

Sen Song ◽

Jian Peng

Keyword(s):

Protein Binding ◽

Binding Affinity ◽

Protein Design ◽

Protein Structures ◽

Three Dimensional ◽

Point Mutations ◽

Dimensional Structure ◽

Gradient Boosting ◽

Benchmark Datasets ◽

The Impact

Modeling the impact of amino acid mutations on protein-protein interaction plays a crucial role in protein engineering and drug design. In this study, we develop GeoPPI, a novel structure-based deep-learning framework to predict the change of binding affinity upon mutations. Based on the three-dimensional structure of a protein, GeoPPI first learns a geometric representation that encodes topology features of the protein structure via a self-supervised learning scheme. These representations are then used as features for training gradient-boosting trees to predict the changes of protein-protein binding affinity upon mutations. We find that GeoPPI is able to learn meaningful features that characterize interactions between atoms in protein structures. In addition, through extensive experiments, we show that GeoPPI achieves new state-of-the-art performance in predicting the binding affinity changes upon both single- and multi-point mutations on six benchmark datasets. Moreover, we show that GeoPPI can accurately estimate the difference of binding affinities between a few recently identified SARS-CoV-2 antibodies and the receptor-binding domain (RBD) of the S protein. These results demonstrate the potential of GeoPPI as a powerful and useful computational tool in protein design and engineering. Our code and datasets are available at: https://github.com/Liuxg16/GeoPPI.

Download Full-text