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Grigas AT, Fisher A, Shattuck MD, O'Hern CS. Connecting polymer collapse and the onset of jamming. Phys Rev E 2024; 109:034406. [PMID: 38632799 DOI: 10.1103/physreve.109.034406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 02/13/2024] [Indexed: 04/19/2024]
Abstract
Previous studies have shown that the interiors of proteins are densely packed, reaching packing fractions that are as large as those found for static packings of individual amino-acid-shaped particles. How can the interiors of proteins take on such high packing fractions given that amino acids are connected by peptide bonds and many amino acids are hydrophobic with attractive interactions? We investigate this question by comparing the structural and mechanical properties of collapsed attractive disk-shaped bead-spring polymers to those of three reference systems: static packings of repulsive disks, of attractive disks, and of repulsive disk-shaped bead-spring polymers. We show that the attractive systems quenched to temperatures below the glass transition T≪T_{g} and static packings of both repulsive disks and bead-spring polymers possess similar interior packing fractions. Previous studies have shown that static packings of repulsive disks are isostatic at jamming onset, i.e., the number of interparticle contacts N_{c} matches the number of degrees of freedom, which strongly influences their mechanical properties. We find that repulsive polymer packings are hypostatic at jamming onset (i.e., with fewer contacts than degrees of freedom) but are effectively isostatic when including stabilizing quartic modes, which give rise to quartic scaling of the potential energy with displacements along these modes. While attractive disk and polymer packings are often considered hyperstatic with excess contacts over the isostatic number, we identify a definition for interparticle contacts for which they can also be considered as effectively isostatic. As a result, we show that the mechanical properties (e.g., scaling of the potential energy with excess contact number and low-frequency contribution to the density of vibrational modes) of weakly attractive disk and polymer packings are similar to those of isostatic repulsive disk and polymer packings. Our results demonstrate that static packings generated via attractive collapse or compression of repulsive particles possess similar structural and mechanical properties.
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Affiliation(s)
- Alex T Grigas
- Graduate Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Aliza Fisher
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06520, USA
| | - Mark D Shattuck
- Benjamin Levich Institute and Physics Department, The City College of New York, New York, New York 10031, USA
| | - Corey S O'Hern
- Graduate Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA
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2
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Sarhangi SM, Matyushov DV. Theory of Protein Charge Transfer: Electron Transfer between Tryptophan Residue and Active Site of Azurin. J Phys Chem B 2022; 126:10360-10373. [PMID: 36459590 DOI: 10.1021/acs.jpcb.2c05258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
One reaction step in the conductivity relay of azurin, electron transfer between the Cu-based active site and the tryptophan residue, is studied theoretically and by classical molecular dynamics simulations. Oxidation of tryptophan results in electrowetting of this residue. This structural change makes the free energy surfaces of electron transfer nonparabolic as described by the Q-model of electron transfer. We analyze the medium dynamical effect on protein electron transfer produced by coupled Stokes-shift dynamics and the dynamics of the donor-acceptor distance modulating electron tunneling. The equilibrium donor-acceptor distance falls in the plateau region of the rate constant, where it is determined by the protein-water dynamics, and the probability of electron tunneling does not affect the rate. The crossover distance found here puts most intraprotein electron-transfer reactions under the umbrella of dynamical control. The crossover between the medium-controlled and tunneling-controlled kinetics is combined with the effect of the protein-water medium on the activation barrier to formulate principles of tunability of protein-based charge-transfer chains. The main principle in optimizing the activation barrier is the departure from the Gaussian-Gibbsian statistics of fluctuations promoting activated transitions. This is achieved either by incomplete (nonergodic) sampling, breaking the link between the Stokes-shift and variance reorganization energies, or through wetting-induced structural changes of the enzyme's active site.
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Affiliation(s)
- Setare Mostajabi Sarhangi
- School of Molecular Sciences and Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona85287-1504, United States
| | - Dmitry V Matyushov
- School of Molecular Sciences and Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona85287-1504, United States
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3
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Nagano C, Takaoka Y, Kamei K, Hamada R, Ichikawa D, Tanaka K, Aoto Y, Ishiko S, Rossanti R, Sakakibara N, Okada E, Horinouchi T, Yamamura T, Tsuji Y, Noguchi Y, Ishimori S, Nagase H, Ninchoji T, Iijima K, Nozu K. Genotype-Phenotype Correlation in WT1 Exon 8 to 9 Missense Variants. Kidney Int Rep 2021; 6:2114-2121. [PMID: 34386660 PMCID: PMC8343804 DOI: 10.1016/j.ekir.2021.05.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 12/05/2022] Open
Abstract
Introduction WT1 missense mutation in exon 8 or 9 causes infantile nephrotic syndrome with early progression to end-stage kidney disease (ESKD), Wilms tumor, and 46,XY female. However, some patients with missense mutations in exon 8 or 9 progress to ESKD in their teens or later. Therefore, we conducted a systematic review and functional analysis of WT1 transcriptional activity. Methods We conducted a systematic review of 174 cases with WT1 exon 8 or 9 missense variants from our cohort (n=13) and previous reports (n=161). Of these cases, mild and severe genotypes were selected for further in vitro functional analysis using luciferase assay. Results The median age of developing ESKD was 1.17 years. A comparative study was conducted among three WT1 genotype classes: mutations of the DNA-binding site (DBS group), mutations outside the DNA-binding site but at sites important for zinc finger structure formation by 2 cysteines and 2 histidines (C2H2 group), and mutations leading to other amino acid changes (Others group). The DBS group showed the severest phenotype and the C2H2 group was intermediate, whereas the Others group showed the mildest phenotype (developing ESKD at 0.90, 2.00, and 3.92 years, respectively, with significant differences). In vitro functional analysis showed dominant-negative effects for all variants; in addition, the DBS and C2H2 mutations were associated with significantly lower WT1 transcriptional activity than the other mutations. Conclusion Not only the DNA-binding site but also C2H2 zinc finger structure sites are important for maintaining WT1 transcriptional activity, and their mutation causes severe clinical symptoms.
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Affiliation(s)
- China Nagano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Yutaka Takaoka
- Division of Medical Informatics and Bioinformatics, Kobe University Hospital, Kobe, Hyogo, Japan
| | - Koichi Kamei
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - Riku Hamada
- Department of Nephrology, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Daisuke Ichikawa
- Division of Nephrology and Hypertension, St. Marianna University Graduate School of Medicine, Kawasaki City, Kanagawa, Japan
| | - Kazuki Tanaka
- Department of Nephrology, Aichi Children's Health and Medical Center, Obu, Aichi, Japan
| | - Yuya Aoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Shinya Ishiko
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Rini Rossanti
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Nana Sakakibara
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Eri Okada
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Yurika Tsuji
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Yuko Noguchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Shingo Ishimori
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Hiroaki Nagase
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Takeshi Ninchoji
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
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4
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Liang CT, Roscow OMA, Zhang W. Recent developments in engineering protein-protein interactions using phage display. Protein Eng Des Sel 2021; 34:6297171. [PMID: 34117768 DOI: 10.1093/protein/gzab014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/09/2021] [Accepted: 05/18/2021] [Indexed: 12/14/2022] Open
Abstract
Targeted inhibition of misregulated protein-protein interactions (PPIs) has been a promising area of investigation in drug discovery and development for human diseases. However, many constraints remain, including shallow binding surfaces and dynamic conformation changes upon interaction. A particularly challenging aspect is the undesirable off-target effects caused by inherent structural similarity among the protein families. To tackle this problem, phage display has been used to engineer PPIs for high-specificity binders with improved binding affinity and greatly reduced undesirable interactions with closely related proteins. Although general steps of phage display are standardized, library design is highly variable depending on experimental contexts. Here in this review, we examined recent advances in the structure-based combinatorial library design and the advantages and limitations of different approaches. The strategies described here can be explored for other protein-protein interactions and aid in designing new libraries or improving on previous libraries.
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Affiliation(s)
- Chen T Liang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G2W1, Canada
| | - Olivia M A Roscow
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G2W1, Canada
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G2W1, Canada.,CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, MaRS Centre West Tower, 661 University Avenue, Toronto, Ontario M5G1M1, Canada
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5
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Novel ARG1 variants identified in a patient with arginase 1 deficiency. Hum Genome Var 2021; 8:8. [PMID: 33542202 PMCID: PMC7862390 DOI: 10.1038/s41439-021-00139-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/15/2020] [Accepted: 12/23/2020] [Indexed: 12/31/2022] Open
Abstract
We report a case of a 13-year-old boy with arginase 1 deficiency carrying a new variant in ARG1. Sanger sequencing identified the compound heterozygous variants: NM_000045.4: c.365G>A (p.Trp122*)/c.820G>A (p.Asp274Asn). Although not previously reported, the p.Asp274Asn variant is predicted to have strong pathogenicity because it is located in a highly conserved domain in the protein core and arginase activity in the patient was below measurement sensitivity.
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6
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Guckeisen T, Hosseinpour S, Peukert W. Effect of pH and urea on the proteins secondary structure at the water/air interface and in solution. J Colloid Interface Sci 2021; 590:38-49. [PMID: 33524719 DOI: 10.1016/j.jcis.2021.01.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 01/09/2023]
Abstract
HYPOTHESIS The secondary structure of proteins affects their functionality and performance in physiological environments or industrial applications. Change of the solution pH or the presence of protein denaturants are the main chemical means that can alter the secondary structure of proteins or lead to protein denaturation. Since proteins in the bulk solution and those residing at the solution/air interface experience different local environments, their response to chemical denaturation can be different. EXPERIMENTS We utilize circular dichroism and chiral/achiral sum frequency generation spectroscopy to study the secondary structure of selected proteins as a function of the solution pH or in the presence of 8 M urea in the bulk solution and at the solution/air interface, respectively. FINDINGS The liquid/air interface can enhance or decrease protein conformation stability. The change in the secondary structure of the surface adsorbed proteins in alkaline solutions occurs at pH values lower than those denaturing the studied proteins in the bulk solution. In contrast, while 8 M urea completely denatures the studied proteins in the bulk solution, the liquid/air interface prevents the urea-induced denaturation of the surface adsorbed proteins by limiting the access of urea to the hydrophobic side chains of proteins protruding to air.
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Affiliation(s)
- Tobias Guckeisen
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität-Erlangen-Nürnberg (FAU), Cauerstraße 4, 91058 Erlangen, Germany.
| | - Saman Hosseinpour
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität-Erlangen-Nürnberg (FAU), Cauerstraße 4, 91058 Erlangen, Germany.
| | - Wolfgang Peukert
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität-Erlangen-Nürnberg (FAU), Cauerstraße 4, 91058 Erlangen, Germany.
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7
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Grigas AT, Mei Z, Treado JD, Levine ZA, Regan L, O'Hern CS. Using physical features of protein core packing to distinguish real proteins from decoys. Protein Sci 2020; 29:1931-1944. [PMID: 32710566 PMCID: PMC7454528 DOI: 10.1002/pro.3914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 07/10/2020] [Accepted: 07/20/2020] [Indexed: 01/06/2023]
Abstract
The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to distinguish real protein structures from decoys is to delineate the important physical features that specify a real protein. For example, it has long been appreciated that the hydrophobic cores of proteins contribute significantly to their stability. We used two sources to obtain datasets of decoys to compare with real protein structures: submissions to the biennial Critical Assessment of protein Structure Prediction competition, in which researchers attempt to predict the structure of a protein only knowing its amino acid sequence, and also decoys generated by 3DRobot, which have user-specified global root-mean-squared deviations from experimentally determined structures. Our analysis revealed that both sets of decoys possess cores that do not recapitulate the key features that define real protein cores. In particular, the model structures appear more densely packed (because of energetically unfavorable atomic overlaps), contain too few residues in the core, and have improper distributions of hydrophobic residues throughout the structure. Based on these observations, we developed a feed-forward neural network, which incorporates key physical features of protein cores, to predict how well a computational model recapitulates the real protein structure without knowledge of the structure of the target sequence. By identifying the important features of protein structure, our method is able to rank decoy structures with similar accuracy to that obtained by state-of-the-art methods that incorporate many additional features. The small number of physical features makes our model interpretable, emphasizing the importance of protein packing and hydrophobicity in protein structure prediction.
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Affiliation(s)
- Alex T. Grigas
- Graduate Program in Computational Biology and BioinformaticsYale UniversityNew HavenConnecticutUSA
- Integrated Graduate Program in Physical and Engineering BiologyYale UniversityNew HavenConnecticutUSA
| | - Zhe Mei
- Integrated Graduate Program in Physical and Engineering BiologyYale UniversityNew HavenConnecticutUSA
- Department of ChemistryYale UniversityNew HavenConnecticutUSA
| | - John D. Treado
- Integrated Graduate Program in Physical and Engineering BiologyYale UniversityNew HavenConnecticutUSA
- Department of Mechanical Engineering and Materials ScienceYale UniversityNew HavenConnecticutUSA
| | - Zachary A. Levine
- Department of PathologyYale UniversityNew HavenConnecticutUSA
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenConnecticutUSA
| | - Lynne Regan
- Institute of Quantitative Biology, Biochemistry and Biotechnology, Centre for Synthetic and Systems Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Corey S. O'Hern
- Graduate Program in Computational Biology and BioinformaticsYale UniversityNew HavenConnecticutUSA
- Integrated Graduate Program in Physical and Engineering BiologyYale UniversityNew HavenConnecticutUSA
- Department of Mechanical Engineering and Materials ScienceYale UniversityNew HavenConnecticutUSA
- Department of PhysicsYale UniversityNew HavenConnecticutUSA
- Department of Applied PhysicsYale UniversityNew HavenConnecticutUSA
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8
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Shiraishi K, Mizuno H, Ikeda A. Vibrational properties of two-dimensional dimer packings near the jamming transition. Phys Rev E 2019; 100:012606. [PMID: 31499851 DOI: 10.1103/physreve.100.012606] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Indexed: 11/07/2022]
Abstract
Jammed particulate systems composed of various shapes of particles undergo the jamming transition as they are compressed or decompressed. To date, sphere packings have been extensively studied in many previous works, where isostaticity at the transition and scaling laws with the pressure of various quantities, including the contact number and the vibrational density of states, have been established. Additionally, much attention has been paid to nonspherical packings, and particularly recent work has made progress in understanding ellipsoidal packings. In this work, we study the dimer packings in two dimensions, which have been much less understood than systems of spheres and ellipsoids. We first study the contact number of dimers near the jamming transition. It turns out that packings of dimers have "rotational rattlers," each of which still has a free rotational motion. After correcting this effect, we show that dimers become isostatic at the jamming, and the excess contact number obeys the same critical law and finite-size scaling law as those of spheres. We next study the vibrational properties of dimers near the transition. We find that the vibrational density of states of dimers exhibits two characteristic plateaus that are separated by a peak. The high-frequency plateau is dominated by the translational degree of freedom, while the low-frequency plateau is dominated by the rotational degree of freedom. We establish the critical scaling laws of the characteristic frequencies of the plateaus and the peak near the transition. In addition, we present detailed characterizations of the real space displacement fields of vibrational modes in the translational and rotational plateaus.
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Affiliation(s)
- Kumpei Shiraishi
- Graduate School of Arts and Sciences, University of Tokyo, Komaba, Tokyo 153-8902, Japan
| | - Hideyuki Mizuno
- Graduate School of Arts and Sciences, University of Tokyo, Komaba, Tokyo 153-8902, Japan
| | - Atsushi Ikeda
- Graduate School of Arts and Sciences, University of Tokyo, Komaba, Tokyo 153-8902, Japan.,Research Center for Complex Systems Biology, Universal Biology Institute, University of Tokyo, Komaba, Tokyo 153-8902, Japan
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9
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Treado JD, Mei Z, Regan L, O'Hern CS. Void distributions reveal structural link between jammed packings and protein cores. Phys Rev E 2019; 99:022416. [PMID: 30934238 DOI: 10.1103/physreve.99.022416] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Indexed: 11/07/2022]
Abstract
Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction ϕ≈0.56, which is the same as dense, random packing of amino-acid-shaped particles. In this article, we compare the structural properties of protein cores and jammed packings of amino-acid-shaped particles in much greater depth by measuring their local and connected void regions. We find that the distributions of surface Voronoi cell volumes and local porosities obey similar statistics in both systems. We also measure the probability that accessible, connected void regions percolate as a function of the size of a spherical probe particle and show that both systems possess the same critical probe size. We measure the critical exponent τ that characterizes the size distribution of connected void clusters at the onset of percolation. We find that the cluster size statistics are similar for void percolation in packings of amino-acid-shaped particles and randomly placed spheres, but different from that for void percolation in jammed sphere packings. We propose that the connected void regions are a defining structural feature of proteins and can be used to differentiate experimentally observed proteins from decoy structures that are generated using computational protein design software. This work emphasizes that jammed packings of amino-acid-shaped particles can serve as structural and mechanical analogs of protein cores, and could therefore be useful in modeling the response of protein cores to cavity-expanding and -reducing mutations.
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Affiliation(s)
- John D Treado
- Department of Mechanical Engineering & Materials Science, Yale University, New Haven, Connecticut 06520, USA.,Integrated Graduate Program in Physical & Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Zhe Mei
- Integrated Graduate Program in Physical & Engineering Biology, Yale University, New Haven, Connecticut 06520, USA.,Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Lynne Regan
- Integrated Graduate Program in Physical & Engineering Biology, Yale University, New Haven, Connecticut 06520, USA.,Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.,Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Corey S O'Hern
- Department of Mechanical Engineering & Materials Science, Yale University, New Haven, Connecticut 06520, USA.,Integrated Graduate Program in Physical & Engineering Biology, Yale University, New Haven, Connecticut 06520, USA.,Department of Physics, Yale University, New Haven, Connecticut 06520, USA.,Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
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10
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Waskasi MM, Martin DR, Matyushov DV. Wetting of the Protein Active Site Leads to Non-Marcusian Reaction Kinetics. J Phys Chem B 2018; 122:10490-10495. [PMID: 30365331 DOI: 10.1021/acs.jpcb.8b10376] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes exist in continuously fluctuating water bath dramatically affecting their function. Water not only forms the solvation shell but also penetrates into the protein interior. Changing the wetting pattern of the protein's active site in response to altering redox state initiates a highly nonlinear structural change and non-Gaussian electrostatic fluctuations at the active site. The free-energy surfaces of electron transfer are highly nonparabolic (non-Marcusian), as shown by atomistic molecular dynamics simulations of hydrated ferredoxin protein and by an analytical model in agreement with simulations. The reorganization energy of electron transfer passes through a spike marking equal probabilities of the wet and dry states of the active site. The activation thermodynamics affected by wetting leads to a non-Arrhenius, passing through a maximum, plot for the reaction rate vs the inverse temperature.
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Affiliation(s)
- Morteza M Waskasi
- School of Molecular Sciences , Arizona State University , P.O. Box 871604, Tempe , Arizona 85287-1604 , United States
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11
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Matyushov DV. Fluctuation relations, effective temperature, and ageing of enzymes: The case of protein electron transfer. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.06.087] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Gaines JC, Acebes S, Virrueta A, Butler M, Regan L, O'Hern CS. Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins. Proteins 2018; 86:581-591. [PMID: 29427530 PMCID: PMC5912992 DOI: 10.1002/prot.25479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/23/2018] [Accepted: 02/06/2018] [Indexed: 12/26/2022]
Abstract
We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA≲0.3, for all 3 protein classes. Our results show that ≈40% of the interface regions in protein complexes are "core", that is, densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins.
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Affiliation(s)
- J C Gaines
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, 06520
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
| | - S Acebes
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut, 06520
| | - A Virrueta
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut, 06520
| | - M Butler
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, 90007
| | - L Regan
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, 06520
- Department of Chemistry, Yale University, New Haven, Connecticut, 06520
| | - C S O'Hern
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, 06520
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut, 06520
- Department of Physics, Yale University, New Haven, Connecticut, 06520
- Department of Applied Physics, Yale University, New Haven, Connecticut, 06520
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13
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VanderWerf K, Jin W, Shattuck MD, O'Hern CS. Hypostatic jammed packings of frictionless nonspherical particles. Phys Rev E 2018; 97:012909. [PMID: 29448406 PMCID: PMC6295208 DOI: 10.1103/physreve.97.012909] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Indexed: 11/07/2022]
Abstract
We perform computational studies of static packings of a variety of nonspherical particles including circulo-lines, circulo-polygons, ellipses, asymmetric dimers, dumbbells, and others to determine which shapes form packings with fewer contacts than degrees of freedom (hypostatic packings) and which have equal numbers of contacts and degrees of freedom (isostatic packings), and to understand why hypostatic packings of nonspherical particles can be mechanically stable despite having fewer contacts than that predicted from naive constraint counting. To generate highly accurate force- and torque-balanced packings of circulo-lines and cir-polygons, we developed an interparticle potential that gives continuous forces and torques as a function of the particle coordinates. We show that the packing fraction and coordination number at jamming onset obey a masterlike form for all of the nonspherical particle packings we studied when plotted versus the particle asphericity A, which is proportional to the ratio of the squared perimeter to the area of the particle. Further, the eigenvalue spectra of the dynamical matrix for packings of different particle shapes collapse when plotted at the same A. For hypostatic packings of nonspherical particles, we verify that the number of "quartic" modes along which the potential energy increases as the fourth power of the perturbation amplitude matches the number of missing contacts relative to the isostatic value. We show that the fourth derivatives of the total potential energy in the directions of the quartic modes remain nonzero as the pressure of the packings is decreased to zero. In addition, we calculate the principal curvatures of the inequality constraints for each contact in circulo-line packings and identify specific types of contacts with inequality constraints that possess convex curvature. These contacts can constrain multiple degrees of freedom and allow hypostatic packings of nonspherical particles to be mechanically stable.
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Affiliation(s)
- Kyle VanderWerf
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Weiwei Jin
- Department of Mechanics and Engineering Science, Peking University, Beijing 100871, China
- Department of Mechanical Engineering & Materials Science, Yale University, New Haven, Connecticut 06520, USA
| | - Mark D Shattuck
- Benjamin Levich Institute and Physics Department, The City College of New York, New York, New York 10031, USA
| | - Corey S O'Hern
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Department of Mechanical Engineering & Materials Science, Yale University, New Haven, Connecticut 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA
- Graduate Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
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