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  • 1.
    Kliuchnikov, Evgenii
    et al.
    Univ Massachusetts, Dept Chem, Lowell, MA 01854 USA..
    Klyshko, Eugene
    Univ Massachusetts, Dept Chem, Lowell, MA 01854 USA.;Univ Toronto, Dept Phys, Toronto, ON M5S 1A7, Canada..
    Kelly, Maria S.
    Univ Cincinnati, Dept Chem, Cincinnati, OH 45221 USA..
    Zhmurov, Artem
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.
    Dima, Ruxandra, I
    Univ Cincinnati, Dept Chem, Cincinnati, OH 45221 USA..
    Marx, Kenneth A.
    Univ Massachusetts, Dept Chem, Lowell, MA 01854 USA..
    Barsegov, Valeri
    Univ Massachusetts, Dept Chem, Lowell, MA 01854 USA..
    Microtubule assembly and disassembly dynamics model: Exploring dynamic instability and identifying features of Microtubules' Growth, Catastrophe, Shortening, and Rescue2022Ingår i: Computational and Structural Biotechnology Journal, E-ISSN 2001-0370, Vol. 20, s. 953-974Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Microtubules (MTs), a cellular structure element, exhibit dynamic instability and can switch stochastically from growth to shortening; but the factors that trigger these processes at the molecular level are not understood. We developed a 3D Microtubule Assembly and Disassembly DYnamics (MADDY) model, based upon a bead-per-monomer representation of the alpha beta-tubulin dimers forming an MT lattice, stabilized by the lateral and longitudinal interactions between tubulin subunits. The model was parameterized against the experimental rates of MT growth and shortening, and pushing forces on the Dam1 protein complex due to protofilaments splaying out. Using the MADDY model, we carried out GPU-accelerated Langevin simulations to access dynamic instability behavior. By applying Machine Learning techniques, we identified the MT characteristics that distinguish simultaneously all four kinetic states: growth, catastrophe, shortening, and rescue. At the cellular 25 mu M tubulin concentration, the most important quantities are the MT length L, average longitudinal curvature kappa(long), MT tip width w, total energy of longitudinal interactions in MT lattice U-long, and the energies of longitudinal and lateral interactions required to complete MT to full cylinder U-long(add) and U-lat(add) . At high 250 mu M tubulin concentration, the most important characteristics are L, kappa(long), number of hydrolyzed alpha beta-tubulin dimers n(hyd) and number of lateral interactions per helical pitch n(lat) in MT lattice, energy of lateral interactions in MT lattice U-lat, and energy of longitudinal interactions in MT tip u(long). These results allow greater insights into what brings about kinetic state stability and the transitions between states involved in MT dynamic instability behavior.

  • 2.
    Kumar, Rajender
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi, Glykovetenskap. KTH, Skolan för bioteknologi (BIO), Centra, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Kumar, Sanjiv
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi, Glykovetenskap. KTH, Skolan för bioteknologi (BIO), Centra, Albanova VinnExcellence Center for Protein Technology, ProNova. Örebro Univ, Fac Med Sci, S-70362 Örebro, Sweden..
    Bulone, Vincent
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi, Glykovetenskap. KTH, Skolan för bioteknologi (BIO), Centra, Albanova VinnExcellence Center for Protein Technology, ProNova. Flinders Univ S Australia, Coll Med & Publ Hlth, Bedford Pk Campus,Sturt Rd, Bedford Pk, SA 5042, Australia..
    Srivastava, Vaibhav
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi, Glykovetenskap. KTH, Skolan för bioteknologi (BIO), Centra, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Biochemical characterization and molecular insights into substrate recognition of pectin methylesterase from Phytophthora infestans2022Ingår i: Computational and Structural Biotechnology Journal, E-ISSN 2001-0370, Vol. 20, s. 6023-6032Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Pectin methylesterases (PMEs) are a class of carbohydrate-active enzymes that act on the O6-methyl ester groups of the homogalacturonan component of pectins, resulting in de-esterification of the sub-strate polymers and formation of pectate and methanol. PMEs occur in higher plants and microorgan-isms, including fungi, oomycetes, bacteria, and archaea. Microbial PMEs play a crucial role in pathogens' invasion of plant tissues. Here, we have determined the structural and functional properties of Pi-PME, a PME from the oomycete plant pathogen Phytophthora infestans. This enzyme exhibits maxi-mum activity at alkaline pH (8.5) and is active over a wide temperature range (25-50 degrees C). In silico deter-mination of the structure of Pi-PME reveals that the protein consists essentially of three parallel 8-sheets interconnected by loops that adopt an overall 8-helix organization. The loop regions in the vicinity of the active site are extended compared to plant and fungal PMEs, but they are shorter than the corresponding bacterial and insect regions. Molecular dynamic simulations revealed that Pi-PME interacts most strongly with partially de-methylated homogalacturonans, suggesting that it preferentially uses this type of sub-strates. The results are compared and discussed with other known PMEs from different organisms, high-lighting the specific features of Pi-PME.

  • 3.
    Li, Jiachen
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi, Teoretisk kemi och biologi. Zhejiang Univ, Dept Chem, Hangzhou 310027, Peoples R China..
    Wang, Qi
    Zhejiang Univ, Dept Chem, Hangzhou 310027, Peoples R China..
    Tu, Yaoquan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi, Teoretisk kemi och biologi.
    Binding modes of prothrombin cleavage site sequences to the factor Xa catalytic triad: Insights from atomistic simulations2022Ingår i: Computational and Structural Biotechnology Journal, E-ISSN 2001-0370, Vol. 20, s. 5401-5408Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Prothrombin is a key zymogen of the coagulation process and can be converted to thrombin by the prothrombinase complex, which consists of factor Xa (FXa), cofactor Va (FVa), and phospholipids. Prothrombin can be activated at two cleavage sites, R271 and R320, which generates two intermediates: prethrombin-2 via the initial cleavage at R271, and meizothrombin via the first cleavage at R320. Several mechanisms have been proposed to explain this activation preference, but the role of cleavage site sequences in prothrombin activation has not been thoroughly investigated. Here, we used an advanced sampling technique, parallel tempering metadynamics with a well-tempered ensemble (PTMetaDWTE), to study the binding modes of prothrombin cleavage site sequences R266AIEGRTATSEY277 (denoted as Pep271) and S315YIDGRIVEGSD326 (denoted as Pep320) to the FXa catalytic triad. Our study indicates that there exist three binding modes for Pep271 to the FXa catalytic triad but only one binding mode for Pep320 to the FXa catalytic triad. Further molecular dynamics simulations revealed that due to the strong electrostatic interactions, especially the H-bond interactions and salt bridges formed between Pep320 and FXa, the binding mode in the Pep320-FXa system is more stable than the binding modes in the Pep271-FXa system. In view of experimental observations and our results that there exists only one binding mode for Pep320 to the FXa catalytic triad and especially R320 in Pep320 can stably bind to the FXa catalytic triad, we believe that the first cleavage at R320 is favored.

  • 4.
    Linder, Mats
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi.
    Computational enzyme design: Advances, hurdles and possible ways forward2012Ingår i: Computational and Structural Biotechnology Journal, E-ISSN 2001-0370, Vol. 2, nr 3, artikel-id e201209009Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

     This mini review addresses recent developments in computational enzyme design. Successful protocols as well as known issues and limitations are discussed from an energetic perspective. It will be argued that improved results can be obtained by including a dynamic treatment in the design protocol. Finally, a molecular dynamics-based approach for evaluating and refining computational designs is presented.

  • 5.
    Nilvebrant, Johan
    et al.
    KTH, Skolan för bioteknologi (BIO), Proteinteknologi.
    Hober, Sophia
    KTH, Skolan för bioteknologi (BIO), Proteinteknologi.
    The albumin-binding domain as a scaffold for protein engineering2013Ingår i: Computational and Structural Biotechnology Journal, E-ISSN 2001-0370, Vol. 6, nr 7, s. a5-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The albumin-binding domain is a small, three-helical protein domain found in various surface proteins expressed by gram-positive bacteria. Albumin binding is important in bacterial pathogenesis and several homologous domains have been identified. Such albumin-binding regions have been used for protein purification or immobilization. Moreover, improvement of the pharmacokinetics, through the non-covalent association to albumin, by fusing such domains to therapeutic proteins has been shown to be successful. Domains derived from streptococcal protein G and protein PAB from Finegoldia magna, which share a common origin and therefore represent an interesting evolutionary system, have been thoroughly studied structurally and functionally. Their albumin-binding sites have been mapped and these domains form the basis for a wide range of protein engineering approaches. By substitution-mutagenesis they have been engineered to achieve a broader specificity, an increased stability or an improved binding affinity, respectively. Furthermore, novel binding sites have been incorporated either by replacing the original albumin-binding surface, or by complementing it with a novel interaction interface. Combinatorial protein libraries, where several residues have been randomized simultaneously, have generated a large number of new variants with desired binding characteristics. The albuminbinding domain has also been utilized to explore the relationship between three-dimensional structure and amino acid sequence. Proteins with latent structural information built into their sequence, where a single amino acid substitution shifts the equilibrium in favor of a different fold with a new function, have been designed. Altogether, these examples illustrate the versatility of the albumin-binding domain as a scaffold for protein engineering.

  • 6.
    Nisar, Harris
    et al.
    Health Care Engineering Systems Center, University of Illinois Urbana Champaign – 1206 W Clark St, Urbana, IL, USA, 61801, 1206 W Clark St.
    Annamraju, Srikar
    Coordinated Science Laboratory, University of Illinois Urbana Champaign – 1308 W Main St, Urbana, IL, USA, 61801, 1308 W Main St.
    Deka, Shankar
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Intelligenta system, Reglerteknik.
    Horowitz, Anne
    Outpatient Rehabilitation, OSF Healthcare Saint Francis Medical Center – 6501 N Sheridan Rd, Peoria, IL, USA, 6501 N Sheridan Rd.
    Stipanović, Dušan M.
    Coordinated Science Laboratory, University of Illinois Urbana Champaign – 1308 W Main St, Urbana, IL, USA, 61801, 1308 W Main St.
    Robotic mirror therapy for stroke rehabilitation through virtual activities of daily living2024Ingår i: Computational and Structural Biotechnology Journal, E-ISSN 2001-0370, Vol. 24, s. 126-135Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Mirror therapy is a standard technique of rehabilitation for recovering motor and vision abilities of stroke patients, especially in the case of asymmetric limb function. To enhance traditional mirror therapy, robotic mirror therapy (RMT) has been proposed over the past decade, allowing for assisted bimanual coordination of paretic (affected) and contralateral (healthy) limbs. However, state-of-the-art RMT platforms predominantly target mirrored motions of trajectories, largely limited to 2-D motions. In this paper, an RMT platform is proposed, which can facilitate the patient to practice virtual activities of daily living (ADL) and thus enhance their independence. Two similar (but mirrored) 3D virtual environments are created in which the patients operate robots with both their limbs to complete ADL (such as writing and eating) with the assistance of the therapist. The recovery level of the patient is continuously assessed by monitoring their ability to track assigned trajectories. The patient's robots are programmed to assist the patient in following these trajectories based on this recovery level. In this paper, the framework to dynamically monitor recovery level and accordingly provide assistance is developed along with the nonlinear controller design to ensure position tracking, force control, and stability. Proof-of-concept studies are conducted with both 3D trajectory tracking and ADL. The results demonstrate the potential use of the proposed system to enhance the recovery of the patients.

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