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Ojeda-May, Pedro, Application ExpertORCID iD iconorcid.org/0000-0001-9179-9441
Publications (10 of 14) Show all publications
Ojeda-May, P. & Vergara, A. (2024). Effects of colored noise in the dynamic motions and conformational exploration of enzymes [Letter to the editor]. Foundations, 4(3), 324-335
Open this publication in new window or tab >>Effects of colored noise in the dynamic motions and conformational exploration of enzymes
2024 (English)In: Foundations, E-ISSN 2673-9321, Vol. 4, no 3, p. 324-335Article in journal, Letter (Refereed) Published
Abstract [en]

The intracellular environment displays complex dynamics influenced by factors such as molecular crowding and the low Reynolds number of the cytoplasm. Enzymes exhibiting active matter properties further heighten this complexity which can lead to memory effects. Molecular simulations often neglect these factors, treating the environment as a “thermal bath” using the Langevin equation (LE) with white noise. One way to consider these factors is by using colored noise instead within the generalized Langevin equation (GLE) framework, which allows for the incorporation of memory effects that have been observed in experimental data. We investigated the structural and dynamic differences in Shikimate kinase (SK) using LE and GLE simulations. Our results suggest that GLE simulations, which reveal significant changes, could be utilized for assessing conformational motions’ impact on catalytic reactions.

Place, publisher, year, edition, pages
MDPI, 2024
Keywords
enzyme, molecular, dynamics, noise, kinase
National Category
Biological Sciences Chemical Sciences
Research subject
Biochemistry
Identifiers
urn:nbn:se:umu:diva-227750 (URN)10.3390/foundations4030021 (DOI)
Available from: 2024-07-08 Created: 2024-07-08 Last updated: 2024-07-10Bibliographically approved
Dinh, V. M., Khokarale, S. G., Ojeda-May, P., Sparrman, T., Irgum, K. & Mikkola, J.-P. (2024). Ionic liquid strategy for chitosan production from chitin and molecular insights. RSC Sustainability, 2(4), 1154-1164
Open this publication in new window or tab >>Ionic liquid strategy for chitosan production from chitin and molecular insights
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2024 (English)In: RSC Sustainability, E-ISSN 2753-8125, Vol. 2, no 4, p. 1154-1164Article in journal (Refereed) Published
Abstract [en]

To produce chitosan is an interesting research. Chitosan is an important polysaccharide in terms of its various applications in industries and is produced from chitin, an abundant biopolymer in crustacean shell biomass wastes. Traditional processes for chitosan manufacture are commonly based on highly concentrated alkaline or acid solutions which are, however, severely eroding and harmful to the environment. In this study, we have described a ‘greener’ method using 1-ethyl-3-methylimidazolium acetate, [Emim][OAc] ionic liquid (IL), for decrystallization of shrimp crystalline chitin flakes followed by a microwave-mediated NaOH or tetrabutylammonium hydroxide, [TBA][OH], solution-based deacetylation for chitosan production. The decrease in crystallinity in IL pre-treated chitin was confirmed by XRD and SEM analysis which subsequently benefited chitosan production with up to 85% degree of deacetylation (%DDA) in shorter time periods (1-2 hours) and lower alkaline concentrations (20-40%). The %DDA in chitin/chitosan was estimated via FT-IR and NMR analysis. Notably, we could regenerate the ionic liquids: in case of [Emim][OAc] 97 wt.% and in case of [TBA][OH] 83 wt.% could be reused. Roles of ionic liquids in the process were discussed. Molecular dynamics (MD) simulations showed the roles of [TBA]+ cations in the molecular driving forces of [TBA][OH]-induced deacetylation mechanism. The strategy promises a sustainable and milder reaction approach to the existing highly corrosive alkaline- or acid-involved processes for chitosan production.

Place, publisher, year, edition, pages
Royal Society of Medicine Press, 2024
National Category
Chemical Sciences
Research subject
sustainability
Identifiers
urn:nbn:se:umu:diva-222314 (URN)10.1039/d4su00053f (DOI)2-s2.0-85189679118 (Scopus ID)
Available from: 2024-03-13 Created: 2024-03-13 Last updated: 2024-07-02Bibliographically approved
Lipskij, A., Arbeitman, C., Rojas, P., Ojeda-May, P. & Garcia, M. E. (2023). Dramatic differences between the structural susceptibility of the S1 pre- and S2 postfusion states of the SARS-CoV-2 spike protein to external electric fields revealed by molecular dynamics simulations [Letter to the editor]. Viruses, 15(12), 2405-2419
Open this publication in new window or tab >>Dramatic differences between the structural susceptibility of the S1 pre- and S2 postfusion states of the SARS-CoV-2 spike protein to external electric fields revealed by molecular dynamics simulations
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2023 (English)In: Viruses, E-ISSN 1999-4915, Vol. 15, no 12, p. 2405-2419Article in journal, Letter (Refereed) Published
Abstract [en]

In its prefusion state, the SARS-CoV-2 spike protein (similarly to other class I viral fusion proteins) is metastable, which is considered to be an important feature for optimizing or regulating its functions. After the binding process of its S1 subunit (S1) with ACE2, the spike protein (S) undergoes a dramatic conformational change where S1 splits from the S2 subunit, which then penetrates the membrane of the host cell, promoting the fusion of the viral and cell membranes. This results in the infection of the host cell. In a previous work, we showed—using large-scale molecular dynamics simulations—that the application of external electric fields (EFs) induces drastic changes and damage in the receptor-binding domain (RBD) of the wild-type spike protein, as well of the Alpha, Beta, and Gamma variants, leaving a structure which cannot be recognized anymore by ACE2. In this work, we first extend the study to the Delta and Omicron variants and confirm the high sensitivity and extreme vulnerability of the RBD of the prefusion state of S to moderate EF (as weak as 104 V/m), but, more importantly, we also show that, in contrast, the S2 subunit of the postfusion state of the spike protein does not suffer structural damage even if electric field intensities four orders of magnitude higher are applied. These results provide a solid scientific basis to confirm the connection between the prefusion-state metastability of the SARS-CoV-2 spike protein and its susceptibility to be damaged by EF. After the virus docks to the ACE2 receptor, the stable and robust postfusion conformation develops, which exhibits a similar resistance to EF (damage threshold higher than 108 V/m) like most globular proteins.

Place, publisher, year, edition, pages
MDPI, 2023
Keywords
SARS-CoV-2, spike protein, structural stability, molecular dynamics simulations, electric fields
National Category
Biophysics
Research subject
biological chemistry
Identifiers
urn:nbn:se:umu:diva-217584 (URN)10.3390/v15122405 (DOI)38140646 (PubMedID)2-s2.0-85180512188 (Scopus ID)
Available from: 2023-12-11 Created: 2023-12-11 Last updated: 2024-01-17Bibliographically approved
Ojeda-May, P. (2023). Exploring the dynamics of holo-shikimate kinase through molecular mechanics. Biophysica, 3(3), 463-475
Open this publication in new window or tab >>Exploring the dynamics of holo-shikimate kinase through molecular mechanics
2023 (English)In: Biophysica, ISSN 2673-4125, Vol. 3, no 3, p. 463-475Article in journal (Refereed) Published
Abstract [en]

Understanding the connection between local and global dynamics can provide valuable insights into enzymatic function and may contribute to the development of novel strategies for enzyme modulation. In this work, we investigated the dynamics at both the global and local (active site) levels of Shikimate Kinase (SK) through microsecond time-scale molecular dynamics (MD) simulations of the holoenzyme in the product state. Our focus was on the wild-type (WT) enzyme and two mutants (R116A and R116K) which are known for their reduced catalytic activity. Through exploring the dynamics of these variants, we gained insights into the role of residue R116 and its contribution to overall SK dynamics. We argue that the connection between local and global dynamics can be attributed to local frustration near the mutated residue which perturbs the global protein dynamics.

Place, publisher, year, edition, pages
MDPI, 2023
Keywords
shikimate kinase, mutants, molecular, dynamics, binding, frustration
National Category
Biophysics
Research subject
Biochemistry
Identifiers
urn:nbn:se:umu:diva-212302 (URN)10.3390/biophysica3030030 (DOI)2-s2.0-85176214833 (Scopus ID)
Available from: 2023-07-21 Created: 2023-07-21 Last updated: 2023-12-12Bibliographically approved
Dulko-Smith, B., Ojeda-May, P., Ådén, J., Wolf-Watz, M. & Nam, K. (2023). Mechanistic basis for a connection between the catalytic step and slow opening dynamics of adenylate kinase. Journal of Chemical Information and Modeling, 63(5), 1556-1569
Open this publication in new window or tab >>Mechanistic basis for a connection between the catalytic step and slow opening dynamics of adenylate kinase
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2023 (English)In: Journal of Chemical Information and Modeling, ISSN 1549-9596, E-ISSN 1549-960X, Vol. 63, no 5, p. 1556-1569Article in journal (Refereed) Published
Abstract [en]

Escherichia coli adenylate kinase (AdK) is a small, monomeric enzyme that synchronizes the catalytic step with the enzyme’s conformational dynamics to optimize a phosphoryl transfer reaction and the subsequent release of the product. Guided by experimental measurements of low catalytic activity in seven single-point mutation AdK variants (K13Q, R36A, R88A, R123A, R156K, R167A, and D158A), we utilized classical mechanical simulations to probe mutant dynamics linked to product release, and quantum mechanical and molecular mechanical calculations to compute a free energy barrier for the catalytic event. The goal was to establish a mechanistic connection between the two activities. Our calculations of the free energy barriers in AdK variants were in line with those from experiments, and conformational dynamics consistently demonstrated an enhanced tendency toward enzyme opening. This indicates that the catalytic residues in the wild-type AdK serve a dual role in this enzyme’s function─one to lower the energy barrier for the phosphoryl transfer reaction and another to delay enzyme opening, maintaining it in a catalytically active, closed conformation for long enough to enable the subsequent chemical step. Our study also discovers that while each catalytic residue individually contributes to facilitating the catalysis, R36, R123, R156, R167, and D158 are organized in a tightly coordinated interaction network and collectively modulate AdK’s conformational transitions. Unlike the existing notion of product release being rate-limiting, our results suggest a mechanistic interconnection between the chemical step and the enzyme’s conformational dynamics acting as the bottleneck of the catalytic process. Our results also suggest that the enzyme’s active site has evolved to optimize the chemical reaction step while slowing down the overall opening dynamics of the enzyme.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2023
National Category
Theoretical Chemistry
Research subject
biological chemistry
Identifiers
urn:nbn:se:umu:diva-205159 (URN)10.1021/acs.jcim.2c01629 (DOI)000936859400001 ()36802243 (PubMedID)2-s2.0-85148862970 (Scopus ID)
Funder
Swedish Research Council, 2021-04513NIH (National Institutes of Health), R01GM132481
Available from: 2023-02-24 Created: 2023-02-24 Last updated: 2023-03-17Bibliographically approved
Ojeda-May, P. (2022). Exploring the dynamics of shikimate kinase through molecular mechanics. Biophysica, 2(3), 194-202
Open this publication in new window or tab >>Exploring the dynamics of shikimate kinase through molecular mechanics
2022 (English)In: Biophysica, ISSN 2673-4125, Vol. 2, no 3, p. 194-202Article in journal (Refereed) Published
Abstract [en]

Shikimate kinase (SK) enzyme is a suitable target for antimicrobial drugs as it is present in pathogenic microorganisms and absent in mammals. A complete understanding of the functioning of this enzyme can unveil novel methods to inactivate it. To do this, a clear understanding of SK performance is needed. Previously, the chemical step of SK was studied in detail, but a study of longer-term scale simulations is still missing. In the present work, we performed molecular dynamics (MD) simulations in the µs time scale that allowed us to explore further regions of the SK energy landscape than previously. Simulations were conducted on the wild-type (WT) enzyme and the R116A and R116K mutants. We analyzed the dynamics of the enzymes through standard MD tools, and we found that the global motions in the mutants were perturbed. These motions can be linked to the observed undetectable binding affinity of the WT enzyme and the R116A and R116K mutants.

Place, publisher, year, edition, pages
MDPI, 2022
Keywords
shikimate, kinase, mutants, molecular, dynamics, binding
National Category
Physical Chemistry Biophysics
Research subject
Biochemistry
Identifiers
urn:nbn:se:umu:diva-198766 (URN)10.3390/biophysica2030020 (DOI)2-s2.0-85176224716 (Scopus ID)
Available from: 2022-08-23 Created: 2022-08-23 Last updated: 2023-11-23Bibliographically approved
Bispo, J., Barbosa, J. G., Silva, P. F., Morales, C., Myllykoski, M., Ojeda-May, P., . . . Shoukourian, H. (2021). Best Practice Guide: Modern Accelerators.
Open this publication in new window or tab >>Best Practice Guide: Modern Accelerators
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2021 (English)Report (Other academic)
Publisher
p. 111
National Category
Computer Sciences
Research subject
Computer Science
Identifiers
urn:nbn:se:umu:diva-190729 (URN)
Available from: 2021-12-22 Created: 2021-12-22 Last updated: 2021-12-28Bibliographically approved
Ojeda-May, P., Ul Mushtaq, A., Rogne, P., Verma, A., Ovchinnikov, V., Grundström, C., . . . Nam, K. (2021). Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions. Biochemistry, 60(28), 2246-2258
Open this publication in new window or tab >>Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions
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2021 (English)In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 60, no 28, p. 2246-2258Article in journal (Refereed) Published
Abstract [en]

Enzymes employ a wide range of protein motions to achieve efficient catalysis of chemical reactions. While the role of collective protein motions in substrate binding, product release, and regulation of enzymatic activity is generally understood, their roles in catalytic steps per se remain uncertain. Here, molecular dynamics simulations, enzyme kinetics, X-ray crystallography, and nuclear magnetic resonance spectroscopy are combined to elucidate the catalytic mechanism of adenylate kinase and to delineate the roles of catalytic residues in catalysis and the conformational change in the enzyme. This study reveals that the motions in the active site, which occur on a time scale of picoseconds to nanoseconds, link the catalytic reaction to the slow conformational dynamics of the enzyme by modulating the free energy landscapes of subdomain motions. In particular, substantial conformational rearrangement occurs in the active site following the catalytic reaction. This rearrangement not only affects the reaction barrier but also promotes a more open conformation of the enzyme after the reaction, which then results in an accelerated opening of the enzyme compared to that of the reactant state. The results illustrate a linkage between enzymatic catalysis and collective protein motions, whereby the disparate time scales between the two processes are bridged by a cascade of intermediate-scale motion of catalytic residues modulating the free energy landscapes of the catalytic and conformational change processes.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2021
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-187197 (URN)10.1021/acs.biochem.1c00221 (DOI)000677482100003 ()34250801 (PubMedID)2-s2.0-85111203330 (Scopus ID)
Available from: 2021-09-08 Created: 2021-09-08 Last updated: 2021-09-08Bibliographically approved
Ojeda-May, P. (2021). Exploring the mechanism of shikimate kinase through quantum mechanical and molecular mechanical (QM/MM) methods. Biophysica, 1(3), 334-343
Open this publication in new window or tab >>Exploring the mechanism of shikimate kinase through quantum mechanical and molecular mechanical (QM/MM) methods
2021 (English)In: Biophysica, ISSN 2673-4125, Vol. 1, no 3, p. 334-343Article in journal (Refereed) Published
Abstract [en]

The chemical step of Shikimate Kinase Helicobacter pylori, involving the transfer of a phosphoryl group, has been studied by using quantum mechanical and molecular mechanical (QM/MM) methods. Understanding the mechanism of this chemical step, present in bacteria and other microorganisms but absent in humans, can lead to the development of novel drugs for the treatment of common diseases caused by those pathogenic organisms. Different mechanisms including associative, dissociative, and concerted have been proposed up to now but there is not a consensus on the type of pathway that the reaction follows. Herein, we found that the mechanism has features from the associative and concerted types. An analysis of the free energy landscape of the chemical step reveals that the reaction is a two-step process without a well-defined intermediate state.

Place, publisher, year, edition, pages
Basel, Switzerland: MDPI, 2021
Keywords
catalysis, shikimate, kinase, quantum, mechanical, phosphoryl, transfer
National Category
Theoretical Chemistry
Research subject
Biochemistry
Identifiers
urn:nbn:se:umu:diva-187901 (URN)10.3390/biophysica1030025 (DOI)2-s2.0-85150905581 (Scopus ID)
Available from: 2021-09-23 Created: 2021-09-23 Last updated: 2023-11-23Bibliographically approved
Arbeitman, C. R., Rojas, P., Ojeda-May, P. & Garcia, M. E. (2021). The SARS-CoV-2 spike protein is vulnerable to moderate electric fields. Nature Communications, 12(1), Article ID 5407.
Open this publication in new window or tab >>The SARS-CoV-2 spike protein is vulnerable to moderate electric fields
2021 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 12, no 1, article id 5407Article in journal (Refereed) Published
Abstract [en]

Most of the ongoing projects aimed at the development of specific therapies and vaccines against COVID-19 use the SARS-CoV-2 spike (S) protein as the main target. The binding of the spike protein with the ACE2 receptor (ACE2) of the host cell constitutes the first and key step for virus entry. During this process, the receptor binding domain (RBD) of the S protein plays an essential role, since it contains the receptor binding motif (RBM), responsible for the docking to the receptor. So far, mostly biochemical methods are being tested in order to prevent binding of the virus to ACE2. Here we show, with the help of atomistic simulations, that external electric fields of easily achievable and moderate strengths can dramatically destabilise the S protein, inducing long-lasting structural damage. One striking field-induced conformational change occurs at the level of the recognition loop L3 of the RBD where two parallel beta sheets, believed to be responsible for a high affinity to ACE2, undergo a change into an unstructured coil, which exhibits almost no binding possibilities to the ACE2 receptor. We also show that these severe structural changes upon electric-field application also occur in the mutant RBDs corresponding to the variants of concern (VOC) B.1.1.7 (UK), B.1.351 (South Africa) and P.1 (Brazil). Remarkably, while the structural flexibility of S allows the virus to improve its probability of entering the cell, it is also the origin of the surprising vulnerability of S upon application of electric fields of strengths at least two orders of magnitude smaller than those required for damaging most proteins. Our findings suggest the existence of a clean physical method to weaken the SARS-CoV-2 virus without further biochemical processing. Moreover, the effect could be used for infection prevention purposes and also to develop technologies for in-vitro structural manipulation of S. Since the method is largely unspecific, it can be suitable for application to other mutations in S, to other proteins of SARS-CoV-2 and in general to membrane proteins of other virus types.

Place, publisher, year, edition, pages
Springer Nature, 2021
National Category
Biophysics Infectious Medicine
Identifiers
urn:nbn:se:umu:diva-187769 (URN)10.1038/s41467-021-25478-7 (DOI)000700373400024 ()2-s2.0-85114892463 (Scopus ID)
Available from: 2021-09-22 Created: 2021-09-22 Last updated: 2023-09-05Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0001-9179-9441

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