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Article ; Online: Properties of water and argon clusters developed in supersonic expansions.

Klíma, Martin / Celný, David / Janek, Jiří / Kolafa, Jiří

2023 Volume 159, Issue 12

Abstract: Using adiabatic molecular dynamics coupled with the fluid dynamics equations, we model nucleation in an expanding beam of water vapor and argon on a microsecond scale. The size distribution of clusters, their temperature, and pickup cross sections in ... ...

Abstract	Using adiabatic molecular dynamics coupled with the fluid dynamics equations, we model nucleation in an expanding beam of water vapor and argon on a microsecond scale. The size distribution of clusters, their temperature, and pickup cross sections in dependence on velocity are investigated and compared to the geometric cross sections and the experiment. The clusters are warmer than the expanding gas because of the time scale of relaxation processes. We also suggest that their translational and rotational kinetic energies are modified due to evaporative cooling. The pickup cross sections determined for the final clusters using molecules of the same kind increase with decreasing velocity, still obeying the (a+bN1/3)2 law.
Language	English
Publishing date	2023-12-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0166912
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Article ; Online: Molecular Dynamics of Heterogeneous Systems on GPUs and Their Application to Nucleation in Gas Expanding to a Vacuum.

Celný, David / Klíma, Martin / Kolafa, Jiří

Journal of chemical theory and computation

2021 Volume 17, Issue 12, Page(s) 7397–7405

Abstract: Expansion of water vapor through a small orifice to a vacuum produces liquid or frozen clusters which in the experiment serve as model particles for atmospheric aerosols. Yet, there are controversies about the shape of these clusters, suggesting that the ...

Abstract	Expansion of water vapor through a small orifice to a vacuum produces liquid or frozen clusters which in the experiment serve as model particles for atmospheric aerosols. Yet, there are controversies about the shape of these clusters, suggesting that the nucleation process is not fully understood. Such questions can be answered by molecular dynamics simulations; however, they require microsecond-scale runs with thousands of molecules and accurate energy conservation. The available highly parallel codes typically utilize domain decomposition and are inefficient for heterogeneous systems as clusters in a dilute gas. In this work, we present an implementation of molecular dynamics on graphics processing units based on the Verlet list and apply it to several systems for which experimental data are available. We reproduce sufficiently sized clusters but not the experimentally observed clusters of irregular shape.
Language	English
Publishing date	2021-11-19
Publishing country	United States
Document type	Journal Article
ISSN	1549-9626
ISSN (online)	1549-9626
DOI	10.1021/acs.jctc.1c00736
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Article ; Online: Does the Sign of Charge Affect the Surface Affinity of Simple Ions?

Hantal, György / Klíma, Martin / McFegan, Louisa / Kolafa, Jiří / Jedlovszky, Pál

The journal of physical chemistry. B

2023 Volume 127, Issue 27, Page(s) 6205–6216

Abstract: The role the charge sign of simple ions plays in determining their surface affinity in aqueous solutions is investigated by computer simulation methods. For this purpose, the free surface of aqueous solutions of fictitious salts is simulated at finite ... ...

Abstract	The role the charge sign of simple ions plays in determining their surface affinity in aqueous solutions is investigated by computer simulation methods. For this purpose, the free surface of aqueous solutions of fictitious salts is simulated at finite concentration both with nonpolarizable point-charge and polarizable Gaussian-charge potential models. The salts consist of monovalent cations and anions that are, apart from the sign of their charge, identical to each other. In particular, we consider the small Na
Language	English
Publishing date	2023-07-03
Publishing country	United States
Document type	Journal Article
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.3c02641
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Article ; Online: Structural basis for RNA-cap recognition and methylation by the mpox methyltransferase VP39.

Skvara, Petr / Chalupska, Dominika / Klima, Martin / Kozic, Jan / Silhan, Jan / Boura, Evzen

Antiviral research

2023 Volume 216, Page(s) 105663

Abstract: Mpox is a zoonotic disease caused by the mpox virus (MPXV), which has gained attention due to its rapid and widespread transmission, with reports from more than 100 countries. The virus belongs to the Orthopoxvirus genus, which also includes variola ... ...

Abstract	Mpox is a zoonotic disease caused by the mpox virus (MPXV), which has gained attention due to its rapid and widespread transmission, with reports from more than 100 countries. The virus belongs to the Orthopoxvirus genus, which also includes variola virus and vaccinia virus. In poxviruses, the RNA cap is crucial for the translation and stability of viral mRNAs and also for immune evasion. This study presents the crystal structure of the mpox 2'-O-methyltransfarase VP39 in complex with a short cap-0 RNA. The RNA substrate binds to the protein without causing any significant changes to its overall fold and is held in place by a combination of electrostatic interactions, π-π stacking and hydrogen bonding. The structure also explains the mpox VP39 preference for a guanine base at the first position; it reveals that guanine forms a hydrogen bond that an adenine would not be able to form.
MeSH term(s)	Humans ; RNA Caps/metabolism ; Methylation ; Methyltransferases/chemistry ; Mpox (monkeypox) ; Binding Sites ; Viral Proteins/genetics
Chemical Substances	RNA Caps ; Methyltransferases (EC 2.1.1.-) ; Viral Proteins
Language	English
Publishing date	2023-07-07
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	306628-9
ISSN	1872-9096 ; 0166-3542
ISSN (online)	1872-9096
ISSN	0166-3542
DOI	10.1016/j.antiviral.2023.105663
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Article ; Online: Direct Molecular Dynamics Simulation of Nucleation during Supersonic Expansion of Gas to a Vacuum.

Klíma, Martin / Kolafa, Jiří

Journal of chemical theory and computation

2018 Volume 14, Issue 5, Page(s) 2332–2340

Abstract: We develop a methodology for direct molecular-level simulation of adiabatic expansion of gas through a small orifice to a vacuum. The gas attains supersonic speeds, cools, and nucleates. The proposed approach combines equations of frictionless fluid ... ...

Abstract	We develop a methodology for direct molecular-level simulation of adiabatic expansion of gas through a small orifice to a vacuum. The gas attains supersonic speeds, cools, and nucleates. The proposed approach combines equations of frictionless fluid dynamics with molecular dynamics simulation in an expanding periodic box. There are two key components of the proposed algorithm: (i) a time-reversible integrator tailored to an expanding system, and (ii) an iterative procedure employed to satisfy the condition of steady flow. For a conical nozzle (opening angle of 60°), the simulations with argon and water vapor predict cluster sizes in agreement with the experiment. Clusters of irregular shapes observed in the experiment [J. Lengyel et al. Phys. Rev. Lett. 2014, 112, 113401] are not reproduced. The role of friction, turbulence, and sonic boom originating at the sharp nozzle edge is discussed.
Language	English
Publishing date	2018-05-08
Publishing country	United States
Document type	Journal Article
ISSN	1549-9626
ISSN (online)	1549-9626
DOI	10.1021/acs.jctc.8b00066
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Article ; Online: Structural analysis of the putative SARS-CoV-2 primase complex.

Konkolova, Eva / Klima, Martin / Nencka, Radim / Boura, Evzen

Journal of structural biology

2020 Volume 211, Issue 2, Page(s) 107548

Abstract: We report the crystal structure of the SARS-CoV-2 putative primase composed of the nsp7 and nsp8 proteins. We observed a dimer of dimers (2:2 nsp7-nsp8) in the crystallographic asymmetric unit. The structure revealed a fold with a helical core of the ... ...

Abstract	We report the crystal structure of the SARS-CoV-2 putative primase composed of the nsp7 and nsp8 proteins. We observed a dimer of dimers (2:2 nsp7-nsp8) in the crystallographic asymmetric unit. The structure revealed a fold with a helical core of the heterotetramer formed by both nsp7 and nsp8 that is flanked with two symmetry-related nsp8 β-sheet subdomains. It was also revealed that two hydrophobic interfaces one of approx. 1340 Å
MeSH term(s)	Betacoronavirus/chemistry ; Binding Sites ; Coronavirus RNA-Dependent RNA Polymerase ; Crystallography, X-Ray ; DNA Primase/chemistry ; DNA Primase/metabolism ; Models, Molecular ; Multiprotein Complexes ; Protein Conformation ; Protein Multimerization ; RNA/metabolism ; SARS-CoV-2 ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/metabolism
Chemical Substances	Multiprotein Complexes ; NS8 protein, SARS-CoV-2 ; Viral Nonstructural Proteins ; RNA (63231-63-0) ; DNA Primase (EC 2.7.7.-) ; Coronavirus RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; NSP7 protein, SARS-CoV-2 (EC 2.7.7.48)
Keywords	covid19
Language	English
Publishing date	2020-06-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1032718-6
ISSN	1095-8657 ; 1047-8477
ISSN (online)	1095-8657
ISSN	1047-8477
DOI	10.1016/j.jsb.2020.107548
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Zs.A 1428: Show issues

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Article: Structural basis for hijacking of the host ACBD3 protein by bovine and porcine enteroviruses and kobuviruses

Smola, Miroslav / Horova, Vladimira / Boura, Evzen / Klima, Martin

Archives of virology. 2020 Feb., v. 165, no. 2

2020

Abstract: Picornaviruses infect a wide range of mammals including livestock such as cattle and swine. As with other picornavirus genera such as Aphthovirus, there is emerging evidence of a significant economic impact of livestock infections caused by members of ... ...

Abstract	Picornaviruses infect a wide range of mammals including livestock such as cattle and swine. As with other picornavirus genera such as Aphthovirus, there is emerging evidence of a significant economic impact of livestock infections caused by members of the genera Enterovirus and Kobuvirus. While the human-infecting enteroviruses and kobuviruses have been intensively studied during the past decades in great detail, research on livestock-infecting viruses has been mostly limited to the genomic characterization of the viral strains identified worldwide. Here, we extend our previous studies of the structure and function of the complexes composed of the non-structural 3A proteins of human-infecting enteroviruses and kobuviruses and the host ACBD3 protein and present a structural and functional characterization of the complexes of the following livestock-infecting picornaviruses: bovine enteroviruses EV-E and EV-F, porcine enterovirus EV-G, and porcine kobuvirus AiV-C. We present a series of crystal structures of these complexes and demonstrate the role of these complexes in facilitation of viral replication.
Keywords	Aichivirus C ; Aphthovirus ; Porcine enterovirus ; cattle ; economic impact ; genomics ; swine ; virus replication
Language	English
Dates of publication	2020-02
Size	p. 355-366.
Publishing place	Springer Vienna
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	7491-3
ISSN	1432-8798 ; 0304-8608
ISSN (online)	1432-8798
ISSN	0304-8608
DOI	10.1007/s00705-019-04490-9
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Coronaviral RNA-methyltransferases: function, structure and inhibition.

Nencka, Radim / Silhan, Jan / Klima, Martin / Otava, Tomas / Kocek, Hugo / Krafcikova, Petra / Boura, Evzen

Nucleic acids research

2022 Volume 50, Issue 2, Page(s) 635–650

Abstract: Coronaviral methyltransferases (MTases), nsp10/16 and nsp14, catalyze the last two steps of viral RNA-cap creation that takes place in cytoplasm. This cap is essential for the stability of viral RNA and, most importantly, for the evasion of innate immune ...

Abstract	Coronaviral methyltransferases (MTases), nsp10/16 and nsp14, catalyze the last two steps of viral RNA-cap creation that takes place in cytoplasm. This cap is essential for the stability of viral RNA and, most importantly, for the evasion of innate immune system. Non-capped RNA is recognized by innate immunity which leads to its degradation and the activation of antiviral immunity. As a result, both coronaviral MTases are in the center of scientific scrutiny. Recently, X-ray and cryo-EM structures of both enzymes were solved even in complex with other parts of the viral replication complex. High-throughput screening as well as structure-guided inhibitor design have led to the discovery of their potent inhibitors. Here, we critically summarize the tremendous advancement of the coronaviral MTase field since the beginning of COVID pandemic.
MeSH term(s)	Amino Acid Sequence ; Amino Acids/chemistry ; Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Binding Sites ; Coronavirus/drug effects ; Coronavirus/enzymology ; Coronavirus/genetics ; Drug Discovery ; Humans ; Methylation ; Methyltransferases/antagonists & inhibitors ; Methyltransferases/chemistry ; Methyltransferases/metabolism ; Models, Molecular ; Molecular Conformation ; Molecular Structure ; Protein Binding ; RNA, Viral/chemistry ; RNA, Viral/genetics ; RNA, Viral/metabolism ; Structure-Activity Relationship
Chemical Substances	Amino Acids ; Antiviral Agents ; RNA, Viral ; Methyltransferases (EC 2.1.1.-)
Language	English
Publishing date	2022-01-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkab1279
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Article ; Online: Crystal Structure of the ORP8 Lipid Transport ORD Domain: Model of Lipid Transport.

Eisenreichova, Andrea / Klima, Martin / Anila, Midhun Mohan / Koukalova, Alena / Humpolickova, Jana / Różycki, Bartosz / Boura, Evzen

Cells

2023 Volume 12, Issue 15

Abstract: ORPs are lipid-transport proteins belonging to the oxysterol-binding protein family. They facilitate the transfer of lipids between different intracellular membranes, such as the ER and plasma membrane. We have solved the crystal structure of the ORP8 ... ...

Abstract	ORPs are lipid-transport proteins belonging to the oxysterol-binding protein family. They facilitate the transfer of lipids between different intracellular membranes, such as the ER and plasma membrane. We have solved the crystal structure of the ORP8 lipid transport domain (ORD8). The ORD8 exhibited a β-barrel fold composed of anti-parallel β-strands, with three α-helices replacing β-strands on one side. This mixed alpha-beta structure was consistent with previously solved structures of ORP2 and ORP3. A large cavity (≈1860 Å
MeSH term(s)	Biological Transport ; Carrier Proteins/metabolism ; Binding Sites ; Cell Membrane/metabolism ; Lipids/chemistry
Chemical Substances	Carrier Proteins ; Lipids
Language	English
Publishing date	2023-07-31
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells12151974
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Article ; Online: Discovery and structural characterization of monkeypox virus methyltransferase VP39 inhibitors reveal similarities to SARS-CoV-2 nsp14 methyltransferase.

Silhan, Jan / Klima, Martin / Otava, Tomas / Skvara, Petr / Chalupska, Dominika / Chalupsky, Karel / Kozic, Jan / Nencka, Radim / Boura, Evzen

Nature communications

2023 Volume 14, Issue 1, Page(s) 2259

Abstract: Monkeypox is a disease with pandemic potential. It is caused by the monkeypox virus (MPXV), a double-stranded DNA virus from the Poxviridae family, that replicates in the cytoplasm and must encode for its own RNA processing machinery including the ... ...

Abstract	Monkeypox is a disease with pandemic potential. It is caused by the monkeypox virus (MPXV), a double-stranded DNA virus from the Poxviridae family, that replicates in the cytoplasm and must encode for its own RNA processing machinery including the capping machinery. Here, we present crystal structures of its 2'-O-RNA methyltransferase (MTase) VP39 in complex with the pan-MTase inhibitor sinefungin and a series of inhibitors that were discovered based on it. A comparison of this 2'-O-RNA MTase with enzymes from unrelated single-stranded RNA viruses (SARS-CoV-2 and Zika) reveals a conserved sinefungin binding mode, implicating that a single inhibitor could be used against unrelated viral families. Indeed, several of our inhibitors such as TO507 also inhibit the coronaviral nsp14 MTase.
MeSH term(s)	Humans ; Methyltransferases/metabolism ; SARS-CoV-2/genetics ; Monkeypox virus/genetics ; Monkeypox virus/metabolism ; COVID-19 ; Viral Nonstructural Proteins/chemistry ; RNA ; Zika Virus/genetics ; Zika Virus Infection ; RNA, Viral/genetics
Chemical Substances	Methyltransferases (EC 2.1.1.-) ; Viral Nonstructural Proteins ; RNA (63231-63-0) ; RNA, Viral
Language	English
Publishing date	2023-04-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-38019-1
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