1
|
Wang K, Molteni C, Haynes PD. Localized Soft Vibrational Modes and Coherent Structural Phase Transformations in Rutile TiO 2 Nanoparticles under Negative Pressure. Nano Lett 2022; 22:5922-5928. [PMID: 35797495 PMCID: PMC9335867 DOI: 10.1021/acs.nanolett.2c01939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We study the effect of size on the vibrational modes and frequencies of nanoparticles, by applying a newly developed, robust, and efficient first-principles-based method that we present in outline. We focus on rutile TiO2, a technologically important material whose bulk exhibits a softening of a transverse acoustic mode close to q=(12,12,14), which becomes unstable with the application of negative pressure. We demonstrate that, under these conditions, nanoparticles above a critical size exhibit unstable localized modes and we calculate their characteristic localization length and decomposition with respect to bulk phonons. We propose that such localized soft modes could initiate coherent structural phase transformations in small nanoparticles above a critical size.
Collapse
Affiliation(s)
- Kang Wang
- Imperial
College London, Department of Materials, Exhibition Road, London SW7 2AZ, U.K.
| | - Carla Molteni
- King’s
College London, Department of Physics, Strand, London WC2R 2LS, U.K.
| | - Peter D. Haynes
- Imperial
College London, Department of Materials, Exhibition Road, London SW7 2AZ, U.K.
| |
Collapse
|
2
|
Shi J, Fulford M, Li H, Marzook M, Reisjalali M, Salvalaglio M, Molteni C. Investigating the quasi-liquid layer on ice surfaces: a comparison of order parameters. Phys Chem Chem Phys 2022; 24:12476-12487. [PMID: 35576067 DOI: 10.1039/d2cp00752e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ice surfaces are characterized by pre-melted quasi-liquid layers (QLLs), which mediate both crystal growth processes and interactions with external agents. Understanding QLLs at the molecular level is necessary to unravel the mechanisms of ice crystal formation. Computational studies of the QLLs heavily rely on the accuracy of the methods employed for identifying the local molecular environment and arrangements, discriminating between solid-like and liquid-like water molecules. Here we compare the results obtained using different order parameters to characterize the QLLs on hexagonal ice (Ih) and cubic ice (Ic) model surfaces investigated with molecular dynamics (MD) simulations in a range of temperatures. For the classification task, in addition to the traditional Steinhardt order parameters in different flavours, we select an entropy fingerprint and a deep learning neural network approach (DeepIce), which are conceptually different methodologies. We find that all the analysis methods give qualitatively similar trends for the behaviours of the QLLs on ice surfaces with temperature, with some subtle differences in the classification sensitivity limited to the solid-liquid interface. The thickness of QLLs on the ice surface increases gradually as the temperature increases. The trends of the QLL size and of the values of the order parameters as a function of temperature for the different facets may be linked to surface growth rates which, in turn, affect crystal morphologies at lower vapour pressure. The choice of the order parameter can be therefore informed by computational convenience except in cases where a very accurate determination of the liquid-solid interface is important.
Collapse
Affiliation(s)
- Jihong Shi
- Department of Physics, King's College London, Strand, London WC2R 2LS, UK.
| | - Maxwell Fulford
- Department of Physics, King's College London, Strand, London WC2R 2LS, UK.
| | - Hui Li
- Department of Physics, King's College London, Strand, London WC2R 2LS, UK.
| | - Mariam Marzook
- Department of Physics, King's College London, Strand, London WC2R 2LS, UK.
| | - Maryam Reisjalali
- Department of Physics, King's College London, Strand, London WC2R 2LS, UK.
| | - Matteo Salvalaglio
- Department of Chemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
| | - Carla Molteni
- Department of Physics, King's College London, Strand, London WC2R 2LS, UK.
| |
Collapse
|
3
|
Badaoui M, Buigues PJ, Berta D, Mandana GM, Gu H, Földes T, Dickson CJ, Hornak V, Kato M, Molteni C, Parsons S, Rosta E. Combined Free-Energy Calculation and Machine Learning Methods for Understanding Ligand Unbinding Kinetics. J Chem Theory Comput 2022; 18:2543-2555. [PMID: 35195418 PMCID: PMC9097281 DOI: 10.1021/acs.jctc.1c00924] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
The
determination of drug residence times, which define the time
an inhibitor is in complex with its target, is a fundamental part
of the drug discovery process. Synthesis and experimental measurements
of kinetic rate constants are, however, expensive and time consuming.
In this work, we aimed to obtain drug residence times computationally.
Furthermore, we propose a novel algorithm to identify molecular design
objectives based on ligand unbinding kinetics. We designed an enhanced
sampling technique to accurately predict the free-energy profiles
of the ligand unbinding process, focusing on the free-energy barrier
for unbinding. Our method first identifies unbinding paths determining
a corresponding set of internal coordinates (ICs) that form contacts
between the protein and the ligand; it then iteratively updates these
interactions during a series of biased molecular dynamics (MD) simulations
to reveal the ICs that are important for the whole of the unbinding
process. Subsequently, we performed finite-temperature string simulations
to obtain the free-energy barrier for unbinding using the set of ICs
as a complex reaction coordinate. Importantly, we also aimed to enable
the further design of drugs focusing on improved residence times.
To this end, we developed a supervised machine learning (ML) approach
with inputs from unbiased “downhill” trajectories initiated
near the transition state (TS) ensemble of the string unbinding path.
We demonstrate that our ML method can identify key ligand–protein
interactions driving the system through the TS. Some of the most important
drugs for cancer treatment are kinase inhibitors. One of these kinase
targets is cyclin-dependent kinase 2 (CDK2), an appealing target for
anticancer drug development. Here, we tested our method using two
different CDK2 inhibitors for the potential further development of
these compounds. We compared the free-energy barriers obtained from
our calculations with those observed in available experimental data.
We highlighted important interactions at the distal ends of the ligands
that can be targeted for improved residence times. Our method provides
a new tool to determine unbinding rates and to identify key structural
features of the inhibitors that can be used as starting points for
novel design strategies in drug discovery.
Collapse
Affiliation(s)
- Magd Badaoui
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom.,Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Pedro J Buigues
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Dénes Berta
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Gaurav M Mandana
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
| | - Hankang Gu
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Tamás Földes
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Callum J Dickson
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Viktor Hornak
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Mitsunori Kato
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Carla Molteni
- Department of Physics, King's College London, London WC2R 2LS, United Kingdom
| | - Simon Parsons
- School of Computer Science, University of Lincoln, Lincoln LN6 7TS, United Kingdom
| | - Edina Rosta
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom.,Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| |
Collapse
|
4
|
Rossi F, Crnjar A, Comitani F, Feliciano R, Jahn L, Malim G, Southgate L, Kay E, Oakey R, Buggs R, Moir A, Kistler L, Rodriguez Mateos A, Molteni C, Schulz R. Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling. PLoS One 2021; 16:e0254971. [PMID: 34793449 PMCID: PMC8601515 DOI: 10.1371/journal.pone.0254971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/27/2021] [Indexed: 11/19/2022] Open
Abstract
Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability of oak heartwood and hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies of the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. In this study, we aimed to establish protocols for the extraction of DNA, the high-throughput sequencing of whole-genome DNA libraries (WGS) and the profiling of DNA methylation by whole-genome bisulfite sequencing (WGBS) for oak (Quercus robur) heartwood drill cores taken from the trunks of living standing trees spanning the AD 1776-2014 time period. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. Whole-genome and DNA methylome library preparation and sequencing consistently failed for oak heartwood samples more than 100 and 50 years of age, respectively. DNA fragmentation increased with sample age and was exacerbated by the additional bisulfite treatment step during methylome library preparation. Relative coverage of the non-repetitive portion of the oak genome was sparse. These results suggest that quantitative methylome studies of oak hardwood will likely be limited to relatively recent samples and will require a high sequencing depth to achieve sufficient genome coverage.
Collapse
Affiliation(s)
- Federico Rossi
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Alessandro Crnjar
- Department of Physics, King’s College London, London, United Kingdom
| | - Federico Comitani
- Department of Chemistry, University College London, London, United Kingdom
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rodrigo Feliciano
- Department of Nutrition, King’s College London, London, United Kingdom
- Division of Cardiology, Pulmonology and Vascular Medicine, University of Dusseldorf, Dusseldorf, Germany
| | - Leonie Jahn
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens, Lyngby, Denmark
| | - George Malim
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Laura Southgate
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Emily Kay
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
- CRUK Beatson Institute, Glasgow, United Kingdom
| | - Rebecca Oakey
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Richard Buggs
- Department of Natural Capital and Plant Health, Royal Botanical Gardens, Richmond, United Kingdom
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Andy Moir
- Tree-Ring Services Limited, Mitcheldean, United Kingdom
| | - Logan Kistler
- Department of Anthropology, National Museum Of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | | | - Carla Molteni
- Department of Physics, King’s College London, London, United Kingdom
| | - Reiner Schulz
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| |
Collapse
|
5
|
Nin-Hill A, Mueller NPF, Molteni C, Rovira C, Alfonso-Prieto M. Photopharmacology of Ion Channels through the Light of the Computational Microscope. Int J Mol Sci 2021; 22:12072. [PMID: 34769504 PMCID: PMC8584574 DOI: 10.3390/ijms222112072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022] Open
Abstract
The optical control and investigation of neuronal activity can be achieved and carried out with photoswitchable ligands. Such compounds are designed in a modular fashion, combining a known ligand of the target protein and a photochromic group, as well as an additional electrophilic group for tethered ligands. Such a design strategy can be optimized by including structural data. In addition to experimental structures, computational methods (such as homology modeling, molecular docking, molecular dynamics and enhanced sampling techniques) can provide structural insights to guide photoswitch design and to understand the observed light-regulated effects. This review discusses the application of such structure-based computational methods to photoswitchable ligands targeting voltage- and ligand-gated ion channels. Structural mapping may help identify residues near the ligand binding pocket amenable for mutagenesis and covalent attachment. Modeling of the target protein in a complex with the photoswitchable ligand can shed light on the different activities of the two photoswitch isomers and the effect of site-directed mutations on photoswitch binding, as well as ion channel subtype selectivity. The examples presented here show how the integration of computational modeling with experimental data can greatly facilitate photoswitchable ligand design and optimization. Recent advances in structural biology, both experimental and computational, are expected to further strengthen this rational photopharmacology approach.
Collapse
Affiliation(s)
- Alba Nin-Hill
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain; (A.N.-H.); (C.R.)
| | - Nicolas Pierre Friedrich Mueller
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany;
- Faculty of Mathematics and Natural Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Carla Molteni
- Physics Department, King’s College London, London WC2R 2LS, UK;
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain; (A.N.-H.); (C.R.)
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain
| | - Mercedes Alfonso-Prieto
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany;
- Cécile and Oskar Vogt Institute for Brain Research, University Hospital Düsseldorf, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| |
Collapse
|
6
|
Taramasso L, De Vito A, Ricci ED, Orofino G, Squillace N, Menzaghi B, Molteni C, Gulminetti R, De Socio GV, Pellicanò GF, Sarchi E, Celesia BM, Calza L, Rusconi S, Valsecchi L, Martinelli CV, Cascio A, Maggi P, Vichi F, Angioni G, Guadagnino G, Cenderello G, Dentone C, Bandera A, Falasca K, Bonfanti P, Di Biagio A, Madeddu G, Bonfanti P, Di Biagio A, Ricci E, Sarchi E, Chichino G, Bolla C, Bellacosa C, Angarano G, Saracino A, Calza L, Menzaghi B, Farinazzo M, Angioni G, Bruno G, Celesia BM, Falasca K, Mastroianni A, Guadagnino G, Vichi F, Salomoni E, Martinelli C, Di Biagio A, Dentone C, Taramasso L, Bassetti M, Cenderello G, Molteni C, Piconi S, Pellicanò GF, Nunnari G, Valsecchi L, Cordier L, Parisini S, Rizzardini G, Rusconi S, Conti F, Bandera A, Gori A, Motta D, Puoti M, Bonfanti P, Squillace N, Migliorino GM, Maggi P, Martini S, Cascio A, Trizzino M, Gulminetti R, Pagnucco L, De Socio GV, Nofri M, Francisci D, Cibelli D, Parruti G, Madeddu G, Mameli MS, Orofino G, Guastavigna M. Durability of Dolutegravir-Based Regimens: A 5-Year Prospective Observational Study. AIDS Patient Care STDS 2021; 35:342-353. [PMID: 34524918 DOI: 10.1089/apc.2021.0089] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
This study evaluates the frequency and causes of dolutegravir (DTG) discontinuation along 5 years of follow-up, in both antiretroviral treatment (ART)-naive and experienced people living with HIV (PLWH). This is a prospective multi-center cohort study enrolling PLWH on DTG from July 2014 until November 2020. DTG-durability was investigated using the Kaplan-Meier survival curve. The Cox proportional-hazards model was used for estimating the hazard ratio (HR) of DTG discontinuation for any cause, and for adverse events (AEs). Nine hundred sixty-three PLWH were included, 25.3% were women and 28.0% were ART-naive. Discontinuations for any causes were 10.1 [95% confidence interval (95% CI) 8.9-11.5] per 100 person-years, similar in most regimens, with the apparent exception of tenofovir alafenamide/emtricitabine+DTG (p < 0.0001). In the multivariable Cox regression model, non-Caucasian ethnicity, age ≥50 years, and lower estimated glomerular filtration rate (eGFR) were associated with a higher probability of DTG interruption. The incidence rate of virological failure was 0.4 (95% CI 0.2-0.7) per 100 person-years, while the estimated discontinuation rate for AEs was 4.0 (3.2-4.9) per 100 person-years. Thirty-four DTG interruptions were due to grade ≥3 events (10 central nervous system, 6 hypersensitivity, 3 renal, 3 myalgia/asthenia, 3 abdominal pain, 2 gastrointestinal, and 7 other events). People with lower body mass index, age ≥50 years, and lower eGFR were at higher risk of AEs, while dual combinations were protective (HR 0.41 compared with abacavir/lamivudine/DTG, 95% CI 0.22-0.77). In this prospective observational study, we found high DTG durability and a low rate of virological failures. Dual therapies seemed protective toward AEs and might be considered, when feasible, a suitable option to minimize drug interactions and improve tolerability.
Collapse
Affiliation(s)
- Lucia Taramasso
- Infectious Disease Clinic, IRCCS Policlinico San Martino Hospital, Genoa, Italy
| | - Andrea De Vito
- Unit of Infectious and Tropical Diseases, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | | | - Giancarlo Orofino
- Unit of Infectious Diseases, “Divisione A”, Amedeo di Savoia Hospital, Torino, Italy
| | - Nicola Squillace
- Infectious Diseases Clinic, San Gerardo Hospital, University of Milano-Bicocca, Monza, Italy
| | - Barbara Menzaghi
- Unit of Infectious Diseases, ASST della Valle Olona, Busto Arsizio Hospital, Busto Arsizio, Italy
| | - Chiara Molteni
- Infectious Disease Unit, Ospedale A. Manzoni, Lecco, Italy
| | - Roberto Gulminetti
- Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
| | - Giuseppe Vittorio De Socio
- Clinic of Infectious Diseases, Department of Medicine 2, Azienda Ospedaliera di Perugia, Santa Maria Hospital, Perugia, Italy
| | - Giovanni Francesco Pellicanò
- Unit of Infectious Diseases, Department of Human Pathology of the Adult and the Developmental Age ‘G. Barresi’, University of Messina, Messina, Italy
| | - Eleonora Sarchi
- Infectious Diseases Unit, SS. Antonio e Biagio e Cesare Arrigo Hospital, Alessandria, Italy
| | | | - Leonardo Calza
- Department of Medical and Surgical Sciences, Clinics of Infectious Diseases, S. Orsola-Malpighi Hospital, “Alma Mater Studiorum” University of Bologna, Bologna, Italy
| | - Stefano Rusconi
- Infectious Diseases Unit, Department of Biomedical and Clinical Sciences ‘Luigi Sacco’, Università degli Studi di Milano, Milan, Italy
| | - Laura Valsecchi
- Infectious Disease Unit (I Divisione), ASST Fatebenefratelli Sacco, Milan, Italy
| | | | - Antonio Cascio
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Paolo Maggi
- Department of Infectious Disease, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Francesca Vichi
- Infectious Diseases Department, SOC 1, USLCENTROFIRENZE, Santa Maria Annunziata Hospital, Florence, Italy
| | | | - Giuliana Guadagnino
- Department of Infectious and Tropical Diseases, St. Annunziata Hospital, Cosenza, Italy
| | | | - Chiara Dentone
- Infectious Disease Clinic, IRCCS Policlinico San Martino Hospital, Genoa, Italy
| | - Alessandra Bandera
- Infectious Disease Unit, Department of Internal Medicine, Fondazione IRCCS Ca’ Granda, University of Milan, Ospedale Maggiore Policlinico, Milan, Italy
| | - Katia Falasca
- Clinic of Infectious Diseases, Department of Medicine and Science of Aging, University ‘G. d'Annunzio’ Chieti-Pescara, Chieti, Italy
| | - Paolo Bonfanti
- Infectious Diseases Clinic, San Gerardo Hospital, University of Milano-Bicocca, Monza, Italy
| | - Antonio Di Biagio
- Infectious Diseases Clinic, Department of Health Sciences, University of Genoa, San Martino Hospital-IRCCS, Genoa, Italy
| | - Giordano Madeddu
- Unit of Infectious and Tropical Diseases, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Vyšniauskas A, Cornell B, Sherin PS, Maleckaitė K, Kubánková M, Izquierdo MA, Vu TT, Volkova YA, Budynina EM, Molteni C, Kuimova MK. Cyclopropyl Substituents Transform the Viscosity-Sensitive BODIPY Molecular Rotor into a Temperature Sensor. ACS Sens 2021; 6:2158-2167. [PMID: 34060823 DOI: 10.1021/acssensors.0c02275] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A quantitative fluorescent probe that responds to changes in temperature is highly desirable for studies of biological environments, particularly in cellulo. Here, we report new cell-permeable fluorescence probes based on the BODIPY moiety that respond to environmental temperature. The new probes were developed on the basis of a well-established BODIPY-based viscosity probe by functionalization with cyclopropyl substituents at α and β positions of the BODIPY core. In contrast to the parent BODIPY fluorophore, α-cyclopropyl-substituted fluorophore displays temperature-dependent time-resolved fluorescence decays showing greatly diminished viscosity dependence, making it an attractive sensor to be used with fluorescence lifetime imaging microscopy (FLIM). We performed theoretical calculations that help rationalize the effect of the cyclopropyl substituents on the photophysical behavior of the new BODIPYs. In summary, we designed an attractive new quantitative FLIM-based temperature probe that can be used for temperature sensing in live cells.
Collapse
Affiliation(s)
- Aurimas Vyšniauskas
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Imperial College London, Exhibition Road, London W12 0BZ, U.K
- Center of Physical Sciences and Technology, Saulėtekio av. 3, Vilnius 10257, Lithuania
| | - Bethan Cornell
- Physics Department, King’s College London, Strand, London WC2R 2LS, U.K
| | - Peter S. Sherin
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Imperial College London, Exhibition Road, London W12 0BZ, U.K
| | - Karolina Maleckaitė
- Center of Physical Sciences and Technology, Saulėtekio av. 3, Vilnius 10257, Lithuania
| | - Markéta Kubánková
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Imperial College London, Exhibition Road, London W12 0BZ, U.K
| | - Maria Angeles Izquierdo
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Imperial College London, Exhibition Road, London W12 0BZ, U.K
| | - Thanh Truc Vu
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Imperial College London, Exhibition Road, London W12 0BZ, U.K
| | - Yulia A. Volkova
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Imperial College London, Exhibition Road, London W12 0BZ, U.K
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky pr. 47, Moscow 119991, Russia
| | - Ekaterina M. Budynina
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Imperial College London, Exhibition Road, London W12 0BZ, U.K
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1-3, Moscow 119991, Russia
| | - Carla Molteni
- Physics Department, King’s College London, Strand, London WC2R 2LS, U.K
| | - Marina K. Kuimova
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Imperial College London, Exhibition Road, London W12 0BZ, U.K
| |
Collapse
|
8
|
Crnjar A, Mesoy SM, Lummis SCR, Molteni C. A Single Mutation in the Outer Lipid-Facing Helix of a Pentameric Ligand-Gated Ion Channel Affects Channel Function Through a Radially-Propagating Mechanism. Front Mol Biosci 2021; 8:644720. [PMID: 33996899 PMCID: PMC8119899 DOI: 10.3389/fmolb.2021.644720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) mediate fast synaptic transmission and are crucial drug targets. Their gating mechanism is triggered by ligand binding in the extracellular domain that culminates in the opening of a hydrophobic gate in the transmembrane domain. This domain is made of four α-helices (M1 to M4). Recently the outer lipid-facing helix (M4) has been shown to be key to receptor function, however its role in channel opening is still poorly understood. It could act through its neighboring helices (M1/M3), or via the M4 tip interacting with the pivotal Cys-loop in the extracellular domain. Mutation of a single M4 tyrosine (Y441) to alanine renders one pLGIC-the 5-HT3A receptor-unable to function despite robust ligand binding. Using Y441A as a proxy for M4 function, we here predict likely paths of Y441 action using molecular dynamics, and test these predictions with functional assays of mutant receptors in HEK cells and Xenopus oocytes using fluorescent membrane potential sensitive dye and two-electrode voltage clamp respectively. We show that Y441 does not act via the M4 tip or Cys-loop, but instead connects radially through M1 to a residue near the ion channel hydrophobic gate on the pore-lining helix M2. This demonstrates the active role of the M4 helix in channel opening.
Collapse
Affiliation(s)
| | - Susanne M. Mesoy
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Sarah C. R. Lummis
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Carla Molteni
- Physics Department, King's College London, London, United Kingdom
| |
Collapse
|
9
|
Abstract
The protein β2-microglobulin can aggregate in insoluble amyloid fibrils. By relying on extensive sampling simulations, we study the Pro32 isomerization as a possible triggering factor leading to structural modifications in β2-m.
Collapse
Affiliation(s)
| | - Jacopo Fregoni
- CNR-Nano S3
- Modena
- Italy
- Department of Chemical Sciences
- University of Padova
| | - Carla Molteni
- Department of Physics
- King's College London
- Strand
- London WC2R 2LS
- UK
| | - Stefano Corni
- CNR-Nano S3
- Modena
- Italy
- Department of Chemical Sciences
- University of Padova
| |
Collapse
|
10
|
Steinmark IE, Chung PH, Ziolek RM, Cornell B, Smith P, Levitt JA, Tregidgo C, Molteni C, Yahioglu G, Lorenz CD, Suhling K. Time-Resolved Fluorescence Anisotropy of a Molecular Rotor Resolves Microscopic Viscosity Parameters in Complex Environments. Small 2020; 16:e1907139. [PMID: 32363742 DOI: 10.1002/smll.201907139] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/14/2020] [Accepted: 03/06/2020] [Indexed: 06/11/2023]
Abstract
Understanding viscosity in complex environments remains a largely unanswered question despite its importance in determining reaction rates in vivo. Here, time-resolved fluorescence anisotropy imaging (TR-FAIM) is combined with fluorescent molecular rotors (FMRs) to simultaneously determine two non-equivalent viscosity-related parameters in complex heterogeneous environments. The parameters, FMR rotational correlation time and lifetime, are extracted from fluorescence anisotropy decays, which in heterogeneous environments show dip-and-rise behavior due to multiple dye populations. Decays of this kind are found both in artificially constructed adiposomes and in live cell lipid droplet organelles. Molecular dynamics simulations are used to assign each population to nano-environments within the lipid systems. The less viscous population corresponds to the state showing an average 25° tilt to the lipid membrane normal, and the more viscous population to the state showing an average 55° tilt. This combined experimental and simulation approach enables a comprehensive description of the FMR probe behavior within viscous nano-environments in complex, biological systems.
Collapse
Affiliation(s)
| | | | | | | | - Paul Smith
- Department of Physics, King's College London, UK
| | - James A Levitt
- Randall Centre for Cell & Molecular Biophysics, King's College London, UK
| | - Carolyn Tregidgo
- Department of Physics, King's College London, UK
- Genomics England, London, EC1M 6BQ, UK
| | | | | | | | | |
Collapse
|
11
|
Crnjar A, Comitani F, Melis C, Molteni C. Mutagenesis computer experiments in pentameric ligand-gated ion channels: the role of simulation tools with different resolution. Interface Focus 2019; 9:20180067. [PMID: 31065340 PMCID: PMC6501341 DOI: 10.1098/rsfs.2018.0067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2019] [Indexed: 12/21/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) are an important class of widely expressed membrane neuroreceptors, which play a crucial role in fast synaptic communications and are involved in several neurological conditions. They are activated by the binding of neurotransmitters, which trigger the transmission of an electrical signal via facilitated ion flux. They can also be activated, inhibited or modulated by a number of drugs. Mutagenesis electrophysiology experiments, with natural or unnatural amino acids, have provided a large body of functional data that, together with emerging structural information from X-ray spectroscopy and cryo-electron microscopy, are helping unravel the complex working mechanisms of these neuroreceptors. Computer simulations are complementing these mutagenesis experiments, with insights at various levels of accuracy and resolution. Here, we review how a selection of computational tools, including first principles methods, classical molecular dynamics and enhanced sampling techniques, are contributing to construct a picture of how pLGICs function and can be pharmacologically targeted to treat the disorders they are responsible for.
Collapse
Affiliation(s)
- Alessandro Crnjar
- King’s College London, Department of Physics, Strand, London WC2R 2LS, UK
| | - Federico Comitani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Claudio Melis
- Universitá degli Studi di Cagliari, Complesso Universitario di Monserrato, Dipartimento di Fisica, S.P. Monserrato-Sestu Km 0,700, Monserrato (CA) 09042, Italy
| | - Carla Molteni
- King’s College London, Department of Physics, Strand, London WC2R 2LS, UK
| |
Collapse
|
12
|
Affiliation(s)
- Maxwell Fulford
- Department of Physics, King’s College London, Strand, London WC2R 2LS, United Kingdom
| | - Matteo Salvalaglio
- Department of Chemical Engineering, University College London, Torrington Place, London WC1E 7JE, United Kingdom
| | - Carla Molteni
- Department of Physics, King’s College London, Strand, London WC2R 2LS, United Kingdom
| |
Collapse
|
13
|
Crnjar A, Comitani F, Hester W, Molteni C. Trans- Cis Proline Switches in a Pentameric Ligand-Gated Ion Channel: How They Are Affected by and How They Affect the Biomolecular Environment. J Phys Chem Lett 2019; 10:694-700. [PMID: 30668119 DOI: 10.1021/acs.jpclett.8b03431] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pentameric ligand-gated ion channels (pLGICs) are important neuroreceptors, embedded in neuronal membranes, that mediate fast synaptic transmission. The molecular details of their working mechanisms have still to be fully unravelled due to their complexity and limited structural information available. Here we focus on a potential molecular switch in a prototypical pLGIC, the serotonin-activated 5-HT3 receptor, consisting of the trans- cis isomerization of a proline at the interface between the extracellular and transmembrane domain. Mutagenesis electrophysiology experiments previously showed that if such isomerization could not take place, the channel would not open, but the hypothetical role of this mechanism as key to channel gating is still debated. We investigate this switch within the receptor with molecular dynamics and enhanced sampling simulations. We analyze how the isomerization free energy landscape is affected by the receptor environment in comparison to simplified models. Moreover, we reveal how the isomerization, in turn, affects the structural and electrostatic properties of the receptor at the extracellular-transmembrane domain interface, e.g., by tuning the ion selectivity filter.
Collapse
Affiliation(s)
- Alessandro Crnjar
- Physics Department , King's College London , Strand, London WC2R 2LS , United Kingdom
| | - Federico Comitani
- Physics Department , King's College London , Strand, London WC2R 2LS , United Kingdom
- Chemistry Department , University College London , Gower Street , London WC1E 6BT , United Kingdom
| | - William Hester
- Physics Department , King's College London , Strand, London WC2R 2LS , United Kingdom
| | - Carla Molteni
- Physics Department , King's College London , Strand, London WC2R 2LS , United Kingdom
| |
Collapse
|
14
|
Badaoui M, Kells A, Molteni C, Dickson CJ, Hornak V, Rosta E. Calculating Kinetic Rates and Membrane Permeability from Biased Simulations. J Phys Chem B 2018; 122:11571-11578. [DOI: 10.1021/acs.jpcb.8b07442] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Magd Badaoui
- Department of Chemistry, King’s College London, SE1 1DB London, United Kingdom
| | - Adam Kells
- Department of Chemistry, King’s College London, SE1 1DB London, United Kingdom
| | - Carla Molteni
- Department of Physics, King’s College London, WC2R 2LS London, United Kingdom
| | - Callum J. Dickson
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Mass Ave., Cambridge, Massachusetts 02139, United States
| | - Viktor Hornak
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Mass Ave., Cambridge, Massachusetts 02139, United States
| | - Edina Rosta
- Department of Chemistry, King’s College London, SE1 1DB London, United Kingdom
| |
Collapse
|
15
|
Comitani F, Rossi K, Ceriotti M, Sanz ME, Molteni C. Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution. J Chem Phys 2017; 146:145102. [DOI: 10.1063/1.4979519] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Federico Comitani
- Department of Physics, King’s College London, Strand, London WC2R 2LS, United Kingdom
| | - Kevin Rossi
- Department of Physics, King’s College London, Strand, London WC2R 2LS, United Kingdom
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - M. Eugenia Sanz
- Department of Chemistry, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Carla Molteni
- Department of Physics, King’s College London, Strand, London WC2R 2LS, United Kingdom
| |
Collapse
|
16
|
Corsini NRC, Hine NDM, Haynes PD, Molteni C. Unravelling the Roles of Size, Ligands, and Pressure in the Piezochromic Properties of CdS Nanocrystals. Nano Lett 2017; 17:1042-1048. [PMID: 28128961 DOI: 10.1021/acs.nanolett.6b04461] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Understanding the effects of pressure-induced deformations on the optoelectronic properties of nanomaterials is important not only from the fundamental point of view but also for potential applications such as stress sensors and electromechanical devices. Here, we describe the novel insights into these piezochromic effects gained from using a linear-scaling density functional theory framework and an electronic enthalpy scheme, which allow us to accurately characterize the electronic structure of CdS nanocrystals with a zincblende-like core of experimentally relevant size. In particular, we focus on unravelling the complex interplay of size and surface (phenyl) ligands with pressure. We show that pressure-induced deformations are not simple isotropic scaling of the original structures and that the change in HOMO-LUMO gap with pressure results from two competing factors: (i) a bulk-like linear increase due to compression, which is offset by (ii) distortions and disorder and, to a lesser extent, orbital hybridization induced by ligands affecting the frontier orbitals. Moreover, we observe that the main peak in the optical absorption spectra is systematically red-shifted or blue-shifted, as pressure is increased up to 5 GPa, depending on the presence or absence of phenyl ligands. These heavily hybridize the frontier orbitals, causing a reduction in overlap and oscillator strength, so that at zero pressure, the lowest energy transition involves deeper hole orbitals than in the case of hydrogen-capped nanocrystals; the application of pressure induces greater delocalization over the whole nanocrystals bringing the frontier hole orbitals into play and resulting in an unexpected red shift for the phenyl-capped nanocrystals, in part caused by distortions. In response to a growing interest in relatively small nanocrystals that can be difficult to accurately characterize with experimental techniques, this work exemplifies the detailed understanding of structure-property relationships under pressure that can be obtained for realistic nanocrystals with state-of-the-art first-principles methods and used for the characterization and design of devices based on these and similar nanomaterials.
Collapse
Affiliation(s)
| | - Nicholas D M Hine
- Department of Physics, University of Warwick , Coventry CV4 7AL, U.K
| | | | - Carla Molteni
- Department of Physics, King's College London , Strand, London WC2R 2LS, U.K
| |
Collapse
|
17
|
Comitani F, Limongelli V, Molteni C. The Free Energy Landscape of GABA Binding to a Pentameric Ligand-Gated Ion Channel and Its Disruption by Mutations. J Chem Theory Comput 2016; 12:3398-406. [PMID: 27228114 DOI: 10.1021/acs.jctc.6b00303] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pentameric ligand-gated ion channels (pLGICs) of the Cys-loop superfamily are important neuroreceptors that mediate fast synaptic transmission. They are activated by the binding of a neurotransmitter, but the details of this process are still not fully understood. As a prototypical pLGIC, here we choose the insect resistance to dieldrin (RDL) receptor involved in resistance to insecticides and investigate the binding of the neurotransmitter GABA to its extracellular domain at the atomistic level. We achieve this by means of μ-sec funnel-metadynamics simulations, which efficiently enhance the sampling of bound and unbound states by using a funnel-shaped restraining potential to limit the exploration in the solvent. We reveal the sequence of events in the binding process from the capture of GABA from the solvent to its pinning between the charged residues Arg111 and Glu204 in the binding pocket. We characterize the associated free energy landscapes in the wild-type RDL receptor and in two mutant forms, where the key residues Arg111 and Glu204 are mutated to Ala. Experimentally these mutations produce nonfunctional channels, which is reflected in the reduced ligand binding affinities due to the loss of essential interactions. We also analyze the dynamical behavior of the crucial loop C, whose opening allows the access of GABA to the binding site and closure locks the ligand into the protein. The RDL receptor shares structural and functional features with other pLGICs; hence, our work outlines a valuable protocol to study the binding of ligands to pLGICs beyond conventional docking and molecular dynamics techniques.
Collapse
Affiliation(s)
- Federico Comitani
- Department of Physics, King's College London , Strand, London WC2R 2LS, United Kingdom
| | - Vittorio Limongelli
- Universitá della Svizzera Italiana (USI) , Faculty of Informatics, Institute of Computational Science - Center for Computational Medicine in Cardiology, via G. Buffi 13, CH-6900 Lugano, Switzerland.,Department of Pharmacy, University of Naples "Federico II" , via D. Montesano 49, I-80131 Naples, Italy
| | - Carla Molteni
- Department of Physics, King's College London , Strand, London WC2R 2LS, United Kingdom
| |
Collapse
|
18
|
Comitani F, Limongelli V, Molteni C. Exploring the Binding of GABA to the Insect RDL Receptor with Metadynamics. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.2435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
19
|
Corsini NRC, Zhang Y, Little WR, Karatutlu A, Ersoy O, Haynes PD, Molteni C, Hine NDM, Hernandez I, Gonzalez J, Rodriguez F, Brazhkin VV, Sapelkin A. Pressure-Induced Amorphization and a New High Density Amorphous Metallic Phase in Matrix-Free Ge Nanoparticles. Nano Lett 2015; 15:7334-7340. [PMID: 26457875 DOI: 10.1021/acs.nanolett.5b02627] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Over the last two decades, it has been demonstrated that size effects have significant consequences for the atomic arrangements and phase behavior of matter under extreme pressure. Furthermore, it has been shown that an understanding of how size affects critical pressure-temperature conditions provides vital guidance in the search for materials with novel properties. Here, we report on the remarkable behavior of small (under ~5 nm) matrix-free Ge nanoparticles under hydrostatic compression that is drastically different from both larger nanoparticles and bulk Ge. We discover that the application of pressure drives surface-induced amorphization leading to Ge-Ge bond overcompression and eventually to a polyamorphic semiconductor-to-metal transformation. A combination of spectroscopic techniques together with ab initio simulations were employed to reveal the details of the transformation mechanism into a new high density phase-amorphous metallic Ge.
Collapse
Affiliation(s)
- Niccolo R C Corsini
- Department of Physics, Blackett Laboratory, Imperial College London , Exhibition Road, London SW7 2AZ, United Kingdom
| | - Yuanpeng Zhang
- School of Physics and Astronomy, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
| | - William R Little
- School of Physics and Astronomy, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
| | - Ali Karatutlu
- School of Physics and Astronomy, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
- Electrical and Electronics Engineering, Yildirim Campus, Bursa Orhangazi University , 16245 Yildirim, Bursa, Turkey
| | - Osman Ersoy
- School of Physics and Astronomy, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
| | - Peter D Haynes
- Department of Physics, Blackett Laboratory, Imperial College London , Exhibition Road, London SW7 2AZ, United Kingdom
| | - Carla Molteni
- Department of Physics, King's College London , Strand, London WC2R 2LS, United Kingdom
| | - Nicholas D M Hine
- TCM Group, Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
- Department of Physics, University of Warwick , Coventry CV4 7AL, United Kingdom
| | - Ignacio Hernandez
- Malta Consolider Team, Departmento CITIMAC, Universidad de Cantabria , Avenida Los Castros s/n, 39005 Santander, Spain
| | - Jesus Gonzalez
- Malta Consolider Team, Departmento CITIMAC, Universidad de Cantabria , Avenida Los Castros s/n, 39005 Santander, Spain
| | - Fernando Rodriguez
- Malta Consolider Team, Departmento CITIMAC, Universidad de Cantabria , Avenida Los Castros s/n, 39005 Santander, Spain
| | - Vadim V Brazhkin
- High Pressure Physics Institute, RAS , 142190 Troitsk, Moscow Region, Russia
| | - Andrei Sapelkin
- School of Physics and Astronomy, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
| |
Collapse
|
20
|
Affiliation(s)
- Dominic Botten
- Physics
Department, King’s College London, Strand, London WC2R 2LS, United Kingdom
| | - Giorgia Fugallo
- Laboratoire
des Solides Irradiés, École Polytechnique, 91128 Palaiseau Cedex, France
| | - Franca Fraternali
- Randall
Division of Cell and Molecular Biophysics, King’s College London, Guy’s Campus, London SE1 1UL, United Kingdom
| | - Carla Molteni
- Physics
Department, King’s College London, Strand, London WC2R 2LS, United Kingdom
| |
Collapse
|
21
|
Comitani F, Cohen N, Ashby J, Botten D, Lummis SCR, Molteni C. Insights into the binding of GABA to the insect RDL receptor from atomistic simulations: a comparison of models. J Comput Aided Mol Des 2014; 28:35-48. [PMID: 24442887 PMCID: PMC3927061 DOI: 10.1007/s10822-013-9704-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 12/26/2013] [Indexed: 01/19/2023]
Abstract
The resistance to dieldrin (RDL) receptor is an insect pentameric ligand-gated ion channel (pLGIC). It is activated by the neurotransmitter γ-aminobutyric acid (GABA) binding to its extracellular domain; hence elucidating the atomistic details of this interaction is important for understanding how the RDL receptor functions. As no high resolution structures are currently available, we built homology models of the extracellular domain of the RDL receptor using different templates, including the widely used acetylcholine binding protein and two pLGICs, the Erwinia Chrysanthemi ligand-gated ion channel (ELIC) and the more recently resolved GluCl. We then docked GABA into the selected three dimensional structures, which we used as starting points for classical molecular dynamics simulations. This allowed us to analyze in detail the behavior of GABA in the binding sites, including the hydrogen bond and cation-π interaction networks it formed, the conformers it visited and the possible role of water molecules in mediating the interactions; we also estimated the binding free energies. The models were all stable and showed common features, including interactions consistent with experimental data and similar to other pLGICs; differences could be attributed to the quality of the models, which increases with increasing sequence identity, and the use of a pLGIC template. We supplemented the molecular dynamics information with metadynamics, a rare event method, by exploring the free energy landscape of GABA binding to the RDL receptor. Overall, we show that the GluCl template provided the best models. GABA forming direct salt-bridges with Arg211 and Glu204, and cation-π interactions with an aromatic cage including Tyr109, Phe206 and Tyr254, represents a favorable binding arrangement, and the interaction with Glu204 can also be mediated by a water molecule.
Collapse
Affiliation(s)
- Federico Comitani
- Physics Department, King's College London, Strand, London, WC2R 2LS, UK
| | | | | | | | | | | |
Collapse
|
22
|
Corsini NRC, Greco A, Hine NDM, Molteni C, Haynes PD. Simulations of nanocrystals under pressure: Combining electronic enthalpy and linear-scaling density-functional theory. J Chem Phys 2013; 139:084117. [DOI: 10.1063/1.4819132] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Niccolò R C Corsini
- Department of Physics and Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | | | | | | | | |
Collapse
|
23
|
Botten D, Fugallo G, Fraternali F, Molteni C. A computational exploration of the interactions of the green tea polyphenol (-)-Epigallocatechin 3-Gallate with cardiac muscle troponin C. PLoS One 2013; 8:e70556. [PMID: 23923004 PMCID: PMC3726641 DOI: 10.1371/journal.pone.0070556] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 06/22/2013] [Indexed: 11/19/2022] Open
Abstract
Thanks to its polyphenols and phytochemicals, green tea is believed to have a number of health benefits, including protecting from heart disease, but its mechanism of action at the molecular level is still not understood. Here we explore, by means of atomistic simulations, how the most abundant of the green tea polyphenols, (-)-Epigallocatechin 3-Gallate (EGCg), interacts with the structural C terminal domain of cardiac muscle troponin C (cCTnC), a calcium binding protein that plays an important role in heart contractions. We find that EGCg favourably binds to the hydrophobic cleft of cCTnC consistently with solution NMR experiments. It also binds to cCTnC in the presence of the anchoring region of troponin I (cTnI(34-71)) at the interface between the E and H helices. This appears to affect the strength of the interaction between cCTnC and cTnI(34-71) and also counter-acts the effects of the Gly159Asp mutation, related to dilated cardiomyopathy. Our simulations support the picture that EGCg interacting with the C terminal domain of troponin C may help in regulating the calcium signalling either through competitive binding with the anchoring domain of cTnI or by affecting the interaction between cCTnC and cTnI(34-71).
Collapse
Affiliation(s)
- Dominic Botten
- Physics Department, King's College London, London, United Kingdom
| | - Giorgia Fugallo
- Physics Department, King's College London, London, United Kingdom
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Carla Molteni
- Physics Department, King's College London, London, United Kingdom
| |
Collapse
|
24
|
Ashby JA, McGonigle IV, Price KL, Cohen N, Comitani F, Dougherty DA, Molteni C, Lummis SCR. GABA binding to an insect GABA receptor: a molecular dynamics and mutagenesis study. Biophys J 2012. [PMID: 23200041 DOI: 10.1016/j.bpj.2012.10.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
RDL receptors are GABA-activated inhibitory Cys-loop receptors found throughout the insect CNS. They are a key target for insecticides. Here, we characterize the GABA binding site in RDL receptors using computational and electrophysiological techniques. A homology model of the extracellular domain of RDL was generated and GABA docked into the binding site. Molecular dynamics simulations predicted critical GABA binding interactions with aromatic residues F206, Y254, and Y109 and hydrophilic residues E204, S176, R111, R166, S176, and T251. These residues were mutated, expressed in Xenopus oocytes, and their functions assessed using electrophysiology. The data support the binding mechanism provided by the simulations, which predict that GABA forms many interactions with binding site residues, the most significant of which are cation-π interactions with F206 and Y254, H-bonds with E204, S205, R111, S176, T251, and ionic interactions with R111 and E204. These findings clarify the roles of a range of residues in binding GABA in the RDL receptor, and also show that molecular dynamics simulations are a useful tool to identify specific interactions in Cys-loop receptors.
Collapse
|
25
|
Bonfanti P, Ricci E, Molteni C, De Socio GV, Rusconi S, Vichi F, Penco G, Antinori A, Cordier L, Maggi P, Celesia BM, Grosso C, Quirino T. Low frequency of skin reactions in a cohort of patients on raltegravir. J Antimicrob Chemother 2012; 67:1800-2. [DOI: 10.1093/jac/dks096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
26
|
Zucca R, Boero M, Massobrio C, Molteni C, Cleri F. Interacting Lewis-X carbohydrates in condensed phase: a first-principles molecular dynamics study. J Phys Chem B 2011; 115:12599-606. [PMID: 21919496 DOI: 10.1021/jp2055816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We performed first-principles molecular dynamics calculations at finite temperature, to study the interacting conformations of Lewis-X (LeX) trisaccharides in the crystalline phase. The calculated cell parameters and detailed atomic structure of the LeX molecule compare well to the experimental data obtained by X-ray diffraction. We identify and characterize the hydrogen-bond network, responsible for the mutual interaction of the LeX pairs, whereas we find the intramolecular conformation and stability to be mainly assured by dispersion forces. The relative contributions to the crystallization energy of the hydrogen bonds and of the dispersion forces are defined and quantified. From this study, candidate configurations for the fully hydrated, in vivo structures of homotypic LeX-LeX interactions at cell surfaces can be proposed. We discuss how these configurations could also be relevant for the adhesion and self-assembly of nanostructures.
Collapse
Affiliation(s)
- Rinaldo Zucca
- Institut d'Electronique, Microelectronique et Nanotechnologie (Cnrs UMR 8520), Université de Lille I , Villeneuve d'Ascq, France
| | | | | | | | | |
Collapse
|
27
|
McCormack TJ, Melis C, Colón J, Gay EA, Mike A, Karoly R, Lamb PW, Molteni C, Yakel JL. Rapid desensitization of the rat α7 nAChR is facilitated by the presence of a proline residue in the outer β-sheet. J Physiol 2010; 588:4415-29. [PMID: 20837638 DOI: 10.1113/jphysiol.2010.195495] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The rat α7 nicotinic acetylcholine receptor (nAChR) has a proline residue near the middle of the β9 strand. The replacement of this proline residue at position 180 (P180) by either threonine (α7-P180T) or serine (α7-P180S) slowed the onset of desensitization dramatically, with half-times of ~930 and 700 ms, respectively, compared to 90 ms for the wild-type receptor. To investigate the importance of the hydroxyl group on the position 180 side-chains, the mutant receptors α7-P180Y and α7-P180F were studied and showed half-times of desensitization of 650 and 160 ms, respectively. While a position 180 side-chain OH group may contribute to the slow desensitization rates, α7-P180S and α7-P180V resulted in receptors with similar desensitization rates, suggesting that increased backbone to backbone H bonding expected in the absence of proline at position 180 would likely exert a great effect on desensitization. Single channel recordings indicated that for the α7-P180T receptor there was a significantly reduced closed time without any change in single channel conductance (as compared to wild-type). Kinetic simulations indicated that all changes observed for the mutant channel behaviour were reproduced by decreasing the rate of desensitization, and increasing the microscopic affinity to resting receptors. Molecular dynamics (MD) simulations on a homology model were used to provide insight into likely H bond interactions within the outer β-sheet that occur when the P180 residue is mutated. All mutations analysed increased about twofold the predicted number of H bonds between the residue at position 180 and the backbone of the β10 strand. Moreover, the α7-P180T and α7-P180S mutations also formed some intrastrand H bonds along the β9 strand, although H bonding of the OH groups of the threonine or serine side-chains was predicted to be infrequent. Our results indicate that rapid desensitization of the wild-type rat α7 nAChR is facilitated by the presence of the proline residue within the β9 strand.
Collapse
Affiliation(s)
- Thomas J McCormack
- Laboratory of Neurobiology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Bealing C, Fugallo G, Martonák R, Molteni C. Constant pressure molecular dynamics simulations for ellipsoidal, cylindrical and cuboidal nano-objects based on inertia tensor information. Phys Chem Chem Phys 2010; 12:8542-50. [DOI: 10.1039/c004053c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Clive Bealing
- King's College London, Physics Department, Strand, London WC2R 2LS, UK
| | | | | | | |
Collapse
|
29
|
Ma Y, Rohlfing M, Molteni C. Modeling the Excited States of Biological Chromophores within Many-Body Green's Function Theory. J Chem Theory Comput 2009; 6:257-65. [PMID: 26614336 DOI: 10.1021/ct900528h] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
First-principle many-body Green's function theory (MBGFT) has been successfully used to describe electronic excitations in many materials, from bulk crystals to nanoparticles. Here we assess its performance for the calculations of the excited states of biological chromophores. MBGFT is based on a set of Green's function equations, whose key ingredients are the electron's self-energy Σ, which is obtained by Hedin's GW approach, and the electron-hole interaction, which is described by the Bethe-Salpeter equation (BSE). The GW approach and the BSE predict orbital energies and excitation energies with high accuracy, respectively. We have calculated the low-lying excited states of a series of model biological chromophores, related to the photoactive yellow protein (PYP), rhodopsin, and the green fluorescent protein (GFP), obtaining a very good agreement with the available experimental and accurate theoretical data; the order of the excited states is also correctly predicted. MBGFT bridges the gap between time-dependent density functional theory and high-level quantum chemistry methods, combining the efficiency of the former with the accuracy of the latter: this makes MBGFT a promising method for studying excitations in complex biological systems.
Collapse
Affiliation(s)
- Yuchen Ma
- Fachbereich Physik, Universität Osnabrück, D-49069 Osnabrück, Germany, and Physics Department, King's College London, Strand, London WC2R 2LS, United Kingdom
| | - Michael Rohlfing
- Fachbereich Physik, Universität Osnabrück, D-49069 Osnabrück, Germany, and Physics Department, King's College London, Strand, London WC2R 2LS, United Kingdom
| | - Carla Molteni
- Fachbereich Physik, Universität Osnabrück, D-49069 Osnabrück, Germany, and Physics Department, King's College London, Strand, London WC2R 2LS, United Kingdom
| |
Collapse
|
30
|
Melis C, Bussi G, Lummis SCR, Molteni C. Trans-cis switching mechanisms in proline analogues and their relevance for the gating of the 5-HT3 receptor. J Phys Chem B 2009; 113:12148-53. [PMID: 19663504 PMCID: PMC2733763 DOI: 10.1021/jp9046962] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Indexed: 12/17/2022]
Abstract
Trans-cis isomerization of a proline peptide bond is a potential mechanism to open the channel of the 5-HT(3) receptor. Here, we have used the metadynamics method to theoretically explore such a mechanism. We have determined the free energy surfaces in aqueous solution of a series of dipeptides of proline analogues and evaluated the free energy difference between the cis and trans isomers. These theoretical results were then compared with data from mutagenesis experiments, in which the response of the 5-HT(3) receptor was measured when the proline at the apex of the M2-M3 transmembrane domain loop was mutated. The strong correlation between the experimental and the theoretical data supports the existence of a trans-cis proline switch for opening the 5-HT(3) receptor ion channel.
Collapse
Affiliation(s)
| | | | | | - Carla Molteni
- Corresponding author. Phone: +44 20 78482170. Fax: +44 20 7848 2420. E-mail:
| |
Collapse
|
31
|
Bealing C, Martoňák R, Molteni C. Pressure-induced structural phase transitions in CdSe: A metadynamics study. J Chem Phys 2009; 130:124712. [DOI: 10.1063/1.3086043] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
32
|
González EM, Guidoni L, Molteni C. Chemical and protein shifts in the spectrum of the photoactive yellow protein: a time-dependent density functional theory/molecular mechanics study. Phys Chem Chem Phys 2009; 11:4556-63. [DOI: 10.1039/b902615k] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
33
|
Bungaro S, Irving J, Tussiwand R, Mura R, Minto L, Molteni C, Citterio M, Hall A, Biondi A, Cazzaniga G. Genomic analysis of different clonal evolution in a twin pair with t(12;21) positive acute lymphoblastic leukemia sharing the same prenatal clone. Leukemia 2007; 22:208-11. [PMID: 17914410 DOI: 10.1038/sj.leu.2404973] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
34
|
Walker BG, Marzari N, Molteni C. In-plane structure and ordering at liquid sodium surfaces and interfaces from ab initio molecular dynamics. J Chem Phys 2007; 127:134703. [DOI: 10.1063/1.2781388] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
35
|
Abstract
The 5-HT3 receptor is a typical ligand-gated ion channel of the Cys-loop superfamily, which is activated by binding of serotonin (5-HT). Models of the binding site of this protein reveal potential interactions between 5-HT and Tyr143, Tyr153, and Tyr234. Here we describe a series of ab initio calculations, based on density functional theory, to assess the effects of mutating these tyrosine residues on the binding of 5-HT. A series of mutations to these tyrosines, previously studied experimentally, were tested, and the binding energies compared with the available experimental data. Our results show that Tyr153 could form a hydrogen bond with the tertiary amine of 5-HT, and that mutation in this location revealed binding energies broadly in line with experimentally determined EC50s. Tyr143 could also form a hydrogen bond, but as EC50s do not relate to binding energies, it is unlikely that such a bond is formed here. Tyr234 is quite distinct in that it may interact with 5-HT via a mixed hydrogen bond/cation-pi interaction.
Collapse
Affiliation(s)
- Claudio Melis
- Physics Department, King’s College London, Strand, London WC2R 2LS, United Kingdom, Bioinformatique Structurale, CNRS URA 2185
| | | | - Kerry L. Price
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Sarah C. R. Lummis
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Carla Molteni
- Physics Department, King’s College London, Strand, London WC2R 2LS, United Kingdom, Bioinformatique Structurale, CNRS URA 2185
- Address correspondence to this author. E-mail:
| |
Collapse
|
36
|
Abstract
We have studied the liquid surface of sodium with extensive ab initio molecular dynamics simulations based on ensemble density-functional theory. We find clear evidence of layering in the direction perpendicular to the surface that persists to temperatures more than 100 K above the melting point. We also observe clear Friedel oscillations in the electronic density response to the presence of a surface, but their direct effect on atomic layering is ruled out. A careful finite-size effect analysis accompanies our results, showing that liquid slabs 20-25 A thick capture the essential details of the surface structure. We conclude that geometrical confinement is the common cause for layer formation, which is similar to what happens at a liquid-solid interface: at a free liquid surface, the rapid decay of the electronic density from the bulk liquid value to zero in the vapor forms a hard wall against which the atoms pack. Finally, we predict x-ray reflectivities from ab initio molecular dynamics data that include some of the large surface-normal wave vector-transfer regions that, for alkali metals, are not accessible to experiments.
Collapse
Affiliation(s)
- Brent G Walker
- Condensed Matter Section, Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, I-34014 Trieste, Italy.
| | | | | |
Collapse
|
37
|
Affiliation(s)
- Carla Molteni
- Physics Department, King's College London, Strand, London WC2R 2LS, UK.
| | | |
Collapse
|
38
|
Artacho E, Rohlfing M, Côté M, Haynes PD, Needs RJ, Molteni C. Structural relaxations in electronically excited poly(para-phenylene). Phys Rev Lett 2004; 93:116401. [PMID: 15447360 DOI: 10.1103/physrevlett.93.116401] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2004] [Indexed: 05/24/2023]
Abstract
Structural relaxations in electronically excited poly(para-phenylene) are studied using many-body perturbation theory and density-functional-theory methods. A sophisticated description of the electron-hole interaction is required to describe the excitonic energies, but the associated structural relaxations can be obtained quite accurately within a constrained density-functional-theory approach. We find that the structural relaxations in the low-energy excitonic states extend over about eight monomers, leading to an energy reduction of 0.22 eV and a Stokes shift of 0.40 eV.
Collapse
Affiliation(s)
- Emilio Artacho
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EQ, United Kingdom
| | | | | | | | | | | |
Collapse
|
39
|
Martoňák R, Colombo L, Molteni C, Parrinello M. Pressure-induced structural transformations in a medium-sized silicon nanocrystal by tight-binding molecular dynamics. J Chem Phys 2002. [DOI: 10.1063/1.1523894] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
40
|
Bandera A, Gori A, Catozzi L, Degli Esposti A, Marchetti G, Molteni C, Ferrario G, Codecasa L, Penati V, Matteelli A, Franzetti F. Molecular epidemiology study of exogenous reinfection in an area with a low incidence of tuberculosis. J Clin Microbiol 2001; 39:2213-8. [PMID: 11376059 PMCID: PMC88113 DOI: 10.1128/jcm.39.6.2213-2218.2001] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In geographical areas with a low incidence of tuberculosis, recurrent tuberculosis is generally due to reactivation of the disease. However, the relative contribution of tuberculosis reinfection increases in parallel with the incidence of disease and is likely to depend on the epidemiological context: factors such as the spread of multidrug resistance, human immunodeficiency virus (HIV) infection, and immigration from developing countries could modify disease transmission in areas at low risk for tuberculosis. A molecular epidemiology study was performed in Lombardy, Northern Italy, where the incidence of tuberculosis is 17.5 cases per 100,000 persons. A total of 2,452 cases of culture-confirmed tuberculosis in 2,127 patients were studied. A group of 32 patients (1.5%), each of whom had two episodes of tuberculosis with cure as the outcome of the first episode and with more than 6 months between the two episodes, were studied by means of restriction fragment length polymorphism DNA fingerprinting analysis. For 5 of the 32 patients (16%), the DNA fingerprinting patterns of Mycobacterium tuberculosis strains responsible for the second episode did not match those of the corresponding isolates of the first episode, indicating exogenous reinfection. Two of these patients developed multidrug-resistant tuberculosis during the second episode, and in three cases the isolates belonged to clusters of M. tuberculosis strains spreading in the community. A fourfold-increased risk for reinfection was observed in immigrant patients compared to Italian subjects. In contrast, a higher risk of relapse rather than reinfection was evidenced in HIV-positive subjects and in patients infected with multidrug-resistant tuberculosis. Episodes of tuberculosis reinfection in areas with a low incidence of tuberculosis are rare compared to those in high-incidence geographical regions. In populations that have immigrated from high-risk areas, reinfection may represent a considerable contributor to the rate of recurrent tuberculosis. This finding emphasizes the importance of containing the spread of epidemic strains in close communities, in order to prevent changes in global tuberculosis trends for developed countries.
Collapse
MESH Headings
- Adult
- Aged
- DNA Fingerprinting
- DNA, Bacterial/analysis
- DNA, Bacterial/genetics
- Emigration and Immigration
- Female
- HIV Infections/complications
- Humans
- Incidence
- Italy/epidemiology
- Male
- Middle Aged
- Molecular Epidemiology
- Mycobacterium tuberculosis/classification
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/isolation & purification
- Polymerase Chain Reaction
- Polymorphism, Restriction Fragment Length
- Recurrence
- Tuberculosis, Multidrug-Resistant/complications
- Tuberculosis, Multidrug-Resistant/epidemiology
- Tuberculosis, Multidrug-Resistant/microbiology
- Tuberculosis, Multidrug-Resistant/prevention & control
- Tuberculosis, Pulmonary/complications
- Tuberculosis, Pulmonary/epidemiology
- Tuberculosis, Pulmonary/microbiology
- Tuberculosis, Pulmonary/prevention & control
Collapse
Affiliation(s)
- A Bandera
- Institute of Infectious Diseases and Tropical Medicine, L. Sacco Hospital, University of Milan, via G.B. Grassi 74, 20157 Milan, Italy
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Ferrario G, Gori A, Rossi A, Catozzi L, Molteni C, Marchetti G, Bandera A, Rossi MC, Esposti AD, Franzetti F. PCR-hybridization assay for Mycobacterium avium complex: optimization of detection in peripheral blood from humans. J Clin Microbiol 2001; 39:1638-43. [PMID: 11283105 PMCID: PMC87988 DOI: 10.1128/jcm.39.4.1638-1643.2001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We evaluated the sensitivity of a DNA amplification test for the detection of Mycobacterium avium in blood samples using different blood components and different DNA extraction methods. M. avium-inoculated blood samples were processed to obtain separate blood components: peripheral blood mononuclear cells (PBMCs), polymorphonuclear cells (PMNCs), and whole-blood sodium dodecyl sulfate (SDS)-lysate pellets. The sensitivity for the detection of the lowest mycobacterial load (1 CFU/ml) was significantly greater (P < 0.01) with DNA extracted from SDS-lysate pellets than with DNA extracted from PBMCs or PMNCs. Subsequently, DNA extraction methods based on guanidine NaOH, and proteinase were compared. The sensitivity of the guanidine-based method was significantly greater (P < 0.01) than those of the others.
Collapse
Affiliation(s)
- G Ferrario
- Institute of Infectious Diseases and Tropical Medicine, Luigi Sacco Hospital, University of Milan, Milan, Varese, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Molteni C, Martoňák R, Parrinello M. First principles molecular dynamics simulations of pressure-induced structural transformations in silicon clusters. J Chem Phys 2001. [DOI: 10.1063/1.1345497] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
43
|
Gori A, Rossi MC, Marchetti G, Trabattoni D, Molteni C, Cogliati M, Bandera A, Clerici M, Franzetti F. Clinical and immunological benefit of adjuvant therapy with thalidomide in the treatment of tuberculosis disease. AIDS 2000; 14:1859-61. [PMID: 10985328 DOI: 10.1097/00002030-200008180-00026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- A Gori
- Institute of Infectious Diseases and Tropical Medicine, University of Milan, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Gori A, Rossi MC, Trabattoni D, Marchetti G, Fusi ML, Molteni C, Clerici M, Franzetti1 F. Tumor necrosis factor-alpha increased production during thalidomide treatment in patients with tuberculosis and human immunodeficiency virus coinfection. J Infect Dis 2000; 182:639-40. [PMID: 10915104 DOI: 10.1086/315721] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
|
45
|
Martonak R, Molteni C, Parrinello M. Ab initio molecular dynamics with a classical pressure reservoir: simulation of pressure-induced amorphization in a Si35H36 cluster. Phys Rev Lett 2000; 84:682-685. [PMID: 11017346 DOI: 10.1103/physrevlett.84.682] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/1999] [Revised: 08/13/1999] [Indexed: 05/23/2023]
Abstract
We present a new constant-pressure ab initio molecular dynamics method suitable for studying, e.g., pressure-induced structural transformations in finite nonperiodic systems such as clusters. We immerse an ab initio treated cluster into a model classical liquid, described by a soft-sphere potential, which acts as a pressure reservoir. The pressure is varied by tuning the parameter of the liquid potential. We apply the method to a Si35H36 cluster, which undergoes a pressure-induced amorphization at approximately 35 GPa, and remains in a disordered state even upon pressure release.
Collapse
Affiliation(s)
- R Martonak
- Max-Planck-Institut fur Festkorperforschung, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
| | | | | |
Collapse
|
46
|
Affiliation(s)
- C. Molteni
- Contribution from the Max-Planck-Institut für Festkörperforschung, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
| | - I. Frank
- Contribution from the Max-Planck-Institut für Festkörperforschung, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
| | - M. Parrinello
- Contribution from the Max-Planck-Institut für Festkörperforschung, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
| |
Collapse
|
47
|
Affiliation(s)
- C. Molteni
- Contribution from the Max-Planck-Institut für Festkörperforschung, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
| | - M. Parrinello
- Contribution from the Max-Planck-Institut für Festkörperforschung, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
| |
Collapse
|
48
|
|
49
|
|
50
|
Molteni C, Colombo L, Miglio L, Benedek G. Barrier height versus confinement efficiency for the optical phonons in GaAs/AlxGa1-xAs heterostructures. Phys Rev B Condens Matter 1994; 50:11684-11686. [PMID: 9975302 DOI: 10.1103/physrevb.50.11684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
|