LIVIVO - Search results -

Search results

Result 1 - 10 of total 29

Search options

Article ; Online: Mechanistic Picture for Monomeric Human Fibroblast Growth Factor 1 Stabilization by Heparin Binding.

Govind Kumar, Vivek / Agrawal, Shilpi / Kumar, Thallapuranam Krishnaswamy Suresh / Moradi, Mahmoud

The journal of physical chemistry. B

2021 Volume 125, Issue 46, Page(s) 12690–12697

Abstract: Human fibroblast growth factor (FGF) 1 or hFGF1 is a member of the FGF family that is involved in various vital processes such as cell proliferation, cell differentiation, angiogenesis, and wound healing. hFGF1, which is associated with low ... ...

Abstract	Human fibroblast growth factor (FGF) 1 or hFGF1 is a member of the FGF family that is involved in various vital processes such as cell proliferation, cell differentiation, angiogenesis, and wound healing. hFGF1, which is associated with low stability
MeSH term(s)	Fibroblast Growth Factor 1 ; Glycosaminoglycans ; Heparin ; Humans ; Molecular Dynamics Simulation ; Protein Binding
Chemical Substances	Glycosaminoglycans ; Fibroblast Growth Factor 1 (104781-85-3) ; Heparin (9005-49-6)
Language	English
Publishing date	2021-11-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.1c07772
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Binding affinity estimation from restrained umbrella sampling simulations.

Govind Kumar, Vivek / Polasa, Adithya / Agrawal, Shilpi / Kumar, Thallapuranam Krishnaswamy Suresh / Moradi, Mahmoud

Nature computational science

2022 Volume 3, Issue 1, Page(s) 59–70

Abstract: The protein-ligand binding affinity quantifies the binding strength between a protein and its ligand. Computer modeling and simulations can be used to estimate the binding affinity or binding free energy using data- or physics-driven methods or a ... ...

Abstract	The protein-ligand binding affinity quantifies the binding strength between a protein and its ligand. Computer modeling and simulations can be used to estimate the binding affinity or binding free energy using data- or physics-driven methods or a combination thereof. Here we discuss a purely physics-based sampling approach based on biased molecular dynamics simulations. Our proposed method generalizes and simplifies previously suggested stratification strategies that use umbrella sampling or other enhanced sampling simulations with additional collective-variable-based restraints. The approach presented here uses a flexible scheme that can be easily tailored for any system of interest. We estimate the binding affinity of human fibroblast growth factor 1 to heparin hexasaccharide based on the available crystal structure of the complex as the initial model and four different variations of the proposed method to compare against the experimentally determined binding affinity obtained from isothermal titration calorimetry experiments.
MeSH term(s)	Humans ; Ligands ; Proteins/metabolism ; Molecular Dynamics Simulation ; Protein Binding ; Entropy
Chemical Substances	Ligands ; Proteins
Language	English
Publishing date	2022-12-29
Publishing country	United States
Document type	Journal Article
ISSN	2662-8457
ISSN (online)	2662-8457
DOI	10.1038/s43588-022-00389-9
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: cpSRP43 Is Both Highly Flexible and Stable: Structural Insights Using a Combined Experimental and Computational Approach.

Benton, Mitchell / Furr, Mercede / Govind Kumar, Vivek / Polasa, Adithya / Gao, Feng / Heyes, Colin David / Suresh Kumar, Thallapuranam Krishnaswamy / Moradi, Mahmoud

Journal of chemical information and modeling

2023 Volume 63, Issue 13, Page(s) 4125–4137

Abstract: The novel multidomain protein, cpSRP43, is a unique subunit of the post-translational chloroplast signal recognition particle (cpSRP) targeting pathway in higher plants. The cpSRP pathway is responsible for targeting and insertion of light-harvesting ... ...

Abstract	The novel multidomain protein, cpSRP43, is a unique subunit of the post-translational chloroplast signal recognition particle (cpSRP) targeting pathway in higher plants. The cpSRP pathway is responsible for targeting and insertion of light-harvesting chlorophyll a/b binding proteins (LHCPs) to the thylakoid membrane. Upon emergence into the stroma, LHCPs form a soluble transit complex with the cpSRP heterodimer, which is composed of cpSRP43 and cpSRP54. cpSRP43 is irreplaceable as a chaperone to LHCPs in their translocation to the thylakoid membrane and remarkable in its ability to dissolve aggregates of LHCPs without the need for external energy input. In previous studies, cpSRP43 has demonstrated significant flexibility and interdomain dynamics. In this study, we explore the structural stability and flexibility of cpSRP43 using a combination of computational and experimental techniques and find that this protein is concurrently highly stable and flexible. In addition to microsecond-level unbiased molecular dynamics (MD), biased MD simulations based on system-specific collective variables are used along with biophysical experimentation to explain the basis of the flexibility and stability of cpSRP43, showing that the free and cpSRP54-bound cpSRP43 has substantially different conformations and conformational dynamics.
MeSH term(s)	Protein Binding ; Chloroplast Proteins/metabolism ; Chlorophyll A ; Chloroplasts/metabolism ; Thylakoids/metabolism ; Light-Harvesting Protein Complexes/chemistry ; Light-Harvesting Protein Complexes/metabolism
Chemical Substances	Chloroplast Proteins ; Chlorophyll A (YF5Q9EJC8Y) ; Light-Harvesting Protein Complexes
Language	English
Publishing date	2023-06-19
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.3c00319
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 1230: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Characterization of the structural forces governing the reversibility of the thermal unfolding of the human acidic fibroblast growth factor.

Agrawal, Shilpi / Govind Kumar, Vivek / Gundampati, Ravi Kumar / Moradi, Mahmoud / Kumar, Thallapuranam Krishnaswamy Suresh

Scientific reports

2021 Volume 11, Issue 1, Page(s) 15579

Abstract: Human acidic fibroblast growth factor (hFGF1) is an all beta-sheet protein that is involved in the regulation of key cellular processes including cell proliferation and wound healing. hFGF1 is known to aggregate when subjected to thermal unfolding. In ... ...

Abstract	Human acidic fibroblast growth factor (hFGF1) is an all beta-sheet protein that is involved in the regulation of key cellular processes including cell proliferation and wound healing. hFGF1 is known to aggregate when subjected to thermal unfolding. In this study, we investigate the equilibrium unfolding of hFGF1 using a wide array of biophysical and biochemical techniques. Systematic analyses of the thermal and chemical denaturation data on hFGF1 variants (Q54P, K126N, R136E, K126N/R136E, Q54P/K126N, Q54P/R136E, and Q54P/K126N/R136E) indicate that nullification of charges in the heparin-binding pocket can significantly increase the stability of wtFGF1. Triple variant (Q54P/K126N/R136E) was found to be the most stable of all the hFGF1 variants studied. With the exception of triple variant, thermal unfolding of wtFGF1 and the other variants is irreversible. Thermally unfolded triple variant refolds completely to its biologically native conformation. Microsecond-level molecular dynamic simulations reveal that a network of hydrogen bonds and salt bridges linked to Q54P, K126N, and R136E mutations, are responsible for the high stability and reversibility of thermal unfolding of the triple variant. In our opinion, the findings of the study provide valuable clues for the rational design of a stable hFGF1 variant that exhibits potent wound healing properties.
MeSH term(s)	Amino Acid Sequence ; Animals ; Binding Sites ; Cell Proliferation/drug effects ; Fibroblast Growth Factor 1/chemistry ; Fibroblast Growth Factor 1/metabolism ; Guanidine/pharmacology ; Heparin/metabolism ; Humans ; Mice ; Mutant Proteins/chemistry ; Mutation/genetics ; NIH 3T3 Cells ; Protein Conformation ; Protein Denaturation/drug effects ; Protein Stability ; Protein Unfolding ; Static Electricity ; Temperature ; Urea/pharmacology
Chemical Substances	Mutant Proteins ; Fibroblast Growth Factor 1 (104781-85-3) ; Urea (8W8T17847W) ; Heparin (9005-49-6) ; Guanidine (JU58VJ6Y3B)
Language	English
Publishing date	2021-08-02
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-95050-2
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Prefusion spike protein conformational changes are slower in SARS-CoV-2 than in SARS-CoV-1.

Govind Kumar, Vivek / Ogden, Dylan S / Isu, Ugochi H / Polasa, Adithya / Losey, James / Moradi, Mahmoud

The Journal of biological chemistry

2022 Volume 298, Issue 4, Page(s) 101814

Abstract: Within the last 2 decades, severe acute respiratory syndrome coronaviruses 1 and 2 (SARS-CoV-1 and SARS-CoV-2) have caused two major outbreaks; yet, for reasons not fully understood, the coronavirus disease 2019 pandemic caused by SARS-CoV-2 has been ... ...

Abstract	Within the last 2 decades, severe acute respiratory syndrome coronaviruses 1 and 2 (SARS-CoV-1 and SARS-CoV-2) have caused two major outbreaks; yet, for reasons not fully understood, the coronavirus disease 2019 pandemic caused by SARS-CoV-2 has been significantly more widespread than the 2003 SARS epidemic caused by SARS-CoV-1, despite striking similarities between these two viruses. The SARS-CoV-1 and SARS-CoV-2 spike proteins, both of which bind to host cell angiotensin-converting enzyme 2, have been implied to be a potential source of their differential transmissibility. However, the mechanistic details of prefusion spike protein binding to angiotensin-converting enzyme 2 remain elusive at the molecular level. Here, we performed an extensive set of equilibrium and nonequilibrium microsecond-level all-atom molecular dynamics simulations of SARS-CoV-1 and SARS-CoV-2 prefusion spike proteins to determine their differential dynamic behavior. Our results indicate that the active form of the SARS-CoV-2 spike protein is more stable than that of SARS-CoV-1 and the energy barrier associated with the activation is higher in SARS-CoV-2. These results suggest that not only the receptor-binding domain but also other domains such as the N-terminal domain could play a crucial role in the differential binding behavior of SARS-CoV-1 and SARS-CoV-2 spike proteins.
MeSH term(s)	Angiotensin-Converting Enzyme 2/metabolism ; COVID-19/virology ; Humans ; Molecular Dynamics Simulation ; Protein Binding ; Protein Conformation ; Protein Domains ; SARS Virus/chemistry ; SARS Virus/metabolism ; SARS-CoV-2/chemistry ; SARS-CoV-2/metabolism ; Severe Acute Respiratory Syndrome/virology ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2022-03-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2022.101814
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Uc I Zs.108: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Geophysical and geostatistical assessment of groundwater and soil quality using GIS, VES, and PCA techniques in the Jaipur region of Western India.

Khan, Jabbar / Gupta, Govind / Singh, Naveen Kumar / Bhave, Vivek Narayan / Bhardwaj, Vinay / Upreti, Pallavi / Singh, Rani / Sinha, Amarendra Kumar

Environmental science and pollution research international

2023 Volume 30, Issue 31, Page(s) 77713–77728

Abstract: In present study, geophysical and geostatistical variability of ground water and agricultural soil investigated in the Jaipur region of Rajasthan (Western India) by applying the geographic information system (GIS), vertical electrical sounding (VES) ,and ...

Abstract	In present study, geophysical and geostatistical variability of ground water and agricultural soil investigated in the Jaipur region of Rajasthan (Western India) by applying the geographic information system (GIS), vertical electrical sounding (VES) ,and statistical analysis. Ground water and soil samples collected from different sites from the selected study area and variation pattern of quality parameters were assessed. A contour map analysis of distribution of metals and other contaminants in the samples was conducted using GIS. Maximum concentration of metals recorded in the soil samples in order of Fe, 11.25 mg kg
MeSH term(s)	Geographic Information Systems ; Soil ; Metals, Heavy/analysis ; India ; Water Pollutants, Chemical/analysis ; Environmental Monitoring/methods ; Groundwater ; Soil Pollutants/analysis ; Risk Assessment
Chemical Substances	Soil ; Metals, Heavy ; Water Pollutants, Chemical ; Soil Pollutants
Language	English
Publishing date	2023-06-01
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-023-28004-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Bonn / Germany

Z 5915: Show issues

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article: Mechanistic Picture for Monomeric Human Fibroblast Growth Factor 1 Stabilization by Heparin Binding

Govind Kumar, Vivek / Agrawal, Shilpi / Kumar, Thallapuranam Krishnaswamy Suresh / Moradi, Mahmoud

Journal of physical chemistry. 2021 Nov. 11, v. 125, no. 46

2021

Abstract	Human fibroblast growth factor (FGF) 1 or hFGF1 is a member of the FGF family that is involved in various vital processes such as cell proliferation, cell differentiation, angiogenesis, and wound healing. hFGF1, which is associated with low stability in vivo, is known to be stabilized by binding heparin sulfate, a glycosaminoglycan that aids the protein in the activation of its cell surface receptor. The poor thermal and proteolytic stability of hFGF1 and the stabilizing role of heparin have long been observed experimentally; however, the mechanistic details of these phenomena are not well understood. Here, we have used microsecond-level equilibrium molecular dynamics (MD) simulations to quantitatively characterize the structural dynamics of monomeric hFGF1 in the presence and absence of heparin hexasaccharide. We have observed a conformational change in the heparin-binding pocket of hFGF1 that occurs only in the absence of heparin. Several intramolecular interactions were also identified within the heparin-binding pocket that form only when hFGF1 interacts with heparin. The loss of both intermolecular and intramolecular interactions in the absence of heparin plausibly leads to the observed conformational change. This conformational transition results in increased flexibility of the heparin-binding pocket and provides an explanation for the susceptibility of apo hFGF1 to proteolytic degradation and thermal instability. This study provides a glimpse into mechanistic details of the heparin-mediated stabilization of hFGF1 and encourages the use of microsecond-level MD in studying the effect of binding on protein structure and dynamics. In addition, the observed differential behavior of hFGF1 in the absence and presence of heparin provides an example, where microsecond-level all-atom MD simulations are necessary to see functionally relevant biomolecular phenomena that otherwise will not be observed on sub-microsecond time scales.
Keywords	angiogenesis ; cell differentiation ; cell proliferation ; fibroblast growth factor 1 ; heparin ; humans ; molecular dynamics ; protein structure ; proteolysis ; sulfates
Language	English
Dates of publication	2021-1111
Size	p. 12690-12697.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.1c07772
Database	NAL-Catalogue (AGRICOLA)

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Characterization of the structural forces governing the reversibility of the thermal unfolding of the human acidic fibroblast growth factor

Shilpi Agrawal / Vivek Govind Kumar / Ravi Kumar Gundampati / Mahmoud Moradi / Thallapuranam Krishnaswamy Suresh Kumar

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 13

Abstract: Abstract Human acidic fibroblast growth factor (hFGF1) is an all beta-sheet protein that is involved in the regulation of key cellular processes including cell proliferation and wound healing. hFGF1 is known to aggregate when subjected to thermal ... ...

Abstract	Abstract Human acidic fibroblast growth factor (hFGF1) is an all beta-sheet protein that is involved in the regulation of key cellular processes including cell proliferation and wound healing. hFGF1 is known to aggregate when subjected to thermal unfolding. In this study, we investigate the equilibrium unfolding of hFGF1 using a wide array of biophysical and biochemical techniques. Systematic analyses of the thermal and chemical denaturation data on hFGF1 variants (Q54P, K126N, R136E, K126N/R136E, Q54P/K126N, Q54P/R136E, and Q54P/K126N/R136E) indicate that nullification of charges in the heparin-binding pocket can significantly increase the stability of wtFGF1. Triple variant (Q54P/K126N/R136E) was found to be the most stable of all the hFGF1 variants studied. With the exception of triple variant, thermal unfolding of wtFGF1 and the other variants is irreversible. Thermally unfolded triple variant refolds completely to its biologically native conformation. Microsecond-level molecular dynamic simulations reveal that a network of hydrogen bonds and salt bridges linked to Q54P, K126N, and R136E mutations, are responsible for the high stability and reversibility of thermal unfolding of the triple variant. In our opinion, the findings of the study provide valuable clues for the rational design of a stable hFGF1 variant that exhibits potent wound healing properties.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-08-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article: Differential Dynamic Behavior of Prefusion Spike Proteins of SARS Coronaviruses 1 and 2.

Govind Kumar, Vivek / Ogden, Dylan S / Isu, Ugochi / Polasa, Adithya / Losey, James / Moradi, Mahmoud

bioRxiv : the preprint server for biology

2021

Abstract: The coronavirus spike protein, which binds to the same human receptor in both SARS-CoV-1 and 2, has been implied to be a potential source of their differential transmissibility. However, the mechanistic details of spike protein binding to its human ... ...

Abstract	The coronavirus spike protein, which binds to the same human receptor in both SARS-CoV-1 and 2, has been implied to be a potential source of their differential transmissibility. However, the mechanistic details of spike protein binding to its human receptor remain elusive at the molecular level. Here, we have used an extensive set of unbiased and biased microsecond-level all-atom molecular dynamics (MD) simulations of SARS-CoV-1 and 2 spike proteins to determine the differential dynamic behavior of prefusion spike protein structure in the two viruses. Our results indicate that the active form of the SARS-CoV-2 spike protein is more stable than that of SARS-CoV-1 and the energy barrier associated with the activation is higher in SARS-CoV-2. Our results also suggest that not only the receptor binding domain (RBD) but also other domains such as the N-terminal domain (NTD) could play a role in the differential binding behavior of SARS-CoV-1 and 2 spike proteins.
Language	English
Publishing date	2021-03-01
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.12.25.424008
Database	MEDical Literature Analysis and Retrieval System OnLINE

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article ; Online: Reconstructive spectrometer using a photonic crystal cavity.

Sharma, Naresh / Kumar, Govind / Garg, Vivek / Mote, Rakesh G / Gupta, Shilpi

Optics express

2021 Volume 29, Issue 17, Page(s) 26645–26657

Abstract: Optical spectrometers have propelled scientific and technological advancements in a wide range of fields. While sophisticated systems with excellent performance metrics are serving well in controlled laboratory environments, many applications require ... ...

Abstract	Optical spectrometers have propelled scientific and technological advancements in a wide range of fields. While sophisticated systems with excellent performance metrics are serving well in controlled laboratory environments, many applications require systems that are portable, economical, and robust to optical misalignment. Here, we propose and demonstrate a spectrometer that uses a planar one-dimensional photonic crystal cavity as a dispersive element and a reconstructive computational algorithm to extract spectral information from spatial patterns. The simple fabrication and planar architecture of the photonic crystal cavity render our spectrometry platform economical and robust to optical misalignment. The reconstructive algorithm allows miniaturization and portability. The intensity transmitted by the photonic crystal cavity has a wavelength-dependent spatial profile. We generate the spatial transmittance function of the system using finite-difference time-domain method and also estimate the dispersion relation. The transmittance function serves as a transfer function in our reconstructive algorithm. We show accurate estimation of various kinds of input spectra. We also show that the spectral resolution of the system depends on the cavity linewidth that can be improved by increasing the number of periodic layers in distributed Bragg mirrors. Finally, we experimentally estimate the center wavelength and linewidth of the spectrum of an unknown light emitting diode. The estimated values are in good agreement with the values measured using a commercial spectrometer.
Language	English
Publishing date	2021-09-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	1491859-6
ISSN	1094-4087 ; 1094-4087
ISSN (online)	1094-4087
ISSN	1094-4087
DOI	10.1364/OE.432831
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

To top

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito