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Article: Stability of 100 homo and heterotypic coiled-coil a-a' pairs for ten amino acids (A, L, I, V, N, K, S, T, E, and R).

Acharya, Asha / Rishi, Vikas / Vinson, Charles

2006 Volume 45, Issue 38, Page(s) 11324–11332

Abstract: ... heterodimers that contain all possible coiled-coil a-a' pairs for 10 amino acids (I, V, L, N, A, K S, T, E, and ... R). This includes the stability of 36 heterodimers for 6 amino acids (I, V, L, N, A, and K ...

Abstract	We present the thermal stability monitored by circular dichroism (CD) spectroscopy at 222 nm of 100 heterodimers that contain all possible coiled-coil a-a' pairs for 10 amino acids (I, V, L, N, A, K S, T, E, and R). This includes the stability of 36 heterodimers for 6 amino acids (I, V, L, N, A, and K) previously described and 64 new heterodimers including the 4 amino acids (S, T, E, and R). We have calculated a double mutant alanine thermodynamic cycle to determine a-a' pair coupling energies to evaluate which a-a' pairs encourage specific dimerization partners. The four new homotypic a-a' pairs (T-T, S-S, R-R, E-E) are repulsive relative to A-A and have destabilizing coupling energies. Among the 90 heterotypic a-a' pairs, the stabilizing coupling energies contain lysine or arginine paired with either an aliphatic or a polar amino acid. The range in coupling energies for each amino acid reveals its potential to regulate dimerization specificity. The a-a' pairs containing isoleucine and asparagine have the greatest range in coupling energies and thus contribute dramatically to dimerization specificity, which is to encourage homodimerization. In contrast, the a-a' pairs containing charged amino acids (K, R, and E) show the least range in coupling energies and promiscuously encourage heterodimerization.
MeSH term(s)	Amino Acid Sequence ; Amino Acids/chemistry ; Amino Acids/metabolism ; Circular Dichroism ; Dimerization ; Humans ; Leucine Zippers ; Mutation/genetics ; Protein Denaturation ; Thermodynamics
Chemical Substances	Amino Acids
Language	English
Publishing date	2006-09-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/bi060822u
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Article: A heterodimerizing leucine zipper coiled coil system for examining the specificity of a position interactions: amino acids I, V, L, N, A, and K.

Acharya, Asha / Ruvinov, Sergei B / Gal, Jozsef / Moll, Jonathan R / Vinson, Charles

Biochemistry

2002 Volume 41, Issue 48, Page(s) 14122–14131

Abstract: ... a-a' interaction to dimer stability for six amino acids (A, V, L, I, K, and N). Circular dichroism (CD ... than either the L-L or V-V interaction, and 7.0 kcal/mol per dimer more stable than the N-N interaction. Only lysine ... energies between the a and a' positions in the heterodimer. The aliphatic amino acids L, V, and I prefer ...

Abstract	We use a heterodimerizing leucine zipper system to examine the contribution of the interhelical a-a' interaction to dimer stability for six amino acids (A, V, L, I, K, and N). Circular dichroism (CD) spectroscopy monitored the thermal denaturation of 36 heterodimers that generate six homotypic and 30 heterotypic a-a' interactions. Isoleucine (I-I) is the most stable homotypic a-a' interaction, being 9.2 kcal/mol per dimer more stable than the A-A interaction and 4.0 kcal/mol per dimer more stable than either the L-L or V-V interaction, and 7.0 kcal/mol per dimer more stable than the N-N interaction. Only lysine was less stable than alanine. An alanine-based double-mutant thermodynamic cycle calculated coupling energies between the a and a' positions in the heterodimer. The aliphatic amino acids L, V, and I prefer to form homotypic interactions with coupling energies of -0.6 to -0.9 kcal/mol per dimer, but the heterotypic aliphatic interactions have positive coupling energies of <1.0 kcal/mol per dimer. The asparagine homotypic interaction has a coupling energy of -0.5 kcal/mol per dimer, while heterotypic interactions with the aliphatic amino acids produce coupling energies ranging from 2.6 to 4.9 kcal/mol per dimer. The homotypic K-K interaction is 2.9 kcal/mol per dimer less stable than the A-A interaction, but the coupling energy is only 0.3 kcal/mol per dimer. Heterotypic interactions with lysine and either asparagine or aliphatic amino acids produce similar coupling energies ranging from -0.2 to -0.7 kcal/mol per dimer. Thus, of the amino acids that were examined, asparagine contributes the most to dimerization specificity because of the large positive coupling energies in heterotypic interactions with the aliphatic amino acids which results in the N-N homotypic interaction.
MeSH term(s)	Alanine/chemistry ; Alanine/genetics ; Amino Acid Sequence ; Amino Acid Substitution/genetics ; Amino Acids/chemistry ; Amino Acids/genetics ; Animals ; Asparagine/chemistry ; Asparagine/genetics ; Avian Proteins ; Basic-Leucine Zipper Transcription Factors ; Carrier Proteins/chemistry ; Carrier Proteins/genetics ; Chickens ; Circular Dichroism ; Dimerization ; Isoleucine/chemistry ; Isoleucine/genetics ; Leucine/chemistry ; Leucine/genetics ; Leucine Zippers/genetics ; Lysine/chemistry ; Lysine/genetics ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Protein Structure, Secondary/genetics ; Protein Structure, Tertiary/genetics ; Thermodynamics ; Transcription Factors/chemistry ; Transcription Factors/genetics ; Ultracentrifugation ; Valine/chemistry ; Valine/genetics
Chemical Substances	Amino Acids ; Avian Proteins ; Basic-Leucine Zipper Transcription Factors ; Carrier Proteins ; Transcription Factors ; Isoleucine (04Y7590D77) ; Asparagine (7006-34-0) ; Leucine (GMW67QNF9C) ; Valine (HG18B9YRS7) ; Lysine (K3Z4F929H6) ; Alanine (OF5P57N2ZX)
Language	English
Publishing date	2002-11-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/bi020486r
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Article ; Online: Machine intelligence-guided selection of optimized inhibitor for human immunodeficiency virus (HIV) from natural products.

Kumar, Neeraj / Acharya, Vishal

Computers in biology and medicine

2023 Volume 153, Page(s) 106525

Abstract: The human immunodeficiency virus (HIV) connects to the cluster of differentiation (CD4) and any of the entry co-receptors (CCR5 and CXCR4); followed by unloading the viral genome, reverse transcriptase, and integrase enzymes within the host cell. The co- ... ...

Abstract	The human immunodeficiency virus (HIV) connects to the cluster of differentiation (CD4) and any of the entry co-receptors (CCR5 and CXCR4); followed by unloading the viral genome, reverse transcriptase, and integrase enzymes within the host cell. The co-receptors facilitate the entry of virus and vital enzymes, leading to replication and pre-maturation of viral particles within the host. The protease enzyme transforms the immature viral vesicles into the mature virion. The pivotal role of co-receptors and enzymes in homeostasis and growth makes the crucial target for anti-HIV drug discovery, and the availability of X-ray crystal structures is an asset. Here, we used the machine intelligence-driven framework (A-HIOT) to identify and optimize target-based potential hit molecules for five significant protein targets from the ZINC15 database (natural products dataset). Following validation with dynamic motion behavior analysis and molecular dynamics simulation, the optimized hits were evaluated using in silico ADMET filtration. Furthermore, three molecules were screened, optimized, and validated: ZINC00005328058 for CCR5 and protease, ZINC000254014855 for CXCR4 and integrase, and ZINC000000538471 for reverse transcriptase. In clinical trials, the ZINC000254014855 and ZINC000254014855 were passed in primary screens for vif-HIV-1, and we reported the specific receptor as well as interactions. As a result, the validated molecules may be investigated further in experimental studies targeting specific receptors in order to design and synergize an anti-HIV regimen.
MeSH term(s)	Humans ; HIV-1 ; Integrases/therapeutic use ; HIV Infections/drug therapy ; Peptide Hydrolases/therapeutic use
Chemical Substances	Integrases (EC 2.7.7.-) ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2023-01-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2022.106525
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Article ; Online: Advances in machine intelligence-driven virtual screening approaches for big-data.

Kumar, Neeraj / Acharya, Vishal

Medicinal research reviews

2023 Volume 44, Issue 3, Page(s) 939–974

Abstract: Virtual screening (VS) is an integral and ever-evolving domain of drug discovery framework. The VS is traditionally classified into ligand-based (LB) and structure-based (SB) approaches. Machine intelligence or artificial intelligence has wide ... ...

Abstract	Virtual screening (VS) is an integral and ever-evolving domain of drug discovery framework. The VS is traditionally classified into ligand-based (LB) and structure-based (SB) approaches. Machine intelligence or artificial intelligence has wide applications in the drug discovery domain to reduce time and resource consumption. In combination with machine intelligence algorithms, VS has emerged into revolutionarily progressive technology that learns within robust decision orders for data curation and hit molecule screening from large VS libraries in minutes or hours. The exponential growth of chemical and biological data has evolved as "big-data" in the public domain demands modern and advanced machine intelligence-driven VS approaches to screen hit molecules from ultra-large VS libraries. VS has evolved from an individual approach (LB and SB) to integrated LB and SB techniques to explore various ligand and target protein aspects for the enhanced rate of appropriate hit molecule prediction. Current trends demand advanced and intelligent solutions to handle enormous data in drug discovery domain for screening and optimizing hits or lead with fewer or no false positive hits. Following the big-data drift and tremendous growth in computational architecture, we presented this review. Here, the article categorized and emphasized individual VS techniques, detailed literature presented for machine learning implementation, modern machine intelligence approaches, and limitations and deliberated the future prospects.
MeSH term(s)	Humans ; Artificial Intelligence ; Ligands ; Drug Discovery/methods ; Algorithms
Chemical Substances	Ligands
Language	English
Publishing date	2023-12-21
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	603210-2
ISSN	1098-1128 ; 0198-6325
ISSN (online)	1098-1128
ISSN	0198-6325
DOI	10.1002/med.21995
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Zs.A 1764: Show issues

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Article: Machine intelligence-driven framework for optimized hit selection in virtual screening.

Kumar, Neeraj / Acharya, Vishal

Journal of cheminformatics

2022 Volume 14, Issue 1, Page(s) 48

Abstract: Virtual screening (VS) aids in prioritizing unknown bio-interactions between compounds and protein targets for empirical drug discovery. In standard VS exercise, roughly 10% of top-ranked molecules exhibit activity when examined in biochemical assays, ... ...

Abstract	Virtual screening (VS) aids in prioritizing unknown bio-interactions between compounds and protein targets for empirical drug discovery. In standard VS exercise, roughly 10% of top-ranked molecules exhibit activity when examined in biochemical assays, which accounts for many false positive hits, making it an arduous task. Attempts for conquering false-hit rates were developed through either ligand-based or structure-based VS separately; however, nonetheless performed remarkably well. Here, we present an advanced VS framework-automated hit identification and optimization tool (A-HIOT)-comprises chemical space-driven stacked ensemble for identification and protein space-driven deep learning architectures for optimization of an array of specific hits for fixed protein receptors. A-HIOT implements numerous open-source algorithms intending to integrate chemical and protein space leading to a high-quality prediction. The optimized hits are the selective molecules which we retrieve after extreme refinement implying chemical space and protein space modules of A-HIOT. Using CXC chemokine receptor 4, we demonstrated the superior performance of A-HIOT for hit molecule identification and optimization with tenfold cross-validation accuracies of 94.8% and 81.9%, respectively. In comparison with other machine learning algorithms, A-HIOT achieved higher accuracies of 96.2% for hit identification and 89.9% for hit optimization on independent benchmark datasets for CXCR4 and 86.8% for hit identification and 90.2% for hit optimization on independent test dataset for androgen receptor (AR), thus, shows its generalizability and robustness. In conclusion, advantageous features impeded in A-HIOT is making a reliable approach for bridging the long-standing gap between ligand-based and structure-based VS in finding the optimized hits for the desired receptor. The complete resource (framework) code is available at https://gitlab.com/neeraj-24/A-HIOT .
Language	English
Publishing date	2022-07-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2486539-4
ISSN	1758-2946
ISSN	1758-2946
DOI	10.1186/s13321-022-00630-7
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Article: Effect of micronutrients, rhizobium, salicylic acid, and effective microorganisms in plant growth and yield characteristics of green gram [

Chaurasia, Jay / Poudel, Balika / Mandal, Taranand / Acharya, Nobel / Ghimirey, Vivek

Heliyon

2024 Volume 10, Issue 5, Page(s) e26821

Abstract: Nepal has a very diverse topography and ecosystem, with mountains in the north and lush plains in the south. Despite the diverse ecology, the production of green gram is still in its minority. This experiment was conducted to assess the effect of ... ...

Abstract	Nepal has a very diverse topography and ecosystem, with mountains in the north and lush plains in the south. Despite the diverse ecology, the production of green gram is still in its minority. This experiment was conducted to assess the effect of micronutrients (Zn, B, Mo, Co, and Mn), rhizobium, effective micro-organisms, and salicylic acid in plant growth, yield, and yield attributes of green gram [Vigna radiata (L.) Wilczek] in Rupandehi district of Nepal in March 2021. Pratikshya variety of green gram was used as a test crop. Different levels of ZnSO
Language	English
Publishing date	2024-02-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2024.e26821
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Article: Acute Cytomegalovirus Colitis Presenting As Exacerbation of Ulcerative Colitis: A Case Report.

Daiya, Varun / Manuja, Nishtha / Acharya, Sourya / Kumar, Sunil / Jaiswal, Sharwari

Cureus

2024 Volume 16, Issue 2, Page(s) e54903

Abstract: This case report presents a 24-year-old female with a history of ulcerative colitis (UC) who sought care for symptoms initially suggestive of the disease exacerbation but was later diagnosed as acute cytomegalovirus (CMV) colitis. The patient's clinical ... ...

Abstract	This case report presents a 24-year-old female with a history of ulcerative colitis (UC) who sought care for symptoms initially suggestive of the disease exacerbation but was later diagnosed as acute cytomegalovirus (CMV) colitis. The patient's clinical course, marked by watery diarrhea, blood in stools, vomiting, and fever, raised suspicion of a UC flare. However, a nuanced diagnostic approach revealed CMV superinfection, including computed tomography, colonoscopy, and tissue polymerase chain reaction (PCR). The patient's immunosuppressive history, with prior treatment, including intravenous infliximab and azathioprine, contributed to CMV infection. Treatment involved initiation of tofacitinib and antiviral therapy with valganciclovir. This case underscores the diagnostic challenges in distinguishing between infectious complications and UC exacerbations, necessitating a tailored, multidisciplinary approach for optimal management. It highlights the delicate balance required when managing UC patients on immunosuppressive regimens, emphasizing the importance of timely diagnosis and individualized treatment strategies in complex clinical scenarios.
Language	English
Publishing date	2024-02-25
Publishing country	United States
Document type	Case Reports
ZDB-ID	2747273-5
ISSN	2168-8184
ISSN	2168-8184
DOI	10.7759/cureus.54903
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Article: An Unusual Presentation of a Corpus Luteum Rupture.

Godhiwala, Parth / Agarwal, Himanshi / Acharya, Sourya / Acharya, Neema / Lahane, Vivek

Gynecology and minimally invasive therapy

2022 Volume 11, Issue 1, Page(s) 57–60

Abstract: Rheumatic heart disease (RHD) is one of the most common cardiac conditions seen in India with mitral stenosis as the most prevalent cause affecting females more than males. With the increasing number of patients undergoing mitral valve replacement (MVR) ... ...

Abstract	Rheumatic heart disease (RHD) is one of the most common cardiac conditions seen in India with mitral stenosis as the most prevalent cause affecting females more than males. With the increasing number of patients undergoing mitral valve replacement (MVR) and mandatory use of anticoagulants post-MVR, the patients presenting with drug-induced coagulopathy have increased. One of the rare complications of coagulopathy-related hemorrhage may be associated with a gynecological cause with maximum risk in women of reproductive age group. This chance of hemorrhage has increased due to various events that occur in reproductive organs, namely, ovulation, menstruation, trauma due to sexual intercourse, or pregnancy-related bleeding. Such bleeding is evident as external vaginal bleeding or hemoperitoneum. Hereby, we present a rare case of a 30-year-old woman, on anticoagulant therapy for MVR who presented with congestive cardiac failure associated with massive hemoperitoneum. On ultrasound-guided paracentesis, the cause of mild-to-moderate ascites was normal ovulatory bleed evident by the bleeding from the corpus luteal cyst.
Language	English
Publishing date	2022-02-14
Publishing country	India
Document type	Case Reports
ZDB-ID	2696587-2
ISSN	2213-3070
ISSN	2213-3070
DOI	10.4103/GMIT.GMIT_135_20
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Article: Fluorescent ureterography with indocyanine green in laparoscopic colorectal surgery: A safe method to prevent intraoperative ureteric injury.

V R Satish, V N / Acharya, Abhijith / Ramachandran, Srinivasan / Narasimhan, Mohan / Ardhanari, Ramesh

Journal of minimal access surgery

2022 Volume 18, Issue 2, Page(s) 320–323

Abstract: Intraoperative injuries to the ureter can occur in complicated colorectal and gynaecologic procedures in minimal access surgery. The majority of these go unrecognised at the time of the operation, which can be disastrous to the patient. The routine use ... ...

Abstract	Intraoperative injuries to the ureter can occur in complicated colorectal and gynaecologic procedures in minimal access surgery. The majority of these go unrecognised at the time of the operation, which can be disastrous to the patient. The routine use of ureteric stents is controversial, with some studies showing that stents only enable detection of ureteric injury but do not prevent it. Fluorescent image-guided surgery with indocyanine green (ICG) to visualise the ureter is a relatively new technique. We report our method of visualisation of the ureter in two patients undergoing laparoscopic anterior resection and Hartmann procedure, respectively. After induction of anaesthesia, retrograde catheterisation of both ureters was performed by the urologist. 2.5 mg ICG was injected into each catheter at the start of the procedure. Both ureters were visualised very well throughout the procedure with no post-operative complications. This technique using ICG adds visual cues to make up for the loss of tactile feedback, making it a safe strategy to prevent intraoperative ureteric injury.
Language	English
Publishing date	2022-01-19
Publishing country	India
Document type	Case Reports
ZDB-ID	2186884-0
ISSN	1998-3921 ; 0972-9941
ISSN (online)	1998-3921
ISSN	0972-9941
DOI	10.4103/jmas.jmas_183_21
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Article ; Online: A novel homozygous mutation, c.662_672del, in DGUOK gene causing mitochondrial DNA depletion syndrome of type hepatocerebral - A case report.

Radhakrishna, Kandula / Rajsekhar, Batchu / Ramesh, K V Raja / Chitturi, Neelima / Pemmasani, Sandhya Kiran / Acharya, Anuradha

Clinics and research in hepatology and gastroenterology

2024 Volume 48, Issue 4, Page(s) 102319

MeSH term(s)	Humans ; Infant ; Homozygote ; DNA, Mitochondrial/genetics ; Mutation
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2024-03-11
Publishing country	France
Document type	Case Reports ; Letter
ZDB-ID	2594333-9
ISSN	2210-741X ; 2210-7401
ISSN (online)	2210-741X
ISSN	2210-7401
DOI	10.1016/j.clinre.2024.102319
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