scholarly journals Molecular-Level Understanding of the Somatostatin Receptor 1 (SSTR1)–Ligand Binding: A Structural Biology Study Based on Computational Methods

ACS Omega ◽  
2020 ◽  
Vol 5 (33) ◽  
pp. 21145-21161
Author(s):  
Santhosh Kumar Nagarajan ◽  
Sathya Babu ◽  
Honglae Sohn ◽  
Thirumurthy Madhavan
Keyword(s):  
Ligand Binding ◽  
Structural Biology ◽  
Computational Methods ◽  
Molecular Level ◽  
Somatostatin Receptor

Molecular-level understanding of the hTAS2R1 receptor-bitter tasting tetra-peptide binding: a structural biology study based on computational approaches

2021 ◽  
Author(s):  
Fangfang Wang ◽  
Wei Yang ◽  
Bo Zhou
Keyword(s):  
Structural Biology ◽  
Molecular Level ◽  
Peptide Binding ◽  
Computational Approaches

Effective computational approaches for bitter-tasting peptides have been developed and analyzed in the present work.

scholarly journals Carbenes. Pincers, chelates, and abnormal binding modes

2003 ◽  
Vol 75 (4) ◽  
pp. 435-443 ◽  
Author(s):  
Robert H. Crabtree
Keyword(s):  
Ligand Binding ◽  
Computational Methods ◽  
Ion Pairing ◽  
Binding Modes ◽  
Carbene Complexes ◽  
Ch Activation

Routes to pincer and chelate carbene complexes of Pd, Rh, and Ir include double geminal CH activation, metallation, and CH activation. Abnormal binding via imidazole C5 can occur, and ion pairing can strongly influence C2 vs. C5 binding. Prior ligand binding via pyridine N before metallation is not essential. Computational methods are used extensively, for example, to compare N vs. C binding in imidazole. The possibility of C binding by histidine in metalloenzymes is discussed.

scholarly journals Molecular and functional properties of densely and sparsely granulated GH-producing pituitary adenomas

2013 ◽  
Vol 169 (4) ◽  
pp. 391-400 ◽  
Author(s):  
Bernhard Mayr ◽  
Rolf Buslei ◽  
Marily Theodoropoulou ◽  
Günter K Stalla ◽  
Michael Buchfelder ◽  
...  
Keyword(s):  
Pituitary Adenomas ◽  
Molecular Level ◽  
Secretory Granules ◽  
Somatostatin Receptor ◽  
Receptor Subtypes ◽  
Membrane Expression ◽  
Cytoplasmic Expression ◽  
Somatotroph Adenoma ◽  
Somatostatin Receptor Subtypes

ObjectiveGH-producing pituitary adenomas display two distinct morphological patterns of cytoplasmic GH-containing secretory granules, namely the densely and sparsely granulated somatotroph adenoma subtype. It is unknown whether these morphological variants reflect distinct pathophysiological entities at the molecular level.MethodsIn 28 GH-producing adenoma tissues from a consecutive set of patients undergoing pituitary surgery for acromegaly, we studied the GH granulation pattern, the expression of somatostatin receptor subtypes (SSTR) as well as the calcium, cAMP and ZAC1 pathways in primary adenoma cell cultures.ResultsThe expression ofGSPoncogene was similar between densely and sparsely granulated somatotroph adenoma cells. There were no differences in the calcium, cAMP and ZAC1 pathways as well as in their regulation by SSTR agonists. SSTR2 was exclusively expressed in densely but not in sparsely granulated tumours (membrane expression 86 vs 0%; cytoplasmic expression 67 vs 0%). By contrast, expression of SSTR5 was only found in sparsely but not in densely granulated somatotroph adenomas (membrane expression 29 vs 0%; cytoplasmic expression 57 vs 0%).ConclusionsOur results indicate that different granulation patterns in GH-producing adenomas do not reflect differences in pathways and factors pivotal for somatotroph differentiation and function.In vitro, the vast majority of both densely and sparsely granulated tumour cells were responsive to SSTR activation at the molecular level. Sparsely granulated adenomas lacking SSTR2, but expressing SSTR5, might be responsive to novel SSTR agonists with increased affinity to SSTR5.

Dissecting the Hydrophobic Effect on the Molecular Level: The Role of Water, Enthalpy, and Entropy in Ligand Binding to Thermolysin

2013 ◽  
Vol 52 (6) ◽  
pp. 1822-1828 ◽  
Author(s):  
Adam Biela ◽  
Nader N. Nasief ◽  
Michael Betz ◽  
Andreas Heine ◽  
David Hangauer ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Molecular Level ◽  
Hydrophobic Effect ◽  
Enthalpy And Entropy

scholarly journals Recent Advances in Structure, Function, and Pharmacology of Class A Lipid GPCRs: Opportunities and Challenges for Drug Discovery

2021 ◽  
Vol 15 (1) ◽  
pp. 12
Author(s):  
R. N. V. Krishna Deepak ◽  
Ravi Kumar Verma ◽  
Yossa Dwi Hartono ◽  
Wen Shan Yew ◽  
Hao Fan
Keyword(s):  
Ligand Binding ◽  
Structural Biology ◽  
Drug Targets ◽  
Molecular Mechanisms ◽  
Structural Features ◽  
Structure Based Drug Design ◽  
Bovine Rhodopsin ◽  
Receptor Dynamics ◽  
Ligand Interactions ◽  
Approaches To Study

Great progress has been made over the past decade in understanding the structural, functional, and pharmacological diversity of lipid GPCRs. From the first determination of the crystal structure of bovine rhodopsin in 2000, much progress has been made in the field of GPCR structural biology. The extraordinary progress in structural biology and pharmacology of GPCRs, coupled with rapid advances in computational approaches to study receptor dynamics and receptor-ligand interactions, has broadened our comprehension of the structural and functional facets of the receptor family members and has helped usher in a modern age of structure-based drug design and development. First, we provide a primer on lipid mediators and lipid GPCRs and their role in physiology and diseases as well as their value as drug targets. Second, we summarize the current advancements in the understanding of structural features of lipid GPCRs, such as the structural variation of their extracellular domains, diversity of their orthosteric and allosteric ligand binding sites, and molecular mechanisms of ligand binding. Third, we close by collating the emerging paradigms and opportunities in targeting lipid GPCRs, including a brief discussion on current strategies, challenges, and the future outlook.

Free Energy of Ligand Binding to Protein: Evaluation of the Contribution of Water Molecules by Computational Methods

2004 ◽  
Vol 11 (23) ◽  
pp. 3093-3118 ◽  
Author(s):  
Pietro Cozzini ◽  
Micaela Fornabaio ◽  
Anna Marabotti ◽  
Donald Abraham ◽  
Glen Kellogg ◽  
...  
Keyword(s):  
Free Energy ◽  
Ligand Binding ◽  
Computational Methods ◽  
Water Molecules
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