scholarly journals Energy Landscape of Ubiquitin Family Proteins - Elucidating the Role of Protein Sequence and Specific Interactions Such as Salt-Bridges in Dictating Folding Pathways

2020 ◽  
Vol 118 (3) ◽  
pp. 198a-199a
Author(s):  
Tathagata Nandi ◽  
Sri Rama ◽  
Koti Ainavarapu
Keyword(s):  
Protein Sequence ◽  
Energy Landscape ◽  
Specific Interactions ◽  
Salt Bridges ◽  
Folding Pathways

Topography of the Free Energy Landscape on the Claisen-Schmidt Condensation: Solvent and Temperature Effect in the Rate-Controlling Step

2021 ◽  
Author(s):  
Nayara Dantas Coutinho ◽  
Hugo Gontijo Machado ◽  
Valter Henrique Carvalho-Silva ◽  
Wender A. Silva
Keyword(s):  
Free Energy ◽  
Temperature Effect ◽  
Strong Influence ◽  
Aldol Condensation ◽  
Energy Landscape ◽  
Bond Formation ◽  
Free Energy Landscape ◽  
Rate Controlling Step ◽  
Formation Step

Recent studies have assigned hydroxide elimination and C=C bond formation step in base-promoted aldol condensation the role of having a strong influence in the overall rate reaction, in contrast to...

Molecular modulation of calcium oxalate crystallization

2006 ◽  
Vol 291 (6) ◽  
pp. F1123-F1132 ◽  
Author(s):  
James J. De Yoreo ◽  
S. Roger Qiu ◽  
John R. Hoyer
Keyword(s):  
Molecular Modeling ◽  
Calcium Oxalate ◽  
Stone Formation ◽  
Energy Levels ◽  
Critical Role ◽  
Specific Interactions ◽  
Crystal Surfaces ◽  
Site Specific

Calcium oxalate monohydrate (COM) is the primary constituent of the majority of renal stones. Osteopontin (OPN), an aspartic acid-rich urinary protein, and citrate, a much smaller molecule, are potent inhibitors of COM crystallization at levels present in normal urine. Current concepts of the role of site-specific interactions in crystallization derived from studies of biomineralization are reviewed to provide a context for understanding modulation of COM growth at a molecular level. Results from in situ atomic force microscopy (AFM) analyses of the effects of citrate and OPN on growth verified the critical role of site-specific interactions between these growth modulators and individual steps on COM crystal surfaces. Molecular modeling investigations of interactions of citrate with steps and faces on COM crystal surfaces provided links between the stereochemistry of interaction and the binding energy levels that underlie mechanisms of growth modification and changes in overall crystal morphology. The combination of in situ AFM and molecular modeling provides new knowledge that will aid rationale design of therapeutic agents for inhibition of stone formation.

scholarly journals Role of salt bridges in the dimer interface of 14-3-3ζ in dimer dynamics, N-terminal α-helical order, and molecular chaperone activity

2017 ◽  
Vol 293 (1) ◽  
pp. 89-99 ◽  
Author(s):  
Joanna M. Woodcock ◽  
Katy L. Goodwin ◽  
Jarrod J. Sandow ◽  
Carl Coolen ◽  
Matthew A. Perugini ◽  
...  
Keyword(s):  
Molecular Chaperone ◽  
Chaperone Activity ◽  
Salt Bridges ◽  
Dimer Interface

The Energy Landscape of Unsolvated Peptides:  The Role of Context in the Stability of Alanine/Glycine Helices

2003 ◽  
Vol 125 (13) ◽  
pp. 3941-3947 ◽  
Author(s):  
Matthew R. Hartings ◽  
Brian S. Kinnear ◽  
Martin F. Jarrold
Keyword(s):  
Energy Landscape ◽  
The Stability

scholarly journals Conformational Destabilization of Immunoglobulin G Increases the Low pH Binding Affinity with the Neonatal Fc Receptor

2015 ◽  
Vol 291 (4) ◽  
pp. 1817-1825 ◽  
Author(s):  
Benjamin T. Walters ◽  
Pernille F. Jensen ◽  
Vincent Larraillet ◽  
Kevin Lin ◽  
Thomas Patapoff ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Hydrogen Exchange ◽  
Dissociation Constants ◽  
Conformational Dynamics ◽  
Fc Receptor ◽  
Salt Bridges ◽  
Neonatal Fc Receptor ◽  
Intermolecular Contacts ◽  
Ph Dependent

Crystallographic evidence suggests that the pH-dependent affinity of IgG molecules for the neonatal Fc receptor (FcRn) receptor primarily arises from salt bridges involving IgG histidine residues, resulting in moderate affinity at mildly acidic conditions. However, this view does not explain the diversity in affinity found in IgG variants, such as the YTE mutant (M252Y,S254T,T256E), which increases affinity to FcRn by up to 10×. Here we compare hydrogen exchange measurements at pH 7.0 and pH 5.5 with and without FcRn bound with surface plasmon resonance estimates of dissociation constants and FcRn affinity chromatography. The combination of experimental results demonstrates that differences between an IgG and its cognate YTE mutant vary with their pH-sensitive dynamics prior to binding FcRn. The conformational dynamics of these two molecules are nearly indistinguishable upon binding FcRn. We present evidence that pH-induced destabilization in the CH2/3 domain interface of IgG increases binding affinity by breaking intramolecular H-bonds and increases side-chain adaptability in sites that form intermolecular contacts with FcRn. Our results provide new insights into the mechanism of pH-dependent affinity in IgG-FcRn interactions and exemplify the important and often ignored role of intrinsic conformational dynamics in a protein ligand, to dictate affinity for biologically important receptors.

Codon usage and protein sequence pattern dependency in different organisms: A Bioinformatics approach

2015 ◽  
Vol 13 (02) ◽  
pp. 1550002
Author(s):  
Mohammad-Hadi Foroughmand-Araabi ◽  
Bahram Goliaei ◽  
Kasra Alishahi ◽  
Mehdi Sadeghi ◽  
Sama Goliaei
Keyword(s):  
Gene Regulation ◽  
Codon Usage ◽  
Protein Sequence ◽  
Multinomial Logistic Regression ◽  
Translation Efficiency ◽  
Translation Rate ◽  
Protein Levels ◽  
Synonymous Codons ◽  
First Time

Although it is known that synonymous codons are not chosen randomly, the role of the codon usage in gene regulation is not clearly understood, yet. Researchers have investigated the relation between the codon usage and various properties, such as gene regulation, translation rate, translation efficiency, mRNA stability, splicing, and protein domains. Recently, a universal codon usage based mechanism for gene regulation is proposed. We studied the role of protein sequence patterns on the codons usage by related genes. Considering a subsequence of a protein that matches to a pattern or motif, we showed that, parts of the genes, which are translated to this subsequence, use specific ratios of synonymous codons. Also, we built a multinomial logistic regression statistical model for codon usage, which considers the effect of patterns on codon usage. This model justifies the observed codon usage preference better than the classic organism dependent codon usage. Our results showed that the codon usage plays a role in controlling protein levels, for genes that participate in a specific biological function. This is the first time that this phenomenon is reported.

scholarly journals A critical role of VLA-4 in erythropoiesis in vivo

Blood ◽  
1996 ◽  
Vol 87 (6) ◽  
pp. 2513-2517 ◽  
Author(s):  
K Hamamura ◽  
H Matsuda ◽  
Y Takeuchi ◽  
S Habu ◽  
H Yagita ◽  
...  
Keyword(s):  
Monoclonal Antibody ◽  
Fetal Liver ◽  
Critical Role ◽  
In Utero ◽  
In Vitro Studies ◽  
Specific Interactions ◽  
Erythroid Progenitors

Hematopoiesis requires specific interactions with the microenvironments, and VLA-4 has been implicated in these interactions based on in vitro studies. To study the role of VLA-4 in hematopoiesis in vivo, we performed in utero treatment of mice with an anti-VLA-4 monoclonal antibody. Although all hematopoietic cells in fetal liver expressed VLA-4, the treatment specifically induced anemia. It had no effect on the development of nonerythroid lineage cells, including lymphoids and myeloids. In the treated liver almost no erythroblast was detected, whereas the erythroid progenitors, which give rise to erythroid colonies in vitro, were present. These results indicate that VLA-4 plays a critical role in erythropoiesis, while it is not critical in lymphopoiesis in vivo.

Role of Glycosphingolipids in HIV-1 Entry: Requirement of Globotriosylceramide (Gb3) in CD4/CXCR4-dependent Fusion

1999 ◽  
Vol 19 (4) ◽  
pp. 317-325 ◽  
Author(s):  
Anu Puri ◽  
Peter Hug ◽  
Kristine Jernigan ◽  
Patrick Rose ◽  
Robert Blumenthal
Keyword(s):  
Structural Analysis ◽  
Cell Fusion ◽  
Envelope Glycoprotein ◽  
Human Erythrocyte ◽  
Head Group ◽  
Specific Interactions ◽  
Cd4 Cells ◽  
Fusion Site ◽  
Hiv 1

We have recently shown that addition of human erythrocyte glycosphingolipids (GSL) to non-human CD4+ or GSL-depleted human CD4+ cells rendered those cells susceptible to gp120-gp41-mediated cell fusion (Puri et al., BBRC, 1998). One GSL fraction (Fraction 3) isolated from human erythrocyte GSL mixture exhibited the highest recovery of fusion following incorporation into CD4+ non-human and GSL-depleted HeLa-CD4 cells (HeLa-CD4/GSL-). Structural analysis of Fraction 3 showed that this GSL had identical head group as the known GSL, Gal(α1→4)Gal(β1→4)Glc-Ceramide (Gb3) (Puri et al., PNAS, 1998). Here we report that presence of Gb3 in CD4+/CXCR4+ cells but not CD4+/CXCR4- cells allows fusion with HIV-1Lai-envelope glycoprotein expressing cells (TF228). Therefore, Gb3 functions in conjunction with HIV-1 co-receptor, CXCR4 to promote fusion. We propose that Gb3 functions by recruiting CD4 and/or CXCR4 at the fusion site through structurally specific interactions.

scholarly journals Ab initio nanofluidics: disentangling the role of the energy landscape and of density correlations on liquid/solid friction

Nanoscale ◽  
2020 ◽  
Vol 12 (20) ◽  
pp. 10994-11000
Author(s):  
Gabriele Tocci ◽  
Maria Bilichenko ◽  
Laurent Joly ◽  
Marcella Iannuzzi
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Energy Landscape ◽  
Two Dimensional ◽  
Two Dimensional Materials ◽  
Order Of Magnitude ◽  
Solid Friction ◽  
Density Correlations

Ab initio molecular dynamics reveals that subtle variations in the energy landscape and density correlations can change by up to one order of magnitude the slippage of water on two-dimensional materials.

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