scholarly journals Low affinity integrin states have faster ligand binding kinetics than the high affinity state

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Jing Li ◽  
Jiabin Yan ◽  
Timothy A Springer

Integrin conformational ensembles contain two low-affinity states, bent-closed and extended-closed, and an active, high-affinity, extended-open state. It is widely thought that integrins must be activated before they bind ligand; however, one model holds that activation follows ligand binding. As ligand-binding kinetics are not only rate limiting for cell adhesion but also have important implications for the mechanism of activation, we measure them here for integrins α4β1 and α5β1 and show that the low-affinity states bind substantially faster than the high-affinity state. On and off-rates are similar for integrins on cell surfaces and as ectodomain fragments. Although the extended-open conformation's on-rate is ~20-fold slower, its off-rate is ~25,000-fold slower, resulting in a large affinity increase. The tighter ligand-binding pocket in the open state may slow its on-rate. Low affinity integrin states not only bind ligand more rapidly, but are also more populous on the cell surface than high affinity states. Thus, our results suggest that integrin binding to ligand may precede, rather than follow, activation by 'inside-out signaling'.

2021 ◽  
Author(s):  
Jing Li ◽  
Jiabin Yan ◽  
Timothy A Springer

Integrin conformational ensembles contain two low-affinity states, bent-closed and extended-closed, and an active, high-affinity, extended-open state. It is widely thought that integrins must be activated before they bind ligand; however, one model holds that activation follows ligand binding. As ligand-binding kinetics are not only rate limiting for cell adhesion but also have important implications for the mechanism of activation, we measure them here for integrins α4β1 and α5β1 and show that the low-affinity states bind substantially faster than the high-affinity state. On and off-rate measurements are similar for integrins on cell surfaces and ectodomain fragments. Although the extended-open conformation's on-rate is ~20-fold slower, its off-rate is ~25,000-fold slower, resulting in a large affinity increase. The tighter ligand-binding pocket in the open state may slow its on-rate. These kinetic measurements, together with previous equilibrium measurements of integrin conformational state affinity and relative free energy on intact cells, are key to a definitive understanding of the mechanism of integrin activation.


2007 ◽  
Vol 28 (6) ◽  
pp. 1915-1923 ◽  
Author(s):  
Kelly Suino-Powell ◽  
Yong Xu ◽  
Chenghai Zhang ◽  
Yong-guang Tao ◽  
W. David Tolbert ◽  
...  

ABSTRACT A common feature of nuclear receptor ligand binding domains (LBD) is a helical sandwich fold that nests a ligand binding pocket within the bottom half of the domain. Here we report that the ligand pocket of glucocorticoid receptor (GR) can be continuously extended into the top half of the LBD by binding to deacylcortivazol (DAC), an extremely potent glucocorticoid. It has been puzzling for decades why DAC, which contains a phenylpyrazole replacement at the conserved 3-ketone of steroid hormones that are normally required for activation of their cognate receptors, is a potent GR activator. The crystal structure of the GR LBD bound to DAC and the fourth LXXLL motif of steroid receptor coactivator 1 reveals that the GR ligand binding pocket is expanded to a size of 1,070 Å3, effectively doubling the size of the GR dexamethasone-binding pocket of 540 Å3 and yet leaving the structure of the coactivator binding site intact. DAC occupies only ∼50% of the space of the pocket but makes intricate interactions with the receptor around the phenylpyrazole group that accounts for the high-affinity binding of DAC. The dramatic expansion of the DAC-binding pocket thus highlights the conformational adaptability of GR to ligand binding. The new structure also allows docking of various nonsteroidal ligands that cannot be fitted into the previous structures, thus providing a new rational template for drug discovery of steroidal and nonsteroidal glucocorticoids that can be specifically designed to reach the unoccupied space of the expanded pocket.


Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 198-198
Author(s):  
Jieqing Zhu ◽  
Chuanmei Zhang ◽  
Jiafu Liu ◽  
Xiuli Jiang ◽  
Nada Haydar ◽  
...  

Abstract Platelet specific integrin αIIbβ3 plays an essential role in hemostasis and thrombosis. It has been used as a prototype for understanding integrin activation and conformational regulation. Crystal structures of αIIbβ3 headpiece composed of the αIIb β-propeller and β3 βI, hybrid, and PSI domains in the absence or presence of RGD-mimetic drugs revealed the headpiece changing from a closed to an open conformation upon ligand binding. A striking change is the swing-out motion of the β3 hybrid domain away from the βI and the αIIb thigh domains. This is accompanied by the changing of the α1/α1'-helix from a bent to a merged and straightened α-helical conformation. The α1/α1'-helix is bent at the α1/α1' junction (β3 Ile-131 to Gly-135) as revealed by the crystal structures of β3, β1, β2, and β7 integrins in the closed headpiece conformation. The β3 Gly-135 at the α1/α1' junction is completely conserved among all the β integrins. We propose that the conserved glycine at the α1/α1' junction is critical for maintaining the bent α1/α1'-helix conformation, and the α1/α1'-helix unbending is required for integrin activation and bidirectional signaling. To test this hypothesis, we mutated the β3 Gly-135 to alanine and showed that the β3-G135A mutation rendered αIIbβ3 integrin constitutively binding the activation-dependent mAb PAC-1. In contrast, the β3-G135P mutation had minor effect on integrin activation. This is consistent with the idea that alanine tends to stabilize a straight α-helical structure, while glycine and proline tend to introduce a bend or kink into the α-helical conformation when present at the internal positions of an α-helix. That is, the conserved β3 Gly-135 is essential for restraining the α1/α1'-helix in the bent conformation. The β3 Gly-135 is partially exposed in the bent conformation of α1/α1'-helix and buried deeply into the hydrophobic environment upon the α1/α1'-helix unbending. We rationalized that the hydrophilic substitutions will restrain, while the hydrophobic substitutions will facilitate the burying of β3 Gly-135, and thus block and induce α1/α1'-helix unbending, respectively. As expected, the β3-G135R and G135K mutations completely blocked PAC-1 binding to αIIbβ3 integrin stimulated by Mn2+ or by the αIIb-R995D mutation that mimics integrin inside-out activation. In sharp contrast, the β3-G135L and G135M mutations constitutively induced PAC-1 binding to αIIbβ3 integrin. To further confirm the α1/α1'-helix unbending is required for integrin activation and signaling, we introduced tandem double or triple glycine substitutions into the α1/α1' junction to reinforce the bent conformation of α1/α1'-helix. Remarkably, all the double or triple glycine mutations completely abolished soluble PAC-1 binding stimulated by Mn2+ from outside or by the αIIb-R995D or αIIb-F993A mutation from inside the cell. This data provide compelling evidence that the integrin α1/α1'-helix unbending is indispensible for high affinity ligand binding. Interestingly, the β3-G135R or double glycine mutant still mediated cell adhesion to immobilized PAC-1 or fibrinogen, but at a reduced level. The cell adhesion could be blocked by eptifibatide, indicating the binding ability of the mutant integrins with the high affinity small molecule ligand. However, eptifibatide failed to induce the ectodomain extension of the mutant integrins. In addition, integrin-mediated outside-in signaling, such as cell spreading, focal adhesion and F-actin stress fiber formation, and focal adhesion kinase activation was inhibited by the β3-G135R or double glycine mutations. This data demonstrated that the conformational communication initiated by ligand binding is interrupted due to the defect of α1/α1'-helix unbending. We further showed that overexpression of talin1 head domain failed to induce PAC-1 binding to the αIIbβ3 integrin with double glycine mutations at the α1/α1' junction, but still induced integrin ectodomain extension. That is, in the inside-out integrin activation, the ectodomain extension alone does not result in high affinity ligand binding. The conformational signal has to be relayed to the ligand binding site through α1/α1'-helix unbending. In conclusion, our data established the structural role of the α1/α1' junction that allows relaxation of the α1/α1'-helix in the resting state and transmission of bidirectional conformational signals by helix unbending upon integrin activation. Disclosures: No relevant conflicts of interest to declare.


2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Jianchuan Wang ◽  
Yang Su ◽  
Roxana E. Iacob ◽  
John R. Engen ◽  
Timothy A. Springer

AbstractIntegrin αVβ8, which like αVβ6 functions to activate TGF-βs, is atypical. Its β8 subunit binds to a distinctive cytoskeleton adaptor and does not exhibit large changes in conformation upon binding to ligand. Here, crystal structures, hydrogen-deuterium exchange dynamics, and affinity measurements on mutants are used to compare αVβ8 and αVβ6. Lack of a binding site for one of three βI domain divalent cations and a unique β6-α7 loop conformation in β8 facilitate movements of the α1 and α1’ helices at the ligand binding pocket toward the high affinity state, without coupling to β6-α7 loop reshaping and α7-helix pistoning that drive large changes in βI domain-hybrid domain orientation seen in other integrins. Reciprocal swaps between β6 and β8 βI domains increase affinity of αVβ6 and decrease affinity of αVβ8 and define features that regulate affinity of the βI domain and its coupling to the hybrid domain.


Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 1151
Author(s):  
Chenyun Guo ◽  
Zhihua Wu ◽  
Weiliang Lin ◽  
Hao Xu ◽  
Ting Chang ◽  
...  

Suramin was initially used to treat African sleeping sickness and has been clinically tested to treat human cancers and HIV infection in the recent years. However, the therapeutic index is low with numerous clinical side-effects, attributed to its diverse interactions with multiple biological macromolecules. Here, we report a novel binding target of suramin, human Raf1 kinase inhibitory protein (hRKIP), which is an important regulatory protein involved in the Ras/Raf1/MEK/ERK (MAPK) signal pathway. Biolayer interference technology showed that suramin had an intermediate affinity for binding hRKIP with a dissociation constant of 23.8 µM. Both nuclear magnetic resonance technology and molecular docking analysis revealed that suramin bound to the conserved ligand-binding pocket of hRKIP, and that residues K113, W173, and Y181 play crucial roles in hRKIP binding suramin. Furthermore, suramin treatment at 160 µM could profoundly increase the ERK phosphorylation level by around 3 times. Our results indicate that suramin binds to hRKIP and prevents hRKIP from binding with hRaf1, thus promoting the MAPK pathway. This work is beneficial to both mechanistically understanding the side-effects of suramin and efficiently improving the clinical applications of suramin.


2021 ◽  
Author(s):  
Sharif Anisuzzaman ◽  
Ivan M Geraskin ◽  
Muslum Ilgu ◽  
Lee Bendickson ◽  
George A Kraus ◽  
...  

The interaction of nucleic acids with their molecular targets often involves structural reorganization that may traverse a complex folding landscape. With the more recent recognition that many RNAs, both coding and noncoding, may regulate cellular activities by interacting with target molecules, it becomes increasingly important to understand the means by which nucleic acids interact with their targets and how drugs might be developed that can influence critical folding transitions. We have extensively investigated the interaction of the Spinach2 and Broccoli aptamers with a library of small molecule ligands modified by various extensions from the imido nitrogen of DFHBI (3,5-difluoro-4-hydroxybenzylidene imidazolinone) that reach out from the Spinach2 ligand binding pocket. Studies of the interaction of these compounds with the aptamers revealed that poly-fluorophenyl-modified ligands initiate a slow change in aptamer affinity that takes an extended time (half-life of ~40 min) to achieve. The change in affinity appears to involve an initial disruption of the entrance to the ligand binding pocket followed by a gradual lockdown for which the most likely driving force is an interaction of the gateway adenine with a nearby 2'OH group. These results suggest that poly-fluorophenyl modifications might increase the ability of small molecule drugs to disrupt local structure and promote RNA remodeling.


2013 ◽  
Vol 182 ◽  
pp. 73-82 ◽  
Author(s):  
Grace Jones ◽  
Peter Teal ◽  
Vincent C. Henrich ◽  
Anna Krzywonos ◽  
Agnes Sapa ◽  
...  

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