PMID- 36279412
OWN - NLM
STAT- MEDLINE
DCOM- 20221109
LR  - 20221215
IS  - 1520-5827 (Electronic)
IS  - 0743-7463 (Linking)
VI  - 38
IP  - 44
DP  - 2022 Nov 8
TI  - Preferential Adsorption of Prominent Amino Acids in the Urease Enzyme of 
      Sporosarcina pasteurii on Arid Soil Components: A Periodic DFT Study.
PG  - 13414-13428
LID - 10.1021/acs.langmuir.2c01854 [doi]
AB  - The urease enzyme is commonly used in microbially induced carbonate precipitation 
      (MICP) and enzyme-induced carbonate precipitation (EICP) to heal and strengthen 
      soil. Improving our understanding of the adsorption of the urease enzyme with 
      various soil surfaces can lead to advancements in the MICP and EICP engineering 
      methods as well as other areas of soil science. In this work, we use density 
      functional theory (DFT) to investigate the urease enzyme's binding ability with 
      four common arid soil components: quartz, corundum, albite, and hematite. As the 
      urease enzyme cannot directly be simulated with DFT due to its size, the amino 
      acids comprising at least 5% of the urease enzyme were simulated instead. An 
      adsorption model incorporating the Gibbs free energy was used to determine the 
      existence of amino acid-mineral binding modes. It was found that the nine 
      simulated amino acids bind preferentially to the different soil components. 
      Alanine favors corundum, glycine and threonine favor hematite, and aspartic acid 
      favors albite. It was found that, under the standard environmental conditions 
      considered here, amino acid binding to quartz is unfavorable. In the polymeric 
      form where the side chains would dominate the binding interactions, hematite 
      favors aspartic acid through its R-OH group and corundum favors glutamic acid 
      through its R-Ket group. Overall, our model predicts that the urease enzyme 
      produced by Sporosarcina pasteurii can bind to various oxides found in arid soil 
      through its alanine, glycine, aspartic/glutamic acid, or threonine residues.
FAU - Pisani, William A
AU  - Pisani WA
AUID- ORCID: 0000-0002-5172-862X
AD  - Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee37830, United 
      States.
AD  - Environmental Laboratory, US Army Engineer Research and Development Center, 
      Vicksburg, Mississippi39180, United States.
FAU - Jenness, Glen R
AU  - Jenness GR
AUID- ORCID: 0000-0001-7636-7229
AD  - Environmental Laboratory, US Army Engineer Research and Development Center, 
      Vicksburg, Mississippi39180, United States.
FAU - Schutt, Timothy C
AU  - Schutt TC
AD  - Environmental Laboratory, US Army Engineer Research and Development Center, 
      Vicksburg, Mississippi39180, United States.
FAU - Larson, Steven L
AU  - Larson SL
AD  - Environmental Laboratory, US Army Engineer Research and Development Center, 
      Vicksburg, Mississippi39180, United States.
FAU - Shukla, Manoj K
AU  - Shukla MK
AUID- ORCID: 0000-0002-7560-1172
AD  - Environmental Laboratory, US Army Engineer Research and Development Center, 
      Vicksburg, Mississippi39180, United States.
LA  - eng
GR  - R01 GM129325/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20221024
PL  - United States
TA  - Langmuir
JT  - Langmuir : the ACS journal of surfaces and colloids
JID - 9882736
RN  - EC 3.5.1.5 (Urease)
RN  - 1K09F3G675 (ferric oxide)
RN  - 0 (Soil)
RN  - 0 (Amino Acids)
RN  - 14808-60-7 (Quartz)
RN  - 30KYC7MIAI (Aspartic Acid)
RN  - H0G9379FGK (Calcium Carbonate)
RN  - 0 (Carbonates)
RN  - TE7660XO1C (Glycine)
RN  - OF5P57N2ZX (Alanine)
RN  - LMI26O6933 (Aluminum Oxide)
RN  - 2ZD004190S (Threonine)
RN  - 0 (Glutamates)
RN  - Sporosarcina pasteurii
SB  - IM
MH  - *Urease/metabolism
MH  - *Soil
MH  - Adsorption
MH  - Amino Acids
MH  - Quartz
MH  - Aspartic Acid
MH  - Calcium Carbonate/chemistry
MH  - Carbonates
MH  - Glycine
MH  - Alanine
MH  - Aluminum Oxide
MH  - Threonine
MH  - Glutamates
EDAT- 2022/10/25 06:00
MHDA- 2022/11/10 06:00
CRDT- 2022/10/24 15:12
PHST- 2022/10/25 06:00 [pubmed]
PHST- 2022/11/10 06:00 [medline]
PHST- 2022/10/24 15:12 [entrez]
AID - 10.1021/acs.langmuir.2c01854 [doi]
PST - ppublish
SO  - Langmuir. 2022 Nov 8;38(44):13414-13428. doi: 10.1021/acs.langmuir.2c01854. Epub 
      2022 Oct 24.